Guanine quadruplexes in Danio rerio: existence, relative abundance, and putative function.

MARGARIT, E.; ARMAS, P.; CALCATERRA, N. B.

Potrero de los Funes

Congreso; XLVII Annual Meeting of the Argentine Society for Biochemestry and Molecular Biology Research.; 2011

Society for Biochemestry and Molecular Biology Research.

Guanine quadruplexes (G4) are secondary structures of singlestrandedDNA or RNA formed by the stacking of planar layers offour guanines interacting by Hoogsteen hydrogen bonds. G4 werecharacterized in several species and related to specific biologicalfunctions, such as gene expression regulation and chromatinstructure modification. Genome-wide studies of these structures inthe model species Danio rerio have not been performed yet. Here,zebrafish genomic, gene, and promoter sequences weredownloaded from Ensembl (version ZV9; www.ensembl.org) andsearched for the existence G4 structures using the Quadparsersoftware (www.quadruplex.org). We found 55,109 G4 in thezebrafish genome. Among them, 25,602 corresponded to 9,517genes and 2% (1,093 G4) were found in mRNAs synthesized from674 genes. In addition, we found 1,023 G4 (1.9%) in 918 genepromoters. Gene ontology categories enriched in G4 containingsequences were measured with the Cytoscape software(www.cytoscape.org). Interestingly, developmental categorieswere significatively enriched among the identified sequences. Thisstudy presents a first draft of the distribution and potential functionof G4 sequences in zebrafish genome and establishes a startingpoint concerning their role in development and disease.