Cell nucleus
Cell nuclei contain most of the cell's genetic material, organized as multiple long linear DNA molecules in a complex with a large variety of proteins, such as histones, to form chromosomes. The genes within these chromosomes are the cell's nuclear genome and are structured in such a way to promote cell function. The nucleus maintains the integrity of genes and controls the activities of the cell by regulating gene expression—the nucleus is, therefore, the control center of the cell. The main structures making up the nucleus are the nuclear envelope, a double membrane that encloses the entire organelle and isolates its contents from the cellular cytoplasm, and the nuclear matrix (which includes the nuclear lamina), a network within the nucleus that adds mechanical support, much like the cytoskeleton, which supports the cell as a whole.
NUMT
Mitochondria, as a major energy factory of the cell, was previously a free-living prokaryote that invades the eukaryotic cells by the endosymbiosis theory, which gained acceptance around the 1970s. Under this theory, symbiotic organelles gradually transferred their genes to the eukaryotic genome, implying that mtDNA was gradually integrated into the nuclear genome. Despite the metabolic alterations and functional adaptations in the host eukaryotes, circular mitochondrial DNA is contained within the organelles. Containing 37 genes, mitochondrial DNA has an essential role in the production of necessary compounds, such as required enzymes for the proper function of mitochondria. Specifically, it has been suggested that certain genes (such as the genes for cytochrome oxidase subunits I and II) within the organelle are necessary to regulate redox balance throughout membrane-associated electron transport chains. These parts of the mitochondrial genome have been reported to be the most frequently employed. Mitochondria is not the only location within which the cell mtDNA, mitochondrial DNA, can be found; sometimes transfer of mitochondrial DNA from organelles to the nucleus can occur; the evidence of such translocation has been seen through the comparison of mitochondrial DNA sequence with the genome sequence of the counterparts. The integration and recombination of cytoplasmic mtDNA into the nuclear DNA is called Nuclear Mitochondrial DNA, which is abbreviated as NUMT.
The possible presence of organelle DNA inside the nuclear genome was suggested after finding of homologous structure to the mitochondrial DNA, which was shortly after the discovery of the presence of an independent DNA within the organelles in 1967. This topic stayed untouched until the 1980s. Initial evidence that DNA could move among cell compartments came when fragments of chloroplast DNA were found in the maize mitochondrial genome with the help of cross-hybridization, between chloroplast and mitochondrial DNA, and physical mapping of homologous regions. After this initial observation, Ellis coined the name "promiscuous DNA" in order to signify the transfer of DNA intracellularly from one organelle to the other and is the presence of organelle DNA in multiple cellular compartments. This is not only an important discovery on its own, but is also highly informative and helpful for understanding the evolutionary process and the time period different occurrence might take place. The searching for mtDNA in nuclear DNA continued until 1994 when the recent remarkable transposition of 7.9 kb of a typically 17.0-kb mitochondrial genome to a specific nuclear chromosomal position in the domestic cat was reported. This is the time that NUMT was coined to designate the large stretches of mitochondrial DNA in the genome.
Up to now, the whole genomes of many eukaryotes, both vertebrate, and invertebrate, have been sequenced and NUMT was observed in the nuclear genome of various organisms, including yeast, "Podospora", sea urchin, locust, honey bee, "Tribolium", rat, maize, rice, and primates. In Plasmodium, "Anopheles gambiae", and "Aedes aegypti" mosquitoes NUMT can barely be detected. In contrast, the conserved fragments of NUMT have now few were identified in genome data for "Ciona intestinalis", "Neurospora crassa", "Schizosaccharomyces pombe", "Caenorhabditis elegans", "Drosophila melanogaster", and "Rattus norvegicus". Antunes and Ramos were found the presence of NUMT in the fish genome for the first time in 2005 using of BLASTN, MAFFT, very vigorous genome mappings, and phylogenic analysis. Across the animal kingdom, "Apis mellifera", from phylum "Arthropoda", and "Hydra magnipapillata", from phylum "Cnidaria", are respectively the first and second animals with the highest ratio of NUMTs to the total size of the nuclear genome while "Monodelphis Domestica", or Gray short-tailed opossum, is the record holder for NUMT frequency among vertebrates. Similar to animals, NUMTs are abundant in the plants and the longest NUMT fragment known so far, a 620-kb partially duplicated insertion of the 367-kb mtDNA of "Arabidopsis thaliana", was reported.