Nuclear gene

A nuclear gene is a gene located in the cell nucleus of a eukaryote. The term is used to distinguish nuclear genes from the genes of the endosymbiotic organelle, that is genes in the mitochondrion, and in case of plants and algae, the chloroplast, which host their own genetic system and can produce proteins from scratch. A nuclear gene is just one of the genetic building blocks of a eukaryotic organism's entire genome.
Structure.
Eukaryotic genomes have distinct higher-order chromatin structures that are closely packaged and ultimately organized in a certain construct that functionally relates to gene expression. These structures function to package the genome in a greatly compressed form into the cell nucleus, while still ensuring that the gene can be accessed when needed, such as during gene transcription, replication, and DNA repair. The function of the genome is directly related to this organizational system, in which there are a number of complex mechanisms and biochemical pathways which can affect the expression of individual genes within the genome.
Endosymbiotic organelle interactions.
Though separated from one another within the cell, nuclear genes and those of mitochondria and chloroplasts can affect each other in a number of ways as well. Nuclear genes play major roles in the expression of chloroplast genes and mitochondrial genes. Additionally, gene products of mitochondria can themselves affect the expression of genes within the cell nucleus. This can be done through metabolites as well as through certain peptides trans-locating from the mitochondria to the nucleus, where they can then affect gene expression.
Protein synthesis.
The majority of proteins in a cell are the product of messenger RNA transcribed from nuclear genes, including most of the proteins of the organelles, which are produced in the cytoplasm like all nuclear gene products and then transported to the organelle. Genes in the nucleus are arranged in a linear fashion upon chromosomes, which serve as the scaffold for replication and the regulation of gene expression. As such, they are usually under strict copy-number control, and replicate a single time per cell cycle. Nuclear cells such as platelets do not possess nuclear DNA and therefore must have alternative sources for the RNA that they need to generate proteins.
Significance.
Many nuclear-derived transcription factors have played a role in respiratory chain expression. These factors may have also contributed to the regulation of mitochondrial functions. Nuclear respiratory factor (NRF-1) fuses to respiratory encoding genes proteins, to the rate-limiting enzyme in biosynthesis, and to elements of replication and transcription of mitochondrial DNA, or mtDNA. The second nuclear respiratory factor (NRF-2) is necessary for the production of cytochrome c oxidase subunit IV (COXIV) and Vb (COXVb) to be maximized.
The studying of gene sequences for the purpose of speciation and determining genetic similarity is just one of the many uses of modern day genetics, and the role that both types of genes have in that process are important. Though both nuclear genes and those within endosymbiotic organelles provide the genetic makeup of an organism, there are distinct features that can be better observed when looking at one compared to the other. Mitochondrial DNA is useful in the study of speciation as it tends to be the first to evolve in the development of a new species, which is different from nuclear genes' chromosomes that can be examined and analyzed individually, each giving its own potential answer as to the speciation of a relatively recently evolved organism.
As nuclear genes are the genetic basis of all eukaryotic organisms, anything that can affect their expression therefore directly affects characteristics about that organism on a cellular level. The interactions between the genes of endosymbiotic organelles like mitochondria and chloroplasts are just a few of the many factors that can act on the nuclear genome.