the eukaryotic genome is functionally and spatially organized . during interphase , chromosomes fold into topologically associated domains ( tads ) and divide into heterochromatin and euchromatin . also , chromosomes associate with nuclear structures and occupy distinct territories within the nucleus . within these territories , individual genes are positioned with respect to each other and with respect to stable nuclear structures . for example , in metazoa large transcriptionally repressed lamina associate domains ( lads ) position along the nuclear periphery and interact with the nuclear lamina . importantly , the spatial organization of the genome is dynamic and the position of individual genes often changes upon activation or repression . for example , during development , lads can be remodeled to accommodate the repositioning of genes ; the -globin and myod genes move away from the nuclear lamina upon transcriptional activation . many active genes also interact with nuclear pore proteins ( nups ) in diverse organisms including yeast , flies , worms , and mammalian cells . in both yeast and metazoa these interactions occur at the nuclear periphery , presumably in contact with the nuclear pore complex ( npc ) , whereas in higher eukaryotes these interactions often occur in the nucleoplasm with soluble nups active genes colocalize with rnap ii foci in subnuclear compartments called transcription factories . in flies , likewise , in yeast , trna genes , silenced telomeres and npc - associated loci each exhibit specific interchromosomal clustering . these observations support the idea that the spatial organization of the eukaryotic genome compartmentalizes the nucleus into functionally distinct subnuclear environments and that the spatial positioning of a gene both impacts and reflects its transcriptional state . as a model for these phenomena , we have studied the spatial repositioning of inducible yeast genes from the nucleoplasm to the nuclear periphery . inducible genes such as ino1 , prm1 and his4 are recruited from the nucleoplasm to the nuclear periphery upon activation . these genes are inducible under very different conditions ( ino1 is activated by inositol starvation , prm1 is induced by mating pheromone and his4 is induced by amino acid starvation ) and they are targeted to the periphery only under the conditions that lead to their expression . this recruitment leads to a physical interaction with the nuclear pore complex ( npc ) and promotes stronger expression . targeting to the periphery is controlled by cis - acting transcription factor ( tf ) binding sites located within the promoters of these genes . these elements and the tfs that bind to them are not only necessary for recruitment , but are also sufficient to target an ectopic locus to the nuclear periphery . thus , these cis - acting binding sites function as dna zip codes to control the dynamic , conditional positioning and interchromosomal clustering of genes . this suggests that one of the functions of tfs is to control the spatial organization of the genome . targeting of ino1 to the nuclear periphery is mediated by 2 dna elements called grs i and grs ii . the tfs put3 ( zn - binuclear cluster family ) and cbf1 ( basic helix - loop - helix family ) bind to grsi and grsii , respectively and these tfs are necessary for grs i- and grs ii - mediated targeting to the nuclear periphery . the grs i element is necessary and sufficient to mediate interchromosomal clustering with other grs i - containing loci . ino1 transcription is regulated by the ino2/ino4 tfs , which bind to the uasino elements in the promoter . such a separation between the elements controlling transcription and gene positioning is also seen in other promoters ( our unpublished results ) . thus , although gene positioning and transcription are coupled , they can be mediated by distinct elements and factors . in contrast , the positioning of his4 and prm1 is controlled by the same tfs that regulate their expression , gcn4 and ste12 , respectively . inserting dna elements corresponding to the binding sites of gcn4 ( gcn4bs ) and ste12 ( pheromone - response elements , 3xpre ) at the ectopic site ura3 , which is normally localized to the nucleoplasm , is sufficient to reposition the locus to the nuclear periphery . furthermore , mutant strains lacking gcn4 or ste12 fail to target his4 or prm1 to the nuclear periphery , respectively . finally , artificially tethering gcn4 or ste12 to the ura3 locus via a lexa dna binding domain is sufficient to cause ura3 to reposition to the nuclear periphery . therefore , these tfs are both necessary and sufficient to control peripheral localization and interchromosomal clustering . put3 , cbf1 , gcn4 and set12 represent 4 different families of transcription factors that mediate spatial repositioning and clustering of these genes . indeed , in erythroid cells , the transcription factor klf1 is necessary for clustering of its target genes into specialized transcription factories and in flies , interactions of genes with nup98 is mediated by the mbd - r2 dna binding factor . however , not all transcription factors possess this function . as mentioned above , ino2/ino4 binding to the uasino element within the ino1 promoter is neither necessary nor sufficient to recruit chromatin to the nuclear periphery . the activation domain of put3 and gcn4 is dispensable for targeting to the nuclear periphery ( our unpublished results ) . furthermore , inactivating rna polymerase ii or promoter mutations that block ino1 transcription does not block zip code - dependent recruitment to the nuclear periphery . one important , unaddressed question is how these changes in gene positioning are dynamically regulated . repositioning of ino1 , his4 and prm1 to the nuclear periphery and interchromosomal clustering is conditional and occurs under specific environmental stimuli . this reflects how each zip code is regulated , which is revealed when the zip code is inserted at an ectopic site . grsi and grsii are regulated through a context - dependent mechanism : when inserted at an ectopic site , these elements lead to constitutive targeting to the nuclear periphery . in other words , they are negatively regulated in the context of the ino1 promoter and only permitted to function when ino1 is induced . using systematic mutagenesis of cis and trans acting regulators , we find that targeting of ino1 to the nuclear periphery by put3 and cbf1 is regulated through local recruitment of rpd3(l ) histone deacetylase complex ( fig .  1 ) . rpd3(l ) is recruited to the ino1 promoter under repressing conditions by the transcriptional repressors opi1 and ume6 . rpd3(l ) regulates zip code activity by blocking transcription factor binding through its histone deacetylase activity . this regulation was abolished by either perturbing the recruitment of rpd3 or inactivating its catalytic activity ( rpd3 h188a ) , resulting in constitutive targeting of ino1 to the nuclear periphery . furthermore , rpd3(l ) regulation could be recapitulated at the ectopic ura3 locus by artificially tethering either opi1 or ume6 near grs i or grs ii , blocking targeting to the nuclear periphery and interchromosomal clustering ( fig .  1 , left panel ) . to test if this was general function of repressors in yeast , 21 different repressors were tethered beside the grs i. a majority of repressors could block grs i function ; 16 of the 21 repressors tested blocked put3-mediated recruitment to the nuclear periphery and 11 of these required rpd3 . thus , 5 repressors block put3 binding by either recruiting a different histone deacetylase or through alternative mechanisms . these results suggest that put3s ability to reposition genes can be blocked through several different mechanisms . because put3 controls the positioning of genes that are not perfectly co - regulated , cells could use these different strategies to independently regulate put3-mediated targeting in different contexts , depending on the environmental stimulus . figure 1.multiple strategies in regulating transcription factor ( tf)-mediated recruitment to the nuclear periphery over different time scales . top : ( left ) put3 and cbf1 bind to grsi and grsii respectively in the promoter of ino1 and mediate its recruitment to the nuclear periphery upon inositol starvation . these tfs are regulated by the local recruitment of rpd3(l ) histone deacetylase by transcriptional repressors opi1 and ume6 . repression is relieved between 60120  min leading to peripheral localization and interchromosomal clustering of ino1 . ( middle ) ste12 mediates the recruitment of prm1 to the nuclear periphery upon mating pheromone stimulation . ( right ) gcn4-mediated recruitment of his4 to the nuclear periphery is controlled by gcn4 abundance . gcn4 is translationally regulated . through increased protein levels of gcn4 , maximal peripheral targeting occurs between 3060  min . multiple strategies in regulating transcription factor ( tf)-mediated recruitment to the nuclear periphery over different time scales . top : ( left ) put3 and cbf1 bind to grsi and grsii respectively in the promoter of ino1 and mediate its recruitment to the nuclear periphery upon inositol starvation . these tfs are regulated by the local recruitment of rpd3(l ) histone deacetylase by transcriptional repressors opi1 and ume6 . repression is relieved between 60120  min leading to peripheral localization and interchromosomal clustering of ino1 . ( middle ) ste12 mediates the recruitment of prm1 to the nuclear periphery upon mating pheromone stimulation . ( right ) gcn4-mediated recruitment of his4 to the nuclear periphery is controlled by gcn4 abundance . gcn4 is translationally regulated . through increased protein levels of gcn4 , maximal peripheral targeting occurs between 3060  min . unlike put3 , regulation of ste12- and gcn4-mediated repositioning is context - independent ; inserting the gcn4bs or the 3xpre at ura3 led to repositioning to the nuclear periphery upon histidine starvation or pheromone treatment , respectively . furthermore , loss of rpd3 had no effect on recruitment of prm1 or his4 to the nuclear periphery and the 3xpre was completely resistant to tethering of opi1 or ume6 . instead ste12 is constitutively bound and ste12-dependent transcription is inhibited by 2 repressors , dig1 and dig2 . upon mating pheromone stimulation , dig1 and dig2 are phosphorylated by the mapk fus3 , causing them to dissociate from ste12 . dissociation of both dig1 and dig2 is required for prm1 transcriptional activation , but loss of dig2 alone led to constitutive ste12-mediated peripheral localization and interchromosomal clustering . furthermore , mutation of serine 34 to alanine in dig2 - blocking phosphorylation - also blocked targeting to the nuclear periphery . likewise , mutation of serine 34 to aspartate - mimicking phosphorylation - led to constitutive targeting to the nuclear periphery . thus , ste12-mediated gene positioning is regulated through post - translational modification of an inhibitor ( fig .  1 , middle panel ) . gcn4-mediated targeting to the nuclear periphery is regulated by a third mechanism ; the occupancy of gcn4 binding to its target genes , controlled by its abundance . unlike the other mechanisms discussed above , which behave in a switch - like manner , gcn4-mediated targeting to the nuclear periphery and interchomosomal clustering occurs at a lower level under uninducing conditions and at a maximal level under inducing conditions . it is well - established that gcn4-mediated transcription is regulated through the abundance of gcn4 . in the presence of amino acids , gcn4 is poorly translated due to several short , upstream open reading frames ( uorfs ) in the 5 end of the gcn4 mrna . when cells are starved for amino acids , translational initiation is slowed , permitting the ribosome to skip the uorfs and increase the translation of gcn4 . increasing gcn4 protein production by mutating the uorfs resulted in constitutive recruitment and clustering of his4 . thus , under uninducing conditions , low levels of gcn4 lead to modest targeting to the nuclear periphery and measurable interchromosomal clustering . however , under inducing conditions , higher gcn4 protein levels increase the occupancy of the gcn4bs and this leads to maximal peripheral targeting and interchromosomal clustering ( fig .  1 a number of factors have been implicated in the targeting of genes to the npc , including mrna export factors , the saga histone acetyltransferase and components of the npc itself . we find that the saga complex , for example , is required for targeting of ino1 and his4 to the nuclear periphery , but is dispensable for targeting of prm1 to the nuclear periphery . if saga functions to bridge the interaction between chromatin and the npc , as has been suggested , this result indicates that transcription factors use more than one mechanism to promote repositioning to the nuclear periphery . the saga complex is a multi - subunit histone modifying enzyme that has broad impacts on gene expression . because the regulation of put3 , cbf1 and gcn4 occurs at the level of tf occupancy whereas ste12 is regulated downstream of binding , it is possible that saga may either facilitate tf dna binding or alter the abundance of the tfs themselves . these results highlight the critical role of tfs in controlling gene positioning and interchromosomal interactions . tf - mediated gene positioning can be regulated through at least 4 different mechanisms : regulation of tf binding by the rpd3(l ) hdac , regulation of tf binding ( or function ) by repressors independent of rpd3(l ) , regulation of tf occupancy through changes in tf abundance and regulation of tf function through post - translational modification of an inhibitor . these different strategies operate over different time scales to alter the positioning of individual genes and the arrangement of chromosomes with respect to each other : mapk signaling leads to rapid repositioning and clustering of ste12 targets within 1530  min , while changes in gcn4 protein levels leads to a moderate rate of repositioning and clustering within 3060  min and rpd3(l ) regulated gene positioning is derepressed over 60120  min ( fig .  1 ) . thus , reflecting the regulation of tf function , cells employ different strategies to regulate dynamic tf - mediated gene positioning over very different temporal regimes . the authors acknowledge members of the brickner lab , past and present , for contributing to the work described and for helpful discussions .