Ruminiclostridium cellulolyticum. We found that there were usually stem-loop structures downstream of SBP genes, which could prematurely terminate the transcription of ABC importers and were putative internal intrinsic terminators, resulting in high transcript levels of upstream SBP genes and low transcript levels of downstream cognate translocator genes. This was determined by their termination efficiencies. Internal terminators had a lower U content in their 3′ U-rich tracts and longer GC-rich stems, which distinguishes them from canonical terminators and potentially endows them with special termination efficiencies. The pairing of U-rich tracts and the formation of unpaired regions in these internal terminators contributed to their folding energies, affecting the stability of their upstream SBP transcripts. Our findings revealed a strategy of internal transcriptional terminators controlling in vivo stoichiometry of their flanking transcripts.The extracellular substrate-binding proteins (SBPs) of ATP-binding cassette (ABC) importers tend to be expressed in excess relative to their cognate translocators, but how the stoichiometry of ABC transporters is controlled remains unclear. Here, we elucidated a mechanism contributing to differential gene expression in operons encoding ABC importers by employing cellulolytic Clostridia species, specifically IMPORTANCE Operons encoding protein complexes or metabolic pathways usually require fine-tuned gene expression ratios to create and maintain the appropriate stoichiometry for biological functions. In this study, a strategy for controlling differential expression of genes in an operon was proposed by utilizing ABC importers from Ruminiclostridium cellulolyticum. We found that a stem-loop structure is introduced into the intergenic regions of operons encoding ABC importers as the putative internal terminator, which results in the premature termination of transcription. Consequently, the stoichiometric ratio of genes flanking terminators is precisely determined by their termination efficiencies and folding energies at the transcriptional level. Thus, it can be utilized as a promising synthetic biology tool to control the differential expression of genes in an operon. ATP-binding cassette (ABC) transporters, found in both prokaryotes and eukaryotes, play an important role in various physiological processes, such as the uptake of nutrients, facilitating multidrug resistance, the secretion of signal molecules or toxins, cell volume regulation, and other processes –3. In ge–Escherichia coli and histidine in Salmonella enterica were found to exist in a 30 to 50-fold excess relative to their cognate translocators  that delivers a substrate to its translocator. These can be periplasmic in Gram-negative bacteria, membrane-tethered in Gram-positive bacteria, or fused to the permease . SBPs ha8–locators . HoweverRuminiclostridium (Clostridium) cellulolyticum, but no genes encoding the PTS system have been predicted , disaccharides, and oligosaccharides , 16, and18–redicted .R. cellulolyticum H10 as a model system. All 16 stem-loop structures predicted in R. cellulolyticum could cause premature transcription termination of ABC importer gene clusters at a certain efficiency and function as putative internal intrinsic terminators. However, the stoichiometric ratio between upstream SBPs and the downstream cognate translocators of stem-loops was not only determined by the transcription efficiency of these stem-loops but was also affected by the folding energy of stem-loops. This was related to the stability of monocistronic transcripts of SBPs. The folding energy of stem-loops was decreased by the pairing of 3′ U-rich tracts, and it was increased by the formation of unpaired regions in stems. Our findings thus unveiled a mechanism linking stem-loop structures and the stoichiometry of transcripts in an operon and have general implications for the designing and engineering of metabolic pathways or protein complexes with specific stoichiometric ratios.In this study, we first predicted and analyzed gene clusters encoding ABC importers in eight anaerobic cellulolytic Clostridia species. We found that 99.5% of SBP genes were located at both ends of gene clusters, especially at the 5′ end. Moreover, stem-loop structures were frequently found immediately downstream of 5′ SBP genes. We further determined the role of these stem-loops in controlling the stoichiometry of ABC importers by employing R. cellulolyticum H10, Ruminiclostridium papyrosolvens DSM2782, Ruminiclostridium sp. BNL1100, Ruminiclostridium josui JCM17888, Ruminiclostridium termitidis CT1112, Ruminiclostridium sp. MA18, Ruminiclostridium sufflavum DSM 19573, and Clostridium cellulovorans 743B (Table S1). We found that the number of gene clusters encoding ABC importers in cellulolytic Clostridia ranged from 29 to 38, except for R. termitidis CT1112, which harbored 156 clusters. According to the position of SBPs in these gene clusters, ABC importer gene clusters could be classified into three types of clusters, namely, those with 5’ end SBPs, 3′ end SBPs, or middle SBPs. However, the majority of SBP genes (99.5%) were located at both ends of clusters, and the number of SBPs located at the 5′ end was much higher than that of SBPs located at the 3′ end in all test Clostridia .Moreover, to find potential elements in the intergenic regions (IRs) between SBPs and their cognate translocator genes, putative stem-loop structures and promoters were predicted in 306 long intergenic regions (more than 50 bp). A total of 213 IRs were predicted to harbor stem-loops . It showed that 87.3% of IRs (193) from the 5′ SBP clusters harbored stem-loops, which is much more than 23.5% of IRs  from theR. cellulolyticum grown on glucose, cellobiose, and cellulose were compared relative to our previous data (accession number GSE57652). The average fold change of SBPs compared to their downstream or upstream genes (SBP/X or X/SBP) was significantly higher than that between TMDs and NBDs (around zero)  . This find zero)  to D. Adnd zero) . A putatnd zero) . Thus, tFurthermore, the cluster Ccel_2112-2110 was employed to analyze the transcription pattern of the ABC importer harboring 5′-end SBPs. This cluster harbors an SBP gene (Ccel_2112) at the 5′ end, followed by two TMD genes (Ccel_2111 and Ccel_2110), and has a 106-bp long intergenic region between Ccel_2112 and Ccel_2111. Ccel_2112, encoding SBPs, was transcribed at significantly higher levels than its downstream genes . NortherR. cellulolyticum had two Type I, five Type II, five Type III, and four Type IV stem-loops , and the RNA secondary structures of intergenic regions between SBPs and their downstream genes were further analyzed. It was found that the long intergenic regions tended to harbor a stem-loop structure but not a C-rich region, suggesting Rho-independent termination. In total, 191 putative stem-loop structures were found, and their folding energy ΔG ranged from −38.3 to −10.1 kcal/mol in eight cellulolytic Clostridia (Table S2). Based on these structures, the stem-loops could be classified into four types: 24 Type I, which had the typical structure of Rho-independent terminators harboring a paired or unpaired 3′ poly(U) tails and the number of U in poly(U) tails of Type I stem-loops was more than 5; 88 Type II, which were similar to Type I, except that they replaced the poly(U) tail with a 3′ U-rich tract and the number of U in 3’tail of stem-loops was less than 5; 62 Type III, which harbored a pair of 3′ U-rich tracts following a 1 to 2 base unpaired region; and 17 Type IV, which were similar to Type III but had a longer paired region with a lower content of 3′ U following the unpaired region. Thus, sequences at the 3′ paired or unpaired U-rich tails for Type I and Type II stem-loops and downstream of unpaired regions in Types III and IV were considered to be putative 3′ U-rich tracts of Rho-independent terminators (Table S2). For instance, em-loops . The difem-loops . In contem-loops . Given tin vivo role of these stem-loops was designed, where these four types of stem-loops from R. cellulolyticum were inserted between the reporter genes fbfp (encoding a green fluorescence protein) and mcherry  had the highest TEs, which were more than 90%, while the TEs of SL-1025, 1252, 3246, 2589, 0220, and 2687 were lower than 50% . Therefore, stem-loop structures could cause premature termination of transcription and function as transcriptional terminators, allowing a percentage of transcripts to read through and resulting in a specific transcriptional stoichiometry between flanking genes.To probe this hypothesis, an experiment testing the cription . Howeverthan 50% . Furtherblotting . The TE By comparing the stem-loop structures from clusters of these ABC importers, we found that these stem-loops had three features: 3′ U-rich tracts, long stems, and middle unpaired regions, all of which could affect the stoichiometric ratio between both flanking transcripts.fbfp-mcherry reporter system, using SL-0885 with no tails as a control   . For exasubtilis .Second, the 3′ U-rich tracts of stem-loops tended to pair with 5′ sequences, resulting in longer stems that could promote the stability of transcripts to RNase digestion but not impact on the TE of stem-loops because it has been reported that pairing between poly(A) and the U-tract is not involved in termination function , 26. To In contrast, to further clarify the effects of the stem length on transcription termination, a series of SL-2112 derivatives was designed by shortening or lengthening its stem in the folding energy range from −9.7 to −30.3 kcal/mol . The resMoreover, we found that each Type III and IV stem-loop had an unpaired region in the middle of the stem. To determine the role of these unpaired regions, SL-2112, SL-2589, and SL-2687 were mutated into paired forms. Mutation of SL-2112 and SL-2687 produced an A-T base pair, while mutation of SL-2589 produced a G-C base pair, resulting in a reduced ΔG ranging from 3.9 to 5.5 kcal/mol . It indi1F0) is a protein complex containing eight subunits  in a specific stoichiometric ratio of 3:3:1:1:1:1:2:10  by predicting RNA secondary structure, suggesting that this same mechanism works in E. coli. This strategy was also mentioned in the recent report  of GC-rich stems from SL-2112 and its derivatives, an 11 bp lengthened stem had the maximum TE of 98.1 ± 0.3%, while a 5 bp shortened stem hardly had any termination activity. Third, although the extended A-U pairing between poly(A) and the U-tract flanking the stem-loop is generally considered to be associated with bidirectional termination  medium. R. cellulolyticum H10 (ATCC 35319) was cultured anaerobically in Hungate tubes at 35°C in GS-2 medium  supplemented with 3.0 g/liter cellobiose as the sole carbon source (default carbon source unless otherwise stated). When required, the media for E. coli and R. cellulolyticum were supplemented with 100 μg/mL ampicillin or 20 μg/mL erythromycin, respectively.The bacterial strains used in this study are listed in Table S4. mcherry gene (encoding a red fluorescence protein) after the fbfp gene (encoding an anaerobic green fluorescence protein) into pMTC6, which is an R. cellulolyticum–E. coli shuttle vector (fbfp and mcherry were expressed in a single operon promoted by the promoter Pthl (the thiolase gene promoter from Clostridium acetobutylicum) (Bgl II restriction site between the two genes for the introduction of various stem-loop structures. The stem-loops were fused with mcherry by single overlap extension PCR (SOE-PCR) using synthetic oligonucleotide primers (Table S5). The fused fragments were subsequently digested with the restriction enzymes Bgl II and EcoR I and then ligated into the shuttle vector pMTC9, which had been previously digested with the same enzymes.All plasmids constructed in this study are listed in Table S4. To analyze the function of various stem-loop structures, a dual fluorescence reporter system was first constructed by inserting the e vector . In the tylicum) , with a http://clostron.com/) (Xho I and BsrG I and cloned between the corresponding sites of pSY6 to generate pSY6-2112. These plasmids were transformed into R. cellulolytiucm H10ΔmspI based on our previous electroporation method (pSY6-2112 for the targeted disruption of Ccel_2112 was constructed based on the targetron plasmid pSY6  (Table Son.com/) . The taron.com/)  (Table Sn method . All thehttp://www.genome.ad.jp/kegg/) to a blast search with eight sequenced genomes of cellulolytic Clostridia, R. cellulolyticum H10, R. papyrosolvens DSM2782, R. sp. BNL1100, R. josui JCM17888, R. termitidis CT1112, R. sp. MA18, R. sufflavum DSM 19573, and C. cellulovorans 743B, from the NCBI database (https://www.ncbi.nlm.nih.gov/). The BLAST threshold of the E value for statistical significance was set to 1×10−5.To predict genes encoding ABC importers in cellulolytic Clostridia, we subjected all types of ABC importers annotated in the Kyoto Encyclopedia of Genes and Genomes (KEGG) database  was used to predict the RNA secondary structures of the intergenic regions between SBPs and their downstream genes using suggested default parameters (On-line Mfold (rameters . The outhttps://www.fruitfly.org)  between SBP genes and their cognate translocator genes were predicted by using BDGP prokaryotic promoter prediction program (fly.org) . The profly.org) . It is cPst I and Mlu I. The digested fragments were then ligated to pMTC6 which was digested with the same enzymes, resulting in the replacement of the original Pthl promoter (promoter for fbfp gene in pMTC6) by P0044 and P0048. The plasmids were transformed into R. cellulolyticum H10ΔmspI. The transformants of R. cellulolyticum were used to analyze the activity of promoters by measuring the fluorescence intensity of FbFP based on our previous method (The predicted promoters of P0044 and P0048 were amplified by PCR using synthetic primers (Table S4). The PCR products of P0044 and P0048 were purified and digested with restriction enzymes s method .R. cellulolyticum cultures on cellobiose in mid-log-phase, and genomic DNA was removed using RNase-Free DNase Set . The RNA quality was determined using a NanoVue Plus spectrophotometer , and electrophoresis on 1% agarose-formaldehyde gels was performed.Total RNA was isolated from Two micrograms of total RNA were electrophoresed on 1% agarose-formaldehyde gels and blotted onto a positively charged nylon membrane  using the NorthernMax kit . DIG-labeled DNA probes for the detection of specific transcripts were generated with a DIG labeling and detection kit , as per the manufacturer’s instructions, using the oligonucleotides listed in Table S5.RNA was reverse transcribed using the HiScript III RT SuperMix kit . qRT-PCR was performed on a CFX96 real-time PCR detection system  using ChamQ Univeral SYBR qPCR Master Mix . Data were normalized against the abundance of Ccel_0312 encoding the β subunit of DNA-directed RNA polymerase. The primer sets for qPCR are listed in Table S5.


Plasmodium parasites, is still one of the biggest global health challenges. P. falciparum is the deadliest species to humans. In this review, we discuss how this parasite develops and adapts to the complex and heterogenous environments of its two hosts thanks to varied chromatin-associated and epigenetic mechanisms. First, one small family of transcription factors, the ApiAP2 proteins, functions as master regulators of spatio-temporal patterns of gene expression through the parasite life cycle. In addition, chromatin plasticity determines variable parasite cell phenotypes that link to parasite growth, virulence and transmission, enabling parasite adaptation within host conditions. In recent years, epitranscriptomics is emerging as a new regulatory layer of gene expression. We present evidence of the variety of tRNA and mRNA modifications that are being characterized in Plasmodium spp., and the dynamic changes in their abundance during parasite development and cell fate. We end up outlining that new biological systems, like the mosquito model, to decipher the unknowns about epigenetic mechanisms in vivo; and novel methodologies, to study the function of RNA modifications; are needed to discover the Achilles heel of the parasite. With this new knowledge, future strategies manipulating the epigenetics and epitranscriptomic machinery of the parasite have the potential of providing new weapons against malaria.Malaria, caused by  Despite being one of the first recorded illness in history , malariaApicomplexan parasites of the genus Plasmodium that infect different mammalian hosts. P. falciparum is the predominant human malaria species, causing the most severe symptomatology and the highest mortality rate [The disease is caused by ity rate .P. falciparum enters our bloodstream, by means of an infected female Anopheles mosquito bite, the sporozoites invade liver hepatocytes where they multiply for two weeks. Thousands of merozoites per liver cell are released, and then re-enter the blood stream and invade the erythrocytes. Then, each parasite cell enters a continuous cycle called the intraerythrocytic developmental cycle (IDC), developing into ring, trophozoite and the schizont stage. After the formation of a mature schizont, several merozoites tear out the erythrocyte and reinfect new red blood cells. Some of these cycling parasites, in response to certain conditions within the host [Once the host , differeAnopheles bites an infected human, taking a blood meal with gametocytes that reaches the mosquito’s midgut, where they become activated and form extracellular gametes induced by changes in temperature, pH and xanthurenic acid [The life cycle in the mosquito starts when a female nic acid . It is iTo survive in such a complex life cycle involving two hosts, intra- and extra-cellular life forms and multiple host tissues, the parasite requires different sets of proteins and a very tight control of cell cycle progression. For such, transcription is precisely regulated in space and time by a relatively small repertoire of transcription factors called ApiAP2 proteins ,6. How aPlasmodium epigenetics shine. Epigenetics is linked to almost every biological process of P. falciparum, controlling a variety of survival strategies such as immune system evasion, transmission and drug resistance.Apart of a very complex life cycle, the most striking and deadly feature of the malaria parasite is its ability to adapt rapidly and reversibly, without changing its genome, to the variable environment of the host. This is achieved thanks to cell plasticity, the generation of alternative phenotypes in the parasite population . And thiP. falciparum cell fate and plasticity. In addition, we will discuss new insights into the role of epitranscriptomics, also named “RNA epigenetics”, as a new layer of gene regulation in parasite development and adaptation. We will end up envisioning future strategies of manipulating the epigenetic and epitranscriptomic machinery of the parasite for malaria eradication.In this review we will deepen into chromatin and epigenetic mechanisms of gene regulation, mainly AP2 transcription factors, histone post-translational modifications and nuclear organisations, that control Plasmodium parasites, sharing the main principles with their eukaryotic relatives, as well as the repertoire of histone post translational modifications [P. falciparum genome that impacts gene expression regulation is its elevated AT content. Indeed, it has one of the highest in all eukaryotes with an average rate of 80%, that surpass the 90% in introns and intergenic regions [Fundamental chromatin organization regulation is conserved in ications ,12,13. O regions . Long AT regions . However regions .P. falciparum is notable for having one of the lowest ratios of predicted specific transcription factors versus total number of genes in eukaryotes [Plasmodium follows a “just-in-time” pattern [Plasmodium: the ApiAP2 family of DNA-binding proteins, comprises 27 members in P. falciparum. These AP2 transcription factors are specific of apicomplexan parasites and analogous to the plant Apetela2/Ethylene Response Factor (AP2/ERF) DNA-binding proteins [During parasite development, chromatin changes dynamically, shaping parasite cell fate . Most ofkaryotes . Differekaryotes . Another pattern . That is pattern ,21,22,23proteins ,6. Despiproteins . This isproteins ,25, AP2-proteins , AP2-SP proteins . These Aproteins ,21,22. TPlasmodium come from studies on the Intraerythrocytic Developmental Cycle (IDC). It is well described that the transcriptome and the epigenome of P. falciparum during the IDC in the human is highly dynamic. The transcriptional start sites of stage-active genes are marked with a combination of histone H3 acetylations H3K18ac and H3K27ac, that associates with an enrichment of AP2-I and bromodomain protein 1 (BDP1) reader protein in those loci [Almost all we know about chromatin regulation in ose loci . The rinose loci ,18. Thisose loci ,30. In aose loci . The eucose loci ,32. Whenose loci ,18, withose loci ,30,33, aose loci ,32. On tose loci ,35,36,37ose loci ,38. Finaose loci ,30. As aose loci . The AP2ose loci ,40,41. Tose loci , contrasTaken together, available evidence shows that the development of the malaria parasite within the erythrocyte is highly regulated at the level of chromatin structure. Whether these patterns and mechanisms are similar in other stages of parasite development, requires further investigation.Mosquito stages remain poorly investigated. This is in part due to technical limitations. The bottleneck in the parasite population following transmission results in very low parasite numbers in the invertebrate host, which makes it difficult to isolate the different mosquito stages at sufficient purity and quantity. Moreover, multiple infections, consisting of multiple strains and/or genotypes, often co-occur in the mosquito resulting in asynchronous and heterogenous parasite populations that hinder bulk transcriptomic and epigenomic analysis. As a consequence, the study chromatin regulation in this part of the parasite life cycle still remains a challenge.Plasmodium. We know that meiosis occurs in the diploid zygote stage and that the parasite possesses the conserved enzymatic machinery (Dmc1 and Rad51) [P. falciparum and rodent parasites [P. falciparum, AP2-EXP (PF3D7_1466400) has its maximum expression in sporozoites, and displays binding sites in the promoters of hundreds of sporozoite-specific genes, pointing to be the master regulator of this stage of development [The few studies that analyse chromatin regulation in mosquito stages, point to dynamic changes in chromatin states that correlate with stage-specific transcriptional programs ,42,43. Hd Rad51) . Howeverd Rad51) . After md Rad51) ,43. In ad Rad51) . Indeed,arasites ,47,48,49arasites . This hearasites . On the arasites ,50,51,52arasites . The ortelopment . In addiSeveral studies have shown that most of the transcripts expressed in sporozoites are not translated into proteins ,53,54. TIn sum, compared to IDC stages, data about chromatin accessibility, AP2 binding and 3D chromatin structure controlling mosquito stages developmental transitions is mostly lacking. Deciphering the many unknowns in the development regulation in the mosquito stages represents a vein with great potential for further studies.Epigenetic regulation plays a crucial role in the cell plasticity of the malaria parasite. This plasticity is a survival strategy shared by many pathogens that allows the parasite to overcome the unpredictable and changing environments within the human and mosquito hosts. In isogenic populations, different phenotypes can arise thanks to epigenetic regulation. The genes whose expression can change between different parasite cells of the same genotype/clone are referred as Clonally Variant Genes (CVGs). These could be found either in an active or repressed state in genetically indistinguishable parasites. These epigenetic states can be inherited. Phenotypic variation can arise by two different processes. Bet-hedging, where transcriptional variants arise a priori, and the new environments act as selective sieve sorting; and adaptive plasticity, where the new phenotypic variants arise as directed transcriptional responses to an environmental change . EvidencGiven that the CVG activation state does not depend on its primary DNA sequence, the basic regulatory mechanisms that control Clonally Variant Gene Expression (CVGE) is truly epigenetic and relies on facultative heterochromatin. This means that the trait is heritable, being passed through multiple rounds of replication . It is aPlasmodium adaptation strategies involving CVGE that are under epigenetic control are explained. Amongst these, the hallmark examples are antigenic variation (bet-hedging strategy) and sexual differentiation (adaptation plasticity). All what we describe occur linked to the blood cycle in the human and in vitro conditions and have used P. falciparum laboratory reference strains.Hereinafter, several examples of P. falciparum genome encodes different gene families of antigens like var, Pfmc-2TM, rifin and stevor. Those families display CVGE, allowing the parasite to switch its antigen during the infection and overcome the immune response. That explains the ability of malaria parasites to maintain chronic infections for a long time [var. This family of around 60 genes encodes for PfEMP1, a transmembrane protein with a hypervariable domain that bind to endothelial surface receptors, determining the parasite tropism [var genes present mutually exclusive expression. This means that only one copy of the family is expressed in a single parasite cell, the other copies remaining silenced [ong time . The dee tropism . In addisilenced ,87.var copies are marked with H3K9me3, associated with HP1, and H3K36me3 [var genes that occupy central positions in the chromosomes cluster via the formation of large chromatin loops [var family is marked with H3K9ac and H3K4me3 and the histone variants H2A.Z, H2B.Z and H3.3 [The mutually exclusive expression implies a complex regulation of activating only one member of the gene family while maintaining the other 59 genes silenced. There are characteristic epigenetic features that accompany the active/silent state. For example, it has been reported that silenced H3K36me3 ,88. Theyin loops ,89,90,91and H3.3 ,93,94. Tand H3.3 ,92,93, bvar gene copy, is ensured by H3K4me2, the histone mark responsible of the epigenetic memory in the malaria parasite [var mutually exclusive expression. These are transcribed by the RNA pol II from the conserved introns placed in the var genes [var genes. The ncRNA expression is essential for a normal var expression, however, their precise mechanism of action is not known [ruf6 family of lncRNAs playing an important role in var mutually exclusive expression [P. falciparum clonal lines, a recent work revealed that only the ruf6 genes flanking the active var gene appear accessible, whereas there were no differences in promoter or gene body accessibility between active and silent var copies. This work proposed that chromatin looping mediated by these ruf6-encoding long ncRNA and unknown proteins could participate in var gene regulation [var gene [The transmission of the active state for a particular parasite . In addiar genes . An antiot known ,97 Accumpression ,98,99. Cgulation . Indeed,var gene ,84.P. falciparum, usually less than 10% of the parasites produce gametocytes in each multiplication cycle [gdv1) or because deletions of entire chromosomes segments [Gametocytes are the essential stage of the parasite in transmission of the malaria disease. Becoming gametocytes represents a milestone in the parasite life cycle. A sub-population of the asexually growing parasites commit to stop multiplication and exit intraerythrocytic developmental cycle differentiating into a no-way-back dormant stage until transmitted to the mosquito. This strong link with transmission makes sexual differentiation and gametocytes an attractive target for research and disease control approaches. In on cycle . Howeveron cycle  due to gsegments . In natusegments ,102,103.ap2-g gene is epigenetically silenced by H3K9me3 and HP1 in cycling parasites [gdv1, is inhibited by its own antisense RNA [gdv1 gene releases from its antisense RNA and is expressed in stress conditions. Then, GDV1 removes HP1 from ap2-g promoter, activating a first wave of its expression [ap2-g epigenetic repression [At the transcription level, the main effector in this process has been analysed in several studies, validating the role of AP2-G as the master regulator of sexual differentiation ,77,104. arasites ,37,105, ense RNA . By unknpression ,106. Oncpression . The devpression . On the ap2-g goes back to the repressive cluster [ap2-g as well as early gametocyte genes, being necessary for gametocyte maturation [Linked to the sexual differentiation pathway and morphological changes, chromatin organization changes drastically in gametogenesis. An enrichment of H4K20me3, H3K27me3 and H3K36me2 is shown in early gametocytes, indicating a general gene silencing process, while euchromatic marks increase in the late gametocyte stage pointing to a slightly more open chromatin state ,13 Howev cluster . AP2-G5 turation ,110. Motturation . This suturation  in orderPfrh and eba, are formed by mostly nonessential and functionally redundant genes [Different gene families encode for invasion genes allowing alternative pathways for merozoite invasion involving different and specific parasite ligands and erythrocyte receptors. Two of these families, nt genes ,113,114.nt genes ,113,115.nt genes ,117. Thint genes ,118. Thant genes ,118. Itsnt genes ,118,119.nt genes . HoweverP. falciparum can adapt its nutrients uptake and metabolism though epigenetic variation and CVGE. The best described case is the clag family. Clag3.1 and Clag3.2 form the plasmodial surface anion channel, which mediates the transport of several nutrients across the erythrocyte membrane [Clag3 family have CVGE, and especially clag3.1 and clag3.2 show mutually exclusive expression [clag3 expression leads to differential nutrient transport, allowing the parasite to adapt to the nutrient environment [clag3.2 and clag3.1, pointing to the role of clag3 and epigenetic factors in controlling nutrient uptake and toxic barring [membrane ,121. Clapression ,36,75. Bpression ,75,122. ironment ,84,123.  barring ,123.P. berghei is able to detect nutrient restriction using the AMPKα homologous kinase KIN and respond through a transcriptional change leading to lower multiplication rates [Similarly, members of the fatty acyl-CoA synthases family PfACS can change its expression within the asexual cycle  adaptingon rates . SimilarPlasmodium parasites have evolved mechanisms to adapt and respond quickly to this increase in the host temperature [hsp70-1 and hsp90 and an uncharacterized gene PF3D7_1421800 [Hsp70-1 and hsp-90 are evolutionary conserved heat response proteins [hsp70-1 [sir2 in the same conditions with asynchronized parasite cultures [P. falciparum adaptive plasticity, the epigenetic basis of AP2-HS mediated heat shock response, the precise mechanism of regulation, and their target genes remain unknown.In each intraerythrocytic developmental cycle, following the red blood cell lysis and the release of the merozoites, one of the key symptoms of malaria is fever. As so, perature . It has perature ,127 and perature ,129. As perature ,130. A rperature . In respperature , activat_1421800 . Hsp70-1proteins ,132. Ind[hsp70-1 . Previou[hsp70-1 ,134. Two[hsp70-1 , althougEpitranscriptomics is the term that encompasses the different RNA modifications that affect gene expression without changing the primary nucleotide sequence . This riPlasmodium [mcm5UCU)ArgGlyGluProSerValLeuAlaIle of the upregulated proteins increases. This effect appears linked to the epitranscriptomic marks in the tRNA anticodon that enhance the recognition of the enriched codons [Various tRNA and mRNA epitranscriptomic marks have been identified in asmodium ,138,139.Asp(GTC). This modification is placed by the methyltransferase PfDNMT2. The PfDNMT2 knockout represses 199 GAC codon biased proteins, and the resulting phenotype displays altered cellular metabolism, protein synthesis and folding. In addition, PfDNMT2 KO parasites are more sensible to nutritional stresses, enhancing the gametocyte production. Without m5C, tRNAAsp(GTC) is degraded under metabolic stress, reducing the expression of the proteins with the GAC codon. However, the RNA nuclease that cleavage m5C-less tRNAAsp(GTC) is not known [A tRNA modification in the Cytosine 38 that have been partially characterized is the m5C of the tRNAot known .Plasmodium. Only m7G, pseudouridine (Ψ), m5C, and m6A have been identified in P. falciparum [Toxoplasma gondii, in which the m6A modification is in the 3′ end of the mRNA. In that parasite, this modification has been linked to mRNA maturation and 3′ end polyadenylation [P. yoelii has been shown to impair the gametocytogenesis [On the other hand, mRNA modifications are less studied in lciparum ,139. Amonylation ,141. Anoogenesis .All the above epitranscriptomic studies focus on the human blood stages of the parasite and in vitro conditions. It is now fundamental to expand the repertoire of modifications studied, validate their function, and apply the methodology to mosquito stages and in vivo conditions.P. falciparum [Given the importance of epiregulation in the malaria parasite, those mechanisms can be exploited in order to design innovative strategies against the disease. Some advances have been made in this area. Apicidin, a histone deacetylase inhibitor, impairs deeply the transcriptional regulation of the intraerythrocytic developmental cycle via HDAC inhibition. It produces the hyperacetylation of H3K9, H4K8 and the tetra-acetyl H4 (H4Ac4) and demethylation of H3K4me3 in lciparum . In addilciparum ,144.P. falciparum but not in humans  [The effect of the epidrugs in gametocytes is key for new malaria strategies that target transmission as this stage is highly resistant to most current malaria treatments . The mai6A, m3U) , so thes6A, m3U) . But thiIndeed, the mosquito stages are still one of the greatest unknowns in malaria transcriptional regulation. Most of the studies are conducted in the blood in vitro stages, however, the mosquito host represents an ideal in vivo biological model to analyse gene regulation in the context of host–parasite interactions. Very strong selective forces act in this part of the parasite life cycle, promoting phenotypic variation and plasticity ,148. TakP. falciparum allowing the malaria parasite to transition and adapt swiftly to the variable and unpredictable environments of its two hosts. The field is now moving towards characterising these regulatory networks in less studied parts of the parasite life cycle, like the mosquito, which are critical to transmission and malaria eradication. On the other hand, the emerging field of epitranscriptomics is revealing the significance of RNA modifications for parasite biology and has the potential to unveil new layers of gene regulation in Plasmodium development and adaptation. New weapons against malaria that exploit this new knowledge, like epidrugs that target DNA or RNA modifications, should now be developed.To conclude, epigenetics represents a fundamental process in


Filamentous fungal pathogens have evolved diverse strategies to infect a variety of hosts including plants and insects. The dynamic infection process requires rapid and fine-tuning regulation of fungal gene expression programs in response to the changing host environment and defenses. Therefore, transcriptional reprogramming of fungal pathogens is critical for fungal development and pathogenicity. Histone post-translational modification, one of the main mechanisms of epigenetic regulation, has been shown to play an important role in the regulation of gene expressions, and is involved in, e.g., fungal development, infection-related morphogenesis, environmental stress responses, biosynthesis of secondary metabolites, and pathogenicity. This review highlights recent findings and insights into regulatory mechanisms of histone methylation and acetylation in fungal development and pathogenicity, as well as their roles in modulating pathogenic fungi–host interactions. Filamentous fungal pathogens such as phytopathogenic fungi and entomopathogenic fungi, have a great impact on crop agriculture. Phytopathogenic fungi cause serious plant diseases that severely decrease crop yield and quality . In contTo successfully infect and colonize the host (plants or insects), pathogenic fungi have evolved complicated and delicate infection strategies which involve host cuticle adhesion and degradation, infection structure differentiation, suppression of host immunity by effectors and toxins, stress management, and nutrient assimilation . The dynN-terminal tails, such as methylation, acetylation, phosphorylation, and ubiquitination, regulate chromatin architecture, and consequently, the accessibility of the transcription machinery to DNA [In eukaryotic cells, genomic DNA is packed into a highly organized nucleoprotein complex known as chromatin. As the basic structural subunit of the chromatin, each nucleosome consists of around 146 base pairs of DNA wrapped around an octamer of core histone proteins, including two subunits of each histone H2A, H2B, H3, and H4. Post-translational modifications of histone y to DNA   to the lysine residues on the N-terminal of H3 or H4 [Histone lysine methylation is a dynamic and reversible histone modification, which plays an important role in modulating the accessibility of DNA to the transcription machinery and providing signal or docking sites for chromatin remodelers, and subsequently regulates gene transcription. The site-specific methylation is catalyzed by histone lysine methyltransferases (HKMTs), mostly with a catalytic Set (Su(var)3–9, enhancer-of-zeste and trithorax) domain, which transfer a methyl group from H3 or H4 . Based oH3 or H4 . ConversH3 or H4 . HistoneH3 or H4 . DependiSaccharomyces cerevisiae [Candida albicans, Set1-mediated H3K4me3 activates mitochondrial protein genes to establish defenses against oxidative stress from host cells during infection [Candida glabrata, is necessary for the azole-induced expression of ergosterol biosynthesis genes that mediate drug resistance [Fusarium graminearum [Fusarium fujikuroi [Magnaporthe oryzae [Brassica anthracnose pathogen Colletotrichum higginsianum is positively regulated by H3K4 methylation [F. graminearum [F. fujikuroi, the methyltransferase Set1 and the demethylase KDM5 are antagonists for H3K4me [aba1 and increases conidiation. H3K4me catalyzed by MoSet1 together with other COMPASS subunits  at the TSS region of pathogenicity related genes facilitates infection structure formation in M. oryzae [S. cerevisiae Bre2 homolog in C. higginsianum, is required for the genome-wide H3K4me3 that facilitates vegetative growth , as well as fungal virulence , yet inhibits the production of some secondary metabolites, including terpenoid compounds [Botrytis cinerea, which causes gray mold disease in more than 200 plant species, knockout of the H3K4 demethylase gene Jar1 (belonging to KDM5 family) causes abnormal genome-wide H3K4me accumulation and attenuates fungal virulence [Metarhizium robertsii, the infection-related morphogenesis is under coordinated regulation by the KMT2-Cre1-Hyd4 regulatory pathway [hyd4 to facilitate fungal appressorium formation and virulence. Similarly, the Set1/KMT2-Cre1-hydrophobin regulatory pathway is later shown to regulate fungal virulence in another important entomopathogenic fungus Beauveria bassiana [B. bassiana.H3K4 methylation is specifically catalyzed by the KMT2 proteins, typified by Set1 that functions as a key component of the COMPASS (Complex Proteins Associated with Set1) complex. COMPASS is a highly conserved protein complex in eukaryotes, which was first discovered in revisiae . COMPASSrevisiae . Two typrevisiae ,17. The nfection . Set1-mesistance . In phytminearum , the ricujikuroi , the rice oryzae , and thehylation . H3K4me minearum . In F. fr H3K4me . H3K4me2. oryzae ,24. CclAompounds . Methyla pathway . KMT2-mebassiana . In addiSchizosaccharomyces pombe Clr4 (Cryptic loci regulator 4) and Neurospora crassa DIM5 (Defective In Methylation 5) [B. bassiana, deletion of dim5 downregulates genes related to cuticle infection and cell wall composition that contribute to fungal virulence [Botrytis cinerea, the loss of dim5 results in nearly abolished H3K9me3 and causes downregulation of pathogenicity genes associated with host signal sensing, host tissue colonization, stress response, toxin synthesis, and response to host immunity [Fusarium verticillioides, H3K9me3 is largely attenuated by dim5 disruption, leading to significant defects in fungal virulence, and unexpectedly, increased expression of melanin synthesis genes for osmotic stress tolerance [Fusarium mangiferae, the loss of kmt1 almost completely inhibits the biosynthesis of the toxins fusapyrone and deoxyfusapyrone [Epichloë festucae, genes associated with biosynthesis of lolitrems, and ergot alkaloids are silenced via H3K9me3 catalyzed by Clr4 (KMT1) under non-symbiotic culture conditions. These genes are activated by the removal of H3K9me3 when the fungus interacts with the plant host [Leptosphaeria maculans, which causes stem canker of oilseed rape, is also repressed by DIM5 and HP1 (Heterochromatin Protein 1) involved in heterochromatin formation and maintenance during axenic growth [H3K9 methylation is specifically catalyzed by KMT1 proteins, the biggest family in HKMT, exemplified by ation 5) . H3K9 meation 5) . Normal irulence . In the immunity . In the olerance . In the sapyrone . In the ant host . Expressc growth .N. crassa, PRC2 is composed of the Set-domain-containing component Ezh1 or Ezh2 (belonging to KMT6 family) with methyltransferase activity, as well as three other proteins, Eed, Npf, and Su(z)12 [Cryptococcus neoformans [E. festucae, H3K27me3 catalyzed by EzhB (KMT6), together with H3K9me3 catalyzed by ClrD (KMT1), silences lolitrems and ergot alkaloids gene clusters under axenic growth condition. H3K27me3 diminishes so that alkaloid biosynthesis is induced in planta [M. oryzae is responsible for H3K27me3 which silences virulence-associated genes (such as effectors) during vegetative growth. During the infection process, H3K27me3 is removed, immediately activating the virulence-related genes [Ustilaginoidea virens and F. graminearum [F. graminearum BP1, a reader of H3K27me, attenuates fungal virulence [H3K27 methylation is catalyzed by KMT6 that functions as a key component of the PRC2 (Polycomb Repressive Complex 2) complex. In  Su(z)12 . Npf is  Su(z)12 . Ezh2 hooformans . Similaroformans . Regulatn planta . In planed genes . Similarminearum ,40. FurtDrosophila melanogaster Ash1  is also identified to catalyze H3K36 methylation [N. crassa, transcription of the circadian gene frequency (frq) is repressed by Set2-mediated H3K36me so that frq is transcribed in a rhythmic manner, which ensures normal development of the fungus [F. verticillioides and E. festucae. In F. verticillioides, genes involved in toxin and pigment synthesis (Fumonisin B1 (FB1) and bikaverin) are activated by Set2-mediated H3K36me3 [E. festucae, transcription of effector genes can be regulated in both positive and negative ways by Set2-mediated H3K36me [F. fujikuroi [B. cinerea that demethylates H3K36me3 has been proved to affect fungal virulence and stress response in a positive way by regulating light-responsive genes [H3K36 methylation is catalyzed by Set2 (belonging to the KMT3 family) conserved from yeasts to human. In fact, Set2 is also an RNA polymerase II-interacting protein, which interacts with the C terminal domain of RNA polymerase II during transcription elongation . H3K36 mhylation ,43. H3K3hylation . H3K36 me fungus . The H3 H3K36me3 . In E. f H3K36me . Ash1, ave genes .S.cerevisiae [Penicillium oxalicum, the loss of Dot1 downregulates genes involved in extracellular glycoside hydrolase biosynthesis [Aspergillus flavus, an opportunistic fungal pathogen of oil crops and animals, Dot1 positively regulates fungal colonization on maize seeds, indicating that Dot1 might be associated with fungal pathogenicity [H3K79 methylation is specifically catalyzed by the Dot1 (disruptor of telomeric silencing 1) protein (belonging to the KMT4 family), which is the only histone methyltransferase without a SET domain . Methylarevisiae  and Dot1revisiae ,51. The ynthesis . In Aspegenicity .S. pombe, H4K20me2 catalyzed by Set9 participates in the cell cycle checkpoint. When DNA damage is detected at the checkpoint, H4K20me2 and H2A phosphorylation sites are exposed and bind with the Crb2 protein (related to DNA damage checkpoint) to start DNA repair [M. oryzae, KMT5 is proved to be responsible for H4K20me3. Deletion of kmt5 slightly inhibits fungal vegetative growth but has no impact on conidium germination, conidiation, appressorium formation, or pathogenicity [F. graminearum, KMT5 has been reported to catalyze H4K20me1/2/3 and be required for full virulence on wheat [H4K20 methylation is specifically catalyzed by the KMT5 family. While fruit flies and mammals possess two types of KMT5, KMT5A and KMT5B/C, responsible for H4K20me1 and H4K20me2/3, respectively , fungi pA repair . In the genicity . Recentlon wheat .Histone acetylation/deacetylation is one of the best-characterized dynamic and reversible histone modifications established by the opposing functions of histone acetyltransferases (HATs) and histone deacetylases (HDACs). In general, histone acetylation is associated with transcriptional activation, whereas histone deacetylation has the opposite effect on gene transcription.N-acetyl lysine. This modification neutralizes the positive charge of lysines and results in a more relaxed, open, and transcriptionally active chromatin (euchromatin) structure, enabling active gene transcription [N-acetyltransferases), MYST , p300/CBP (CREB-binding protein), basal transcription factors, and nuclear receptor coactivators [Histone acetyltransferases (HATs) are enzymes that acetylate lysines within the amino-terminal tails of histone proteins by transferring an acetyl group from acetyl-coenzyme A (acetyl-CoA) to form ɛ-cription . There ativators . Among tGNAT Familygcn5 can not derepress the expressions of amino acid biosynthesis genes [C. neoformans, Gcn5 regulates the expression of specific genes such as Kre61 that encode a β-glucan synthase involved in cell wall biosynthesis, which enables the fungus to respond appropriately to hosts [N-acetylglucosamine (GlcNAc) on host cell surface and survive in various host niches, the commensal and pathogenic yeast of humans, C. albicans GCN5-related N-acetyltransferase can bind GlcNAc through its N-terminal β-N-acetylglucosaminidase domain, which further activates N-acetyltransferase activity in the C-terminal GCN5-related N-acetyltransferase domain, resulting in promoter histone acetylation and transcription of all GlcNAc-induced genes [HATs of GNAT family have high similarity with yeast histone acetyltransferase Gcn5 . Gcn5 acts as the catalytic subunit and coordinates with other different regulatory factors in multiple high-molecular-weight protein complexes such as SAGA (Spt-Ada-Gcn5-Acetyltransferase), ADA (Ada2-Gcn5-Ada3), and SLIK/SALSA (SAGA-like). Gcn5 can acetylate nucleosomal H2B lysines K11, K16, H3 lysines K9, K14, K18, K23, and K27 in either the manner of acting alone or being associated with the HAT complexes. Because of different histone sites targeted by Gcn5 for transcriptional regulation, Gcn5 has been found to be functionally differentiated in the fungi that adapt to different hosts and environments. Gcn5 was the first identified HAT via a screen of sensitive yeast mutants in growth under conditions of amino acid limitation. Deletion of is genes . Additiois genes ,61. In tto hosts . To sensed genes .brlA promoter, the central transcription factor gene regulating fungal conidiation [B. bassiana, the absence of gcn5 blocks the normal infection against Galleria mellonella through cuticular penetration, which could be largely attribute to the repression of two cuticle-degrading proteinase genes, CDEP1 and CDEP2, in the Δgcn5 mutant  [B. bassiana, which modulates development, cell cycle progression, multi-stress responses, and virulence [gcn5 in Ustilago maydis (corn smut) results in long mycelial cells and fuzz-like colonies and influences dimorphism and virulence [A. flavus, Gcn5 is also crucial for morphological development, aflatoxin biosynthesis, stress responses, and pathogenicity [F. graminearum Gcn5 is essential for the acetylation of H3K9, H3K18, and H3K27. Deletion of FgGcn5 results in reduced perithecium formation, increased sensitivity to oxidative and osmotic stresses, and most importantly, no production of the mycotoxin deoxynivalenol (DON) that is a virulence factor enabling the fungus to spread from infected florets into the wheat rachis [Growing evidence implicates the regulatory role of Gcn5 in fungal morphogenesis, stress responses, and virulence of pathogenic filamentous fungi. Fungal conidia are required for the infection cycle of a filamentous fungal pathogen on plants and insects. Gcn5 in the SAGA complex activates an asexual development pathway by acetylating H3K14 on the chromatin of idiation . In B. bnfirmed) . Anotherirulence . Deletioirulence . In the genicity . F. gramt rachis .Aspergillus nidulans and the soil-dwelling bacterium Streptomyces rapamycinicus triggers the fungal SAGA/ADA complex containing Gcn5 and Ada2 proteins, and subsequently leads to an increased acetylation of H3K9 specific for the induction of the secondary metabolite gene cluster involved in orsellinic acid biosynthesis in A. nidulans [Pseudomonas piscium isolated from the wheat head microbiome secrets the compound phenazine-1-carboxamide that directly inhibits the activity of Gcn5 in F. graminearum, leading to the deregulation of histone acetylation, repression of gene expression, and suppression of fungal growth and pathogenicity [Interestingly, several studies show that alterations of histone acetylation in fungi could be triggered by the interacting bacteria via targeting fungal Gcn5. The intimate contact between nidulans . The bacgenicity . TherefoM. oryzae is important for the establishment of rice blast disease, and Gcn5 negatively regulates light- and nitrogen-starvation-induced autophagy by acetylating the autophagy protein Atg7 in cytoplasm [M. oryzae [Notably, HATs of the GNAT family can also catalyze non-histone proteins . Gcn5 diytoplasm . In cont. oryzae .MYST FamilyThe MYST family is named after the founding members, including MOZ (monocytic leukemia zinc-finger protein), YBF2 (yeast binding factor 2)/SAS3 (something about silencing 3), SAS2 (something about silencing 2), and TIP60 (Tat interactive protein-60). The MYST proteins are the largest HAT family, mediate a diverse variety of biological functions, and preferentially acetylate histones H4 and H2A . These MB. cinerea, Sas2 regulates the transcription of plant cell wall degradation and oxidative stress-response genes by controlling the acetylation level of H4K16, thereby affecting the virulence and oxidative sensitivity [Sas2 is the catalytic subunit of the SAS HAT complex (Sas2p-Sas4p-Sas5p) and responsible for the acetylation of H4K16 . Sas2 issitivity .S. cerevisiae. However, its simultaneous disruption of Gcn5 causes extensive, global loss of H3 acetylation and cell cycle arrest that is synthetically lethal to cells [M. oryzae alone has a profound effect on pre-penetration development, including asexual reproduction, germination, and appressorium formation [F. graminearum, Sas3 is indispensable for the acetylation of H3K4, while FgGcn5 is essential for the acetylation of H3K9, H3K18, and H3K27. Both are required for DON biosynthesis and pathogenicity [A. flavus, including MystA (Sas2 orthologue) and MystB (Sas3 orthologue), with opposite functions have been identified. MystA acetylates H4K16 and plays a negative role in sclerotia formation and aflatoxin B1 production, while MystB acetylates H3K14, H3K18, and H3K23 and positively affects sclerotia formation and aflatoxin B1 production [M. robertsii, results in a decrease in global H3 acetylation and activation of orphan secondary metabolite genes [B. bassiana has shown to mediate global gene transcription and/or post-translation through H3K14 acetylation, which enables regulating multiple stress responses and plays an essential role in sustaining the biological control potential of the fungus against arthropod pests [Sas3, as a catalytic subunit of the NuA3  complex, is responsible for H3 acetylation  . Since Sto cells . Unlike ormation . In F. ggenicity . Two Mysoduction . Deletiote genes . Mst2  complex that is more complex and consists of 13 proteins. Esa1/NuA4 is capable of acetylating multiple sites, most notably H4K5, K8 and K12, H2AK7 and H2BK16 . Esa1 istylation ,90,91. Ealbicans . Overexpnidulans . H4 acetminearum . Interesminearum . Esa1 isrevisiae , which r. oryzae . HoweverRtt109C. albicans pathogenicity, suggesting a unique target for therapeutic antifungal compounds [Aspergillus fumigatus, the loss of Rtt109 also attenuates virulence in the G. mellonella model, as well as hypersensitivity to genotoxic agent [rtt109 in B. bassiana abolishes H3K56 acetylation and triggers H2A-S129 phosphorylation that affects global gene activity, and consequently results in increased sensitivity to multiple stresses and reduced virulence through normal cuticle infection [A. flavus [Rtt109  is fungal-specific, responsible for the acetylation of H3K9, H3K27, and mostly H3K56 . Activatompounds ,102. In ic agent . Deletionfection . In addi. flavus .N-terminal tails. This restores the positive charge on the histone tails [2+ that acts as a coactivator for deacetylase activity. Class III HDACs are homologous to yeast Sir2 (NAD+-dependent silent information regulator 2). Class I, II, and III HDACs have been extensively studied in fungi. However, Class IV HDAC has only one member, HDAC11, that is highly conserved and presents in all eukaryotes except fungi [Histone deacetylases (HDACs) are a group of enzymes that catalyze the deacetylation by removing acetyl residues from the ε-amino group of lysine residues in the histone ne tails . In contne tails . Based one tails . Class Ipt fungi .Class I HDACsS. cerevisiae, which deacetylates the histones H3 and H4 [B. bassiana, Rpd3 plays essential roles in regulating transcription and posttranscriptional lysine modification of genes in the central development pathway, and the deletion of Rpd3 causes severe growth defects, reduction in conidiation, and drastic attenuation in virulence [F. pseudograminearum [A. nidulans, A. fumigatus, B. cinerea and M. oryzae, is lethal [B. cinerea and M. oryzae results in dramatically impaired infection structure formation, oxidative stress response, and virulence [B. cinerea [M. oryzae [Rpd3 (Reduced potassium dependency 3) is the founding member of the Class I HDACs in 3 and H4 . In fila3 and H4 . Rpd3 fu3 and H4 ,112. In 3 and H4 ,114. Yea3 and H4 . In B. birulence . Dep1, aminearum . Howevers lethal ,118,119.irulence . Transcr. oryzae .S. cerevisiae [Cochliobolus carbonum, a fungal pathogen of maize, Hos2 affects extracellular depolymerase expression and virulence [F. graminearum HDF1, an ortholog of Hos2, is involved in spore formation, DON production, and plant infection [C. albicans attenuates cAMP-PKA signaling to repress yeast-to-filament transition and modulate white–opaque switching [U. maydis, Hos2 acts as a downstream component of the cAMP-PKA pathway to directly control the expression of mating-type genes via H4K16 deacetylation, and thus is required for the dimorphic switch and pathogenic development [M. oryzae, indicating that it is likely to be conserved in filamentous fungal pathogens [M. oryzae Hos2, as the core component of the Tig1 complex, deacetylates H3K18 and H4K16 and is required for full virulence through transcriptional regulation of ROS detoxifying genes and effector genes [B. bassiana not only directly deacetylates H4K16 but also indirectly affects H3K56 acetylation and phosphorylation of H2A serine129 (H2A-S129) and cyclin-dependent kinase 1 (CDK1) tyrosine 15 (CDK1-Y15), which further regulates sensitivity to DNA damage and oxidative stress, cell cycle, and fungal virulence [M. robertsii HDAC1 is downregulated due to the decreased HAT1-mediated H3K4 acetylation in its promoter bound chromatin, which further leads to the derepression of H3K56 acetylation and activation of the regulatory protein COH1 (colonization of hemocoel 1) gene. COH1 physically contacts the transcription factor COH2 (colonization of hemocoel 2) to reduce COH2 stability, which thus switches off genes for cuticle penetration and switches on key genes for hemocoel colonization. This regulatory cascade precisely controls a distinct set of genes of M. robertsii in response to cuticle and hemocoel microenvironments during infection of insects [Hos2 (Hda one similar 2), another member of Class I HDACs, is a component of the Set3 (Su(var)3–9, enhancer-of-zeste and trithorax 3) complex (Set3C) . Hos2 sprevisiae . Growingirulence . F. gramnfection . The Setwitching ,128. Howelopment . The relathogens . M. oryzor genes ,131. Morirulence . When pe insects .Class II HDACsF. fujikuroi is required for normal germination, vegetative growth, and fungal virulence [U. maydis, Hda1 is essential for teliospore development, and acts as a repressor of the biotrophic marker gene mig1 that encodes a small, secreted, cysteine-containing hydrophilic protein specifically expressed during infection [HDA is a Class II histone deacetylase complex consisting of three subunits: the catalytic subunit Hda1 (Histone deacetylase 1) and accessory factors Hda2 and Hda3. HDA complex specifically deacetylates acetylated lysines on H3  and H2B (K11 and K16) , and antirulence . In U. mnfection ,143.C. albicans, leading to its compromised chaperone function [C. albicans that controls the expression of hypha-specific genes to modulate the yeast-hyphal transition [Some Class I and Class II HDACs have also been proved to target nonhistone proteins. Rpd3 has been identified as a negative regulator of autophagy since deletion of Rpd3 increases Atg3 acetylation and accelerates autophagy in yeast . Hda1 anfunction . The aceansition .Class III HDACs+ [C. albicans, Sir2 controls phenotypic switching and chromosome stability by organizing chromatin structure [C. glabrata, Sir2 suppresses the expression of EPA1 that encodes the major epithelial adhesin important for fungal survival and proliferation in the host environment [C. neoformans shortens the replicative lifespan, impairs fitness, and decreases virulence [M. oryzae, Sir2 is dispensable for appressorium development and rice cuticle penetration but is essential for biotrophic growth due to its role in neutralizing host ROS [B. bassiana, Sir2 regulates a distinct set of cellular targets that affect conidiation, carbon utilization, stress responses, blastospore development, and virulence [Class III HDACs are sirtuin family enzymes that are related to the transcriptional repressor Sir2 (Silent information regulator 2) in budding yeast . In cont+ . Sir2 de+ . Sir2-de+ ,150,151.+ . Therefotructure . In the ironment . The losirulence ,155. Asihost ROS . The undirulence . In addi2+ sites via a hydroxamic acid group [A. fumigatus via the inhibition of the RpdA C-terminal [C. albicans sensitivity to azoles and the related antifungals [M. oryzae with HDAC inhibitors of the Rpd3/Hda1 family and TSA results in the inhibition of appressorium formation and decreased pathogenicity, respectively [C. neoformans, both of TSA and NaBut can attenuate fungal virulence by affecting their growth at 37 °C, capsule expansion, and melanin synthesis [C. neoformans. Otherwise, a synthetic fungal-specific HDACI, MGCD290, described to be specific for Hos2 in Candida species, also functions as an inhibitor of several clinical pathogens’ growth, such as Candida and Aspergillus species, in combination with fluconazole, voriconazole, and posaconazole [Since HDACs are involved in regulating genes required for fungal survival, development, and pathogenicity, they are considered as potential targets of antifungal agents . The epiid group . NaBut iid group . TSA treterminal . TSA treifungals . Treatmeectively . In the ynthesis . Furtherconazole . Apart fEpigenetic mechanisms such as histone modifications have been elucidated to play a pivotal role in regulating gene expression in filamentous fungal pathogens, and thus modulate a wide range of biological processes, including fungal sporulation, morphological differentiation, environmental stress responses, biosynthesis of secondary metabolites, and pathogenicity , Table 1Histone modifications regulate gene transcription via changing the chromatin structure and controlling the access of transcription factors to gene promoters ,106. GenIt is becoming clearer that the antagonistic activity of modification writers and their corresponding erasers determines the dynamic regulation of gene expression in fungi ,135,145.Verticillium dahliae is able to secrete an effector  to the plant nucleus to interfere with the nuclear export of AGO1-miRNA complexes, resulting in the inhibition of antifungal RNAi and increased virulence in plants [Phytophthora sojae binds to the ADA2 subunit of SAGA complex in the host, and disrupts the association of ADA2 with the catalytic subunit GCN5 to suppress H3K9 acetylation and thus increase plant susceptibility [P. sojae, recruits a host cytoplasmic transacetylase into the nucleus that acetylates histones H2A and H3, and thus promotes susceptibility to the pathogen [Rhizophagus irregularis is translocated into the host nucleus where it interacts with the plant core nucleosome protein H2B and impairs the mono-ubiquitination of H2B, which results in the suppression of defense gene expression [In addition, small RNAs (sRNAs), another type of epigenetic regulator, have been recently recognized as trafficking effectors to mediate bidirectional transkingdom RNAi in interacting organisms ,171. Then plants . The cyttibility . PsAvh52pathogen . Nuclearpression . Aside fpression ,182. In pression ,70. Howe


Arabidopsis thaliana, Gossypium hirsutum, Oryza sativa, Cucumis sativus, Solanum lycopersicum, Nicotiana tabacum, and Artemisia annua. Here, we review current knowledge of the molecular mechanisms underlying fate determination and initiation, elongation, and maturation of unicellular, bicellular and multicellular trichomes in several representative plants. We emphasize the regulatory roles of plant hormones, transcription factors, the cell cycle and epigenetic modifications in different stages of trichome development. Finally, we identify the obstacles and key points for future research on plant trichome development, and speculated the development relationship between the salt glands of halophytes and the trichomes of non-halophytes, which provides a reference for future studying the development of plant epidermal cells.Plant trichomes, protrusions formed from specialized aboveground epidermal cells, provide protection against various biotic and abiotic stresses. Trichomes can be unicellular, bicellular or multicellular, with multiple branches or no branches at all. Unicellular trichomes are generally not secretory, whereas multicellular trichomes include both secretory and non-secretory hairs. The secretory trichomes release secondary metabolites such as artemisinin, which is valuable as an antimalarial agent. Cotton trichomes, also known as cotton fibers, are an important natural product for the textile industry. In recent years, much progress has been made in unraveling the molecular mechanisms of trichome formation in  Trichomes are visible on leaves, stems and flower organs of many terrestrial plants . These hSolanum lycopersicum), and cause the appearance of a “hairy plant,” while others are small, such as the shield coat of mint species , tobacco (Nicotiana tabacum), tomato and snapdragon (Antirrhinum majus) are multicellular  trichomes (cotton fibers) play an important role in resisting pests such as cotton boll weevil  proteins, bHLH transcription factors and C2H2 zinc finger proteins, and negative regulators, such as R3-MYB transcription factors, play a key role in this process .Arabidopsis. GLABROUS INFLORESCENCE STEMS (GIS), GIS2, GIS3, ZINC FINGER PROTEIN 1 (ZFP1), ZFP5, ZFP6, and ZFP8 all encode C2H2 zinc finger proteins that play important roles in trichome development (GIS functions upstream of the trichome initiation complex GLABRA1 (GL1)-GLABRA3 (GL3)-TRANSPARENT TESTA GLABRA 1 (TTG1) (GL1-GL3-TTG1) and downstream of the gibberellin (GA) signal repressor SPINDLY (SPY). It responds to GA and promotes inflorescence trichome initiation. This pathway is negatively regulated by SPY and the DELLA repressor GIBBERELLIC ACID INSENSITIVE (GAI) (GIS3 receives GA and cytokinin (CTK) signal transduction and directly targets the downstream genes GIS and GIS2 to regulate the production of trichomes  . GIS3 rerichomes . ZFP6 re of ZFP5 . ZFP5 ac of ZFP5 , 2012. Ibidopsis . TRICHOMrichomes .GL1 was the first factor found by researchers to control the development of plant trichomes (GL3 encodes a bHLH transcription factor and has redundancy with ENHANCER GLABRA3 (EGL3) (GL3 and EGL3 leads to a trichome defect. TRANSPARENT TESTA GLABRA (TTG) has been studied since the 1990s  encodes an importin β-domain protein that has the same function as GL1, GL2 and GL3 in regulating trichome development  and CAPRICE (CPC) negatively regulate the development of trichomes; they mainly encode R3-MYB transcription factors  gene is also a negative regulator of trichome development. SPL temporally controls trichome distribution during flowering. Increasing SPL transcription levels were associated with progressive loss of stem hair cells. SPL9 directly activates its expression by binding to TCL1 and TRY promoters, which is independent of GL1; GIS-dependent pathways do not affect SPL9 regulation of TCL1 and TRY (TTG2 is regulated by MYB and bHLH genes. TTG2 mutations lead to phenotypic defects in trichome development (reviewed by ttg2 mutants are unbranched (> 95%), and the number of trichomes formed per leaf is approximately halved, and even glassy and twisted trichomes appear  . A doublhe 1990s , 1999. Tntiation . The semelopment . SUPER Selopment . SAD2 ca and GL2 . TRIPTYC factors . They carichomes . The R3-al cells . etc1 mue mutant . SQUAMOS and TRY . SPL is  and TRY . TTG2, t and TRY . Analysis appear . GL2, a elopment . The upsrichomes . Furtherrichomes .SIAMESE (SIM), CONSTITUTIVE EXPRESSION OF PR GENES 5 (CPR5) and RETINOBLASTOMA-RELATED (RBR) negatively regulate trichome branching by controlling nuclear replication (sim mutant has fewer branched trichomes than the wild type because the transition of trichome cells from mitosis to intranuclear replication is inhibited (reviewed by SIM is likely a direct target for GL3 to control intracellular replication. In a chromatin immunoprecipitation (ChIP) experiment, GL1 and GL3 bound to the promoter region of SIM (CELL CYCLE SWITCH PROTEIN 52 A1 (CCS52A1) and SIM cooperate to inhibit the accumulation of mitotic cyclin to establish the inner loop of trichomes  acts upstream of CYCLIN-DEPENDENT KINASE B1;1 , affecting endonuclear replication and cell growth in Arabidopsis. The da3-1 inhibitor SUPPRESSOR OF DA3-1 6; SUD6, which encodes CYCLIN-DEPENDENT KINASE G2 (CDKG2), promotes nuclear replication and cell growth and ultimately increases the number of trichome branches  and SIM  and RBR genes and plays a key role in endonuclear replication (ANGUSTIFOLIA (AN) enriches high concentrations of microtubules at the top of trichome cells (ZWICHEL (ZWI) is involved in the initiation of trichome branching (STI and TUBULIN FOLDING COFACTOR A/C (TFCA/C) are involved in the formation of trichome branching (FASS/TONNEAU2 (TON2) and SPIKE are involved in trichome branching by regulating microtubule tissue (INHIBITOR/INTERACTOR OF CDK 1 (ICK1)/KIP RELATED PROTEIN 1 (KRP1) positively regulates trichome branching. Overexpression of ICK1/KRP1 in Arabidopsis reduces intranuclear replication and cell size and induces cell death (ROOT HAIRLESS 2 (RHL2) and HYPOCOTYL6 (HYP6) encode subunits of DNA topoisomerase VI, indicating the existence of DNA replication pathways specific to internally replicating cells  mutants, trichomes are smaller, defective, branched, and have lower nuclear DNA content than in the wild type (kaktus (kak) mutants, trichome branching increases , DISTORTED (DIS) and ROP are involved in trichome cell actin cytoskeleton expansion  leads to significantly more leaf trichomes  can degrade under the action of JA, release MYB-bHLH-WD40 activity and promote trichome development. NUCLEOREDOXIN 2 (NRX2) promotes JA-mediated trichome formation in Arabidopsis; trichome formation is significantly reduced in the nrx2 mutant compared to in the wild type. JMJ29 is a histone demethylase-containing JMJC domain belonging to the JHDM2/KDM3 group. It participates in epidermal hair development by directly regulating GL3 expression  are involved in trichome differentiation in richomes . Salicylrichomes . CTK andrichomes . In addirichomes . GAI andelopment . TEM1 anitiation . A ChIP pression . The celild type . These mynthesis .TRY  promotes GL3 and EGL3 degradation, which in turn inhibits epidermal branching. As a histone chaperone, CAF-1 participates in trichome development through a pathway independent of internal duplication (reviewed by N6-methyladenosine (m6A) is the most common genomic marker. Similar to DNA methylation, known regulatory genes can express m6A, and factors of different functions can also write, clear and read m6A ] is similar to that of Arabidopsis genes have been cloned and identified. GhMYB2 has a similar sequence to Arabidopsis GL1 and controls cotton fiber cell fate determination  in the TRANS-ACTING SIRNA GENE 4 (TAS4) family. Four families of genes encoding ta-siRNA were found in Arabidopsis, namely TASl, TAS2, TAS3, and TAS4. TAS4 was discovered when a special algorithm clustered 21-base fragments within the genome. After the primary transcript of TAS4 was recognized by miR828, it was cleaved to generate the corresponding ta-siRNA. miR828 directs the cleavage of RNA derived from TAS4 and initiates the production of phasic small interfering RNA (siRNA) dependent on RNA-DEPENDENT RNA POLYMERASE 6 (RDR6)  or RDR6 of ta-siRNAs in gl1 GhMYB2D overexpressing body can restore trichome development  . Overexpelopment . The funTAS site . RNA-indTAS site . CleavedTAS site , which crichomes . GhMYB25GhMYB109 . GhMYB10eriments . GhMYB10d GhACT1 . The gend GhACT1 . The MYBr length . A yeast complex . In the ild type . The probidopsis .PROTODERMAL FACTOR1 (GbPDF1) encodes the homologous framework HD-ZIP protein, which plays a role in fiber initiation and early elongation by interacting with PPIP1, PPIP2, and PPIP3. Knockout of GbPDF1 can result in delayed fiber initiation, fiber shortening, and decreased lint percentage, indicating that GbPDF1 plays an important role in fiber development  is necessary for cotton fiber initiation, and RNAi-mediated inhibition of GhVIN1 leads to a significant decrease in VIN activity, thereby forming a fiber-free seed phenotype in a dose-dependent manner  encodes CYP734A1, which degrades brassinosteroid (BR) through C26 hydroxylation and negatively regulates fiber development. As an acidic protein, Gh14-3-3 not only interacts with GhBZR1, but also regulates BR signals, thereby promoting fiber initiation and elongation  biosynthesis and transport plays a major role in the accumulation of AUX in the ovule and fiber. The AUX efflux mediated by the IAA efflux transporter (PIN) in the ovule participates in the accumulation of AUX and the development of cotton fiber . Excessielopment . The AUXd fibers . Overexpet genes . GhARF2-itiation . Similarn cotton . During on fiber . Exogenoin fiber . PAGODA1ongation .Transcription factors and hormone signaling pathways are also involved in the cotton trichome elongation stage (3–20 DPA).GhMYB212 also controls expression of the sucrose transporter gene GhSWEET12, mediates the transport of sucrose and glucose, and mediates fiber development  of fiber length . Yeast one-hybrid and transient dual-luciferase assays showed that GhbHLH13 can activate GhPEL76 and regulate cotton fiber elongation by binding to the G-box in the promoter region of GhPEL76  have been cloned from cotton fiber  is an important structural phospholipid, and exogenous PtdIns application can promote cotton fiber elongation . In tranongation . ARABINOon fiber . GhAGP4  quality . Transcr quality . Northerer cells .MAT (GA_Ed0052D12f), which is a homolog of GhMAT4 (Arabidopsis gene ANKYRIN REPEAT PROTEIN 2A (AKR2A) promotes cotton fiber elongation by increasing ETH biosynthesis and synergistic action with AUX accumulation , a set of enzymes synthesize secondary cell walls (SCWs). The NAC-MYB-CESAs module defines the central pathway of SCW cellulose biosynthesis.Gossypium hirsutum, GhFSN1 is a NAC transcription factor; it regulates SCW biosynthesis in cotton fibers. GhFSN1 positively regulates the formation of cotton fiber SCWs by regulating the expression of its downstream genes GhIRX12, GhMYB1, GhGUT1, and GhDUF231L1. Overexpression of GhFSN1 by the 35S promoter increases cotton fiber SCW thickness and slightly reduces fiber length  transcription factors act as the main switch in the NAC-MYB-cellulose synthases (CESAs) pathway . In Gossr length .GhMYB46_D13 and GhMYB46_D9, are highly expressed in 20 DPA fibers. Both GhMYB46_D13 and GhMYB46_D9 can bind the promoter of the cotton fiber SCW cellulose synthase gene, enhancing its expression and promoting fiber SCW thickening , and GhMYB1 is specifically expressed in 19 DPA fibers. A yeast one-hybrid assay showed that GhMYB1 binds to the GhGDSL promoter, indicating that GhMYB1 can regulate GhGDSL during fiber development  genes in cotton are divided into six subclasses, of which GhCESA4, GhCESA7, and GhCESA8 are mainly involved in SCW development , overexpression of the marshmallow sucrose synthase gene pocotyls . GhBRI1 n stages .A regulation model of cotton trichome (fiber) initiation, elongation, secondary cell wall deposition and maturation are shown in Oryza sativa) leaf trichomes are bicellular. They are arranged in a cylindrical shape between the stem veins of the upper and lower epidermis of the leaves, the morphological photographs of rice leaf trichomes were shown in Rice  was located within 21 kb between chromosome 5 markers M6 and M7. In a complementary experiment, weakening the expression of GLR1 significantly reduced or completely removed the number of trichomes, and the constitutive expression of GLR1 in the knockout line NILglr1 rescued the hairless phenotype of T0 generation transgenic lines (DEGENERATIVE PALEA (DEP) can restore the formation of bristle-type trichomes on the leaves and glumes of hairless rice, indicating that DEP can regulate trichome formation on leaves and glumes , DEP and NUDA encode a homologous domain protein similar to that encoded by WUSCHEL (WUS); these genes are located at the same site on chromosome 5 and regulate rice trichome formation  was induced in the light-leaf mutant and that of one gene (LOC_Os01g70100) was repressed in the optica mutant. Therefore, LOC_Os01g70100 is a candidate gene for GLR2 (ESTRICTION FRAGMENT LENGTH POLYMORPHISM (RFLP) marker was used to preliminarily map nd RG403 . Researcnd RG403 . The ligic lines . Complemd glumes . GLR1, Wormation . The NUD OsWOX3B . GLR2 hafor GLR2 .SQUAMOSA PROMOTER BINDING PROTEIN-LIKE10 (OsSPL10) also controls trichome initiation and positively regulates rice trichome formation   family gene ormation . Knockouhenotype . At the id (NAA) . OsTCL1 e plants . HAIRY LOsYUCCA5 .OsGL6 localizes to the lower 79-kb region of chromosome 6. OsGL6 is a natural allele of OsHL6, which can stimulate the initiation of trichomes. In OsGL6 overexpressing rice, OsGL6 can promote trichome initiation but does not affect trichome elongation  is an indica rice variety from Sri Lanka with hairy leaves. SWWRHL6 is a novel allele of the reported HL6 locus that regulates trichome formation in rice. Transgene complementation and knockout experiments confirmed that SWWRHL6 regulates rice trichome elongation  is a common vegetable worldwide. From stems and leaves to flowers, branches, fruits, and tendrils, their surface is covered with trichomes. The trichomes on its fruit are called thorns, and they have a multi-layered tubercule underneath (Cucumber (derneath . Both thderneath .csgl1 and csgl3), type I trichomes exist on the fruits of all cucumber varieties. Type I trichomes consist of a single short stalk with 3–5 cells and a 4–8-cell head region with glandular functions  and CsGL3 are two alleles of the HD-ZIP IV family; they play an important role in the fate determination and initiation of cucumber glandular hairs. Mutations in these two genes present a completely hairless phenotype on leaves, stems, flowers, sepals, and fruits , TINY BRANCHED HAIR (CsTBH), and MICRO-TRICHOME (CsMICT) genes of the HD-ZIP I family are involved in the formation of cucumber trichomes. Under scanning electron microscopy (SEM), many papillae can be observed on the epidermis of csgl1 mutant leaves. The density of papillae is similar to that of wild type trichomes, indicating that CsGL1 may be involved in the development of trichomes of leaves but not in fate determination and initiation  gene and regulate its expression, thereby affecting the development of multicellular fruit trichomes  into Arabidopsis can significantly inhibit the development of leaf trichomes. Researchers speculate that the CsTRY gene inhibits the development of cucumber trichomes, and the CsMYB6 gene, which is similar to CsTRY, negatively regulates the formation of cucumber trichomes (The MYB-type transcription factors CsMYB6 (Csa3G824850) and CsTRY (Csa5G139610) negatively regulate cucumber fruit spine initiation . Transforichomes , 2021.Tu is specifically expressed in cucumber tumor cells  lines and completely absent in all 56 non-wart (nWty) lines. Moreover, Tu was required for the Wty fruit phenotype in Tu transgenic cucumber plants (The C2H2 zinc finger protein gene or cells . Tu is aormation . CsGL1 h nodules . Tu was r plants .CsTTG1 (Csa4Gm097650) plays a key role in cucumber flowering and trichome and fruit tumor formation. Silencing of CsTTG1 inhibits the formation of fruit thorns  is highly expressed in cucumber pericarp (including tubercule and thorns). A mutant of the pression .CsGA20ox1 reduces the length of cucumber fruit spines (NUMEROUS SPINES (NS) (Csa2G264590) gene encodes AUX transporter-like protein 3, which is a key negative regulator gene that determines the thorn density of cucumber fruit  and GA3 effect epidermal differentiation and fruit thorn development. They affect the number of trichomes in each fruit. Both 6-Benzylaminopurine (6-BAP) and GA stimulate the formation of trichomes in cucumber fruit in a concentration-dependent manner . GA oxidt spines . The NUMer fruit . Through pathway .A regulation model of cucumber trichome development was shown in Nicotiana tabacum L.), including Nicotiana benthamiana L., is commonly used as a heterogeneous production platform as an important model plant for basic biological research. It is a multicellular hairy plant that is widely cultivated worldwide. Most studies on multicellular trichomes in tobacco have primarily focused on morphological observations and identification of their secretions; few studies have investigated the molecular mechanisms of multicellular trichome differentiation in tobacco. Tobacco has three types of trichomes: long-stalked glandular trichomes (LGT), short-stalked glandular trichomes (SGT) and non-glandular trichomes (NGT) (Tobacco (es (NGT) . The glaes (NGT) .NbGIS has a positive regulatory effect on the development of tobacco glandular trichomes. In response to GA signals, it can control glandular trichome initiation and significantly affects the accumulation and expression of GA biosynthesis marker genes, which may lead to tobacco growth and maturity  gene is an HD Zip IV transcription factor  can promote the formation of LGT, while overexpression of NtCycB2 (NtCycB2-OE) can reduce LGT density  and its wild relative (Lycopersicon esculentum) have seven different trichome types. Types II, III, and V are non-glandular hairs composed of a neck and base. They act as a physical barrier to function in resisting diseases and insects. Types I, IV, VI, and VII are glandular hairs, the morphological photographs of tomato trichomes were shown in Cultivated tomato  gene encodes an HD-ZIP IV transcription factor that regulates tomato type I trichome formation mainly through heterodimer formation with the B-type cyclin SlCycB2 . SlWo also actively regulates mitosis in multicellular trichomes  than that in the wild type (NCK-ASSOCIATED PROTEIN 1 named as Hairless-2 (Hl-2) in tomato caused serious distortions in all trichome types  directly interacts with SlWo to regulate tomato trichome initiation  to regulate trichome initiation and elongation by regulating SlZFP6 expression in tomato (C2H2 zinc finger proteins have been isolated and identified in tomato trichome formation. The C2H2 zinc finger protein gene is homologous with richomes . H overe of SlWo . In addiitiation . Overexprichomes . Researcn tomato .SlMYC1) is involved in glandular hair regulation but not non-glandular hair regulation. SlMYC1 is a bHLH transcription factor that regulates the development of type VI glandular hairs in tomato . Non-secretory glandular trichomes are also called T-shaped trichomes (TSTs) or T-type non-glandular trichome (TNGTs) because their appearance is similar to the letter “T.” The morphological photographs of Artemisia trichomes were shown in In recent years, artemisinin has received widespread attention due to its antimalarial effects. The glandular hair of A. annua are similar to those in tomato, and most of them belong to the R2R3-MYB and HD-ZIP subfamilies , indicating that AaMYB1 expression rescues the Atmyb61-2 mutant phenotype  had 20 and 66% more trichomes with 1.4 and 2.56% higher artemisinin content on leaves and inflorescences, respectively (The AP2 transcription factor TRICHOME AND ARTEMISININ REGULATOR 1 (TAR1) regulates trichome development in henotype . In addiectively .AaSPL9 increases the density of glandular hairs by 45–60% and the artemisinin content by 33–60%, indicating that AaSPL9 positively regulates the initiation of glandular hairs. Yeast one-hybrid, dual-luciferase and electrophoretic mobility shift assay (EMSA) demonstrated that AaSPL9 activates the expression of AaHD1 by directly binding the GTAC-box of the AaHD1 promoter to regulate the initiation of glandular hairs in A. annua (SQUAMOSA promoter-binding protein-like (SPL) is a kind of plant-specific transcription factor, studies have shown that overexpression of A. annua .A. annua trichome initiation. Trichome formation is mainly regulated by JA. AaJAZ8 is a repressor of the JA signaling pathway in A. annua. It can inhibit the activity of the positive regulator AaHD1 and reduce the density of glandular hairs  leaves: microscopic bicellular hairs, macrohairs, and prickle hairs (OCL4 in Arabidopsis resulted in a glabrous rosette leaf phenotype (GLOSSY1 (ZmGL1) gene is a component of the pathway leading to maize seedling epidermal wax biosynthesis. zmgl1 mutants have altered maize epidermal development, including altered trichome size and impaired cuticle structure  distributes on its leaves, stems, branches, sepals, pedicels and fruit, and the trichomes on the fruit are often called thorns; they affect the appearance and sensory quality of the plant  in tobacco resulted in more trichomes, suggesting that AmMIXTA regulates trichome development in snapdragon (AmMIXTA has a role in regulating snapdragon trichome development (reviewed by AmMYBML1 can promote trichome development in floral tissues (Overexpression of the MYB-like gene apdragon . Under t tissues .Trichomes are small structures on plant arial parts. Their developmental regulation involves many hormones, transcription factors and metabolic pathways. The key genes in development of different trichome types are summarized in Arabidopsis. Development of special forms of trichomes has been studies less, such as thorns on cucumber fruit and roses, which affect field management and picking efficiency. In addition, little research progress has been made on trichomes of monocotyledonous plants such as rice. Extensive research is needed on trichome development in various horticultural plants from multiple perspectives. Future research should focus on determining internal connections and interactions of trichomes with seeds and other organs; key regulatory factors related to trichome development; and how these regulatory factors change with environmental or developmental changes. This will provide new insights and genetic resources for plant development and crop improvement. Depending on the trichome-specific genes, corresponding promoters, such as FBP7 and E6, can also improve crop yield and quality. Therefore, the identification and application of tissue-specific promoters and specific genes are of great significance to the research of plant development and the advancement of crop genetics.Many trichome development studies have focused on model plants such as Many positive regulators and pathways in trichome development have been identified, but our understanding of negative regulatory mechanisms and key factors is still limited. For example, many C2H2 zinc finger protein transcription factors that positively regulate trichome development have been found in different species, but similar negative regulator have not been reported.Plant hormones play an important role in trichome development. However, the regulatory mechanism of these plant hormones requires further research. AUX, BR, GA, and JA positively regulate cotton fiber initiation, whereas ABA and CTK negatively regulate cotton fiber initiation. The important roles of plant hormones in trichome development are well known, but the interactions among these hormones and their molecular mechanism requires further study. This will help identify and analyze the positive and negative factors in trichome development.A. annua and cucumber have shown that C2H2 zinc finger proteins, and HD-ZIP- and MYB-type transcription factors play a key role in the glandular hair initiation and development. The biosynthesis of cytoskeleton and cutin also has an important role in the morphogenesis of glandular hairs. Interestingly, the reported glandular hair development genes often also affect the development of non-glandular hairs in plants. Therefore, it is necessary to further explore the relationship between glandular and non-glandular hair development and genes that independently regulate glandular hair development.Glandular hairs development is closely related to their density on the plant surface and the types and contents of secondary metabolites. Studies in tomato, Limonium bicolor has no trichomes but has multicellular salt glands. The salt-secreting capacity of the salt glands significantly improves the salt tolerance of L. bicolor. The excess salt in the plant tissue can be excreted through salt glands to regulate the ion balance in the plant. In the epidermal structure of non-halophytes, such as Arabidopsis, tobacco and tomato, there are trichomes but not salt glands, while the leaf epidermal structure of L. bicolor has salt glands but not trichomes. The distribution of salt glands on L. bicolor leaves is similar to that of trichomes in Arabidopsis, they are both arranged in an interval pattern (L. bicolor salt glands at different developmental stages showed that many differentially expressed genes in the early stage of salt gland development were homologous to the key genes in trichomes development in plants such as Arabidopsis (A. annua and tobacco have a strong secretory ability. Similarly, L. bicolor secretes salt through salt glands. Therefore, we speculate that there are certain similarities between salt-secreting glands and secretory trichomes. This raises many questions. Is there a homologous relationship between the development of trichomes and salt glands? Are the key genes that determine salt gland development homologous with the key genes in trichome development? What is the molecular evolutionary relationship between trichomes and salt glands? We propose the “common origin hypothesis” of salt glands and plant trichomes in non-halophytes, that is, there is a “common ancestor gene” that controls the differentiation of proepidermal cells, and separation may occur at a certain node in the long-term evolution of plants. One gene type controls the differentiation and development of proepidermal cells into salt glands to adapt to high salt environments, while another type controls the development into trichomes to survive under other biotic and abiotic stressors, such as arid and semiarid regions (Similarities between trichomes and salt glands are also worthy of future study. Most plants have trichomes; however, the aerial part of the salt-secreting halophyte  pattern . Both sa pattern . In summbidopsis . Further regions . To explInnovation and application of cutting-edge science and technology and experimental methods will help future research on the molecular mechanisms of plant trichome development. These include chloroplast genetic engineering, nanoparticle bombardment transformation, the VIGS method, omics technology, single-cell sequencing and CRISPR-Cas9. With the rapid development and effective application of modern technologies in model plants, horticultural plants and crops, more genes and signaling pathways involved in trichome development will be identified.GH and YL wrote this manuscript. ZY, CW, and YZ participated in the writing and modification of this manuscript. BW and GH conceptualized the idea. All authors read and approved the final manuscript.The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. 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