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All Journal Journal of Tropical Life Science : International Journal of Theoretical, Experimental, and Applied Life Sciences
Maria A. Endriga
Department of Biology, College of Arts and Sciences, University of the Philippines Manila, 1000 Ermita, Manila, Philippines
Agriculture, Biological Sciences & Forestry Environmental Science

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Segmental Duplications: A Possible Mechanism of Hominid Uplift through MicroRNA Diversification Maria A. Endriga; Aldrich Ivan Lois D. Burog; Denise Lauren V. Dalmacion; Custer C. Deocaris
Journal of Tropical Life Science Vol. 1 No. 1 (2010)
Publisher : Journal of Tropical Life Science

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.11594/jtls.1.1.%x

Abstract

MicroRNAs (miRNA) are ~21 nucleotide-long gene silencers. Segmental duplications (SD) are among the driving forces in acquiring new genes. Both miRNA and SD are believed to have played a significant role in evolution, particularly in the divergence of humans (Homo sapiens) from the chimpanzee (Pan troglodytes). This study determines the distribution of miRNAs in humans and in chimpanzees, and presents a hypothesis on its significance in the occurrence of segmental duplications. MiRNA sequences from miRBASE were subjected to BLAT and BLAST to determine if miRNAs are located in SD regions or not. Homology between miRNAs was determined with ClustalW. BLAST was then used to determine whether the non-homologous human miRNA are homologous to any other part of the chimpanzee genome. We found that all 695 human miRNAs are found exclusively in SD regions, and that 67 are de novo miRNAs. Thirteen are homologues of chimpanzee miRNA, and 11 were possibly derived from non-miRNA regions in chimp. Of these, 6 were located in SD regions of the chimpanzee genome. Results indicate that miRNA evolution occurs within regions of segmental duplication and suggest that the presence of miRNA duplicates allows more exposure to mutations that could necessitate diversification, and possibly evolution, through sub- and neofunctionalization.Keywords:
HOX Gene Promoter Prediction and Inter-genomic Comparison: An Evo-Devo Study Maria A. Endriga; Victoria Karenina R. de la Paz; Jezreel Marie G. Sazon; Elisa L. Co; Custer C. Deocaris
Journal of Tropical Life Science Vol. 1 No. 1 (2010)
Publisher : Journal of Tropical Life Science

Show Abstract | Download Original | Original Source | Check in Google Scholar | DOI: 10.11594/jtls.1.1.%x

Abstract

Homeobox genes direct the anterior-posterior axis of the body plan in eukaryotic organisms. Promoter regions upstream of the Hox genes jumpstart the transcription process. CpG islands found within the promoter regions can cause silencing of these promoters. The locations of the promoter regions and the CpG islands of Homeo sapiens sapiens (human), Pan troglodytes (chimpanzee), Mus musculus (mouse), and Rattus norvegicus (brown rat) are compared and related to the possible influence on the specification of the mammalian body plan. The sequence of each gene in Hox clusters A-D of the mammals considered were retrieved from Ensembl and locations of promoter regions and CpG islands predicted using Exon Finder. The predicted promoter sequences were confirmed via BLAST and verified against the Eukaryotic Promoter Database. The significance of the locations was determined using the Kruskal-Wallis test. Among the four clusters, only promoter locations in cluster B showed significant difference. HOX B genes have been linked with the control of genes that direct the development of axial morphology, particularly of the vertebral column bones. The magnitude of variation among the body plans of closely-related species can thus be partially attributed to the promoter kind, location and number, and gene inactivation via CpG methylation.
Co-Authors Aldrich Ivan Lois D. Burog Custer C. Deocaris Denise Lauren V. Dalmacion Elisa L. Co Jezreel Marie G. Sazon Victoria Karenina R. de la Paz