Chlamydomonas reinhardtii genome reveals regulatory elements
Xi Xue, Navid Darouian, David Lopez, Manav Sidhu, Jesus Guillen, and Gaston Pfluegl
Department of Molecular Cell and Developmental Biology, University of California at Los Angeles, Los Angeles, CA 90095, USA.
The genome of Chlamydomonas reinhardtii, a unicellular green alga with both plant-like and animal-like attributes, has been sequenced and provided a valuable resource to further explore, identify, and analyze genes involved in many intracellular processes. The goal of the UCLA Undergraduate Genomics Research Initiative (UGRI) is to annotate and analyze the C. reinhardtii genome. UGRI is a collaborative, cross-discipline effort among undergraduates where students conduct cutting-edge research in genomic biology and biotechnology. Using over 250 gene models previously annotated by undergraduates at UCLA, we examined regions of high intra and inter-species conservation, as well as the existence of potential regulatory sequences in the Chlamydomonas genome. We proposed that the introns not only serve as buffer regions but also contain sequences essential for transcription factor binding. In addition, we hypothesized that Kozak sequence, transcriptional initiation site, may exist in the conserved 5' untranslated regions. We used in silico methods including the usage of the National Center for Biotechnology Information's Basic Local Alignment Search Tool function, Joint Genome Institute's Genome Browser Database, University of California at Santa Cruz's Genome Browser, and other Genome Browsers to analyze the 250 manually curated genes for biologically relevant regulatory elements and motifs. Results will advance our knowledge of diseases caused by faulty regulation and may also allow for the understanding of the origin of diseases. Motifs may also be targets for novel gene therapy aimed at correcting defective regulatory mechanisms.
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