The Chromosomal and Functional Clustering of Markedly Divergent Human-mouse Orthologs Run Parallel To Their Compositional Features - The Chromosomal and Functional Clustering of Markedly Divergent Human-mouse Orthologs Run Parallel To Their Compositional Features - Open Access Pub

It was, previously, reported that the specific pattern of the compositional features of particular human-mouse orthologs defining in human two clusters, named C2 and C5, are present in different clusters in mouse. Since, thus, these orthologs can harbor a significant number of nucleotide differences a large sample of human-mouse orthologs having in human the C2 and C5 compositional features were collected in order to identify the orthologs that have been conserved or diverged during speciation. From the collection, 945 and 1051 orthologs had in human the C2 and C5 profile, respectively, while in mouse only 77 and 125, respectively, had these profiles. We further analyzed whether or not the frequency-usage of trinucleotides having the same gross composition computed from the reading of all nearest-neighbors of the DNA sequence might convey a layer of biological information in terms of chromosomal topology and function. In human, more than 50% of the C2 and C5 genes were found distributed in six chromosomes and preferentially located in GC-rich bands of chromosomes 11, 16 and 19. It was, also, found that 80% of the entire set of genes of band 19p13.3 had the C2 and C5 profile. The data shown also indicate that the proteins codified by the C5 genes have a bias towards nucleus and cytoplasm and specific post-translational modifications while the proteins codified by the C2 genes are mainly located in the cellular membrane or secreted to the external cellular milieu and particular post-transcriptional modifications DOI10.14302/issn.2575-7881.jdrr-15-863 Several studies have revealed that chromosomal gene-clusters are common in eukaryotic species1, 2 and that various mechanisms may be responsible for their formation leading to levels of organization that range from small to large ones. The occurrences of chromosomal clusters may entail that clustering confers some type of selective advantage suggesting that evolutionary mechanisms exists to promote their formation and maintenance3. There may be a link between the compositional, the chromosomal and the functional clustering since genes in chromosomal clusters could belong to common metabolic pathways, codify for proteins that may form interactive networks or serve as ligands and receptors in signaling pathways2, 4. Classically, gene-clusters have been obtained on the basis of expression data and the biological knowledge has been a posteriori used to make the most of the clusters. However, gene-clustering on the basis of expression data alone allows isolating co-expressed, -but not necessarily- biologically