Editing Comparative genomics (section)

====Mouse models in immunology====
[[T cells]] (also known as a T lymphocytes or a thymocytes) are [[immune cells]] that grow from stem cells in the bone marrow. They assist to defend the body from infection and may aid in the fight against cancer. Because of their morphological, physiological, and genetic resemblance to humans, mice and rats have long been the preferred species for biomedical research [[animal model]]s. Comparative Medicine Research is built on the ability to use information from one species to understand the same processes in another. We can get new insights into molecular pathways by comparing human and mouse T cells and their effects on the immune system utilizing comparative genomics. In order to comprehend its TCRs and their genes, Glusman conducted research on the sequencing of the human and mouse T cell receptor loci. TCR genes are well-known and serve as a significant resource for supporting functional genomics and understanding how genes and intergenic regions of the genome contribute to biological processes.<ref name=glusman2001/>

T-cell immune receptors are important in seeing the world of pathogens in the cellular immune system. One of the reasons for sequencing the human and mouse TCR loci was to match the orthologous gene family sequences and discover conserved areas using comparative genomics. These, it was thought, would reflect two sorts of biological information: (1) exons and (2) [[regulatory sequence]]s. In fact, the majority of V, D, J, and C exons could be identified in this method. The variable regions are encoded by multiple unique DNA elements that are rearranged and connected during T cell (TCR) differentiation: variable (V), diversity (D), and joining (J) elements for the and polypeptides; and V and J elements for the and polypeptides.[Figure 1] However, several short noncoding conserved blocks of the genome had been shown. Both human and mouse motifs are largely clustered in the 200 bp [Figure 2], the known 3′ [[Enhancer (genetics)|enhancer]]s in the TCR/ were identified, and a conserved region of 100 bp in the mouse J intron was subsequently shown to have a regulatory function.

[[File:Mouse and Human Comparison (2) (2).png|thumb|upright=1.15|[Figure 2] Gene structure of the human (top) and mouse (bottom) V, D, J, and C gene segments. The arrows represent the transcriptional direction of each TCR gene. The squares and circles represent going in a direct and reverse direction. Modified after Glusman et al. 2001.<ref name=glusman2001/>]]

Comparisons of the genomic sequences within each physical site or location of a specific gene on a chromosome (locs) and across species allow for research on other mechanisms and other regulatory signals. Some suggest new hypotheses about the evolution of TCRs, to be tested (and improved) by comparison to the TCR gene complement of other vertebrate species. A comparative genomic investigation of humans and mice will obviously allow for the discovery and annotation of many other genes, as well as identifying in other species for regulatory sequences.<ref name=glusman2001>{{cite journal | vauthors = Glusman G, Rowen L, Lee I, Boysen C, Roach JC, Smit AF, Wang K, Koop BF, Hood L | title = Comparative genomics of the human and mouse T cell receptor loci | journal = Immunity | volume = 15 | issue = 3 | pages = 337–349 | date = September 2001 | pmid = 11567625 | doi = 10.1016/s1074-7613(01)00200-x | doi-access = free }}</ref>