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

EZEQUIEL MARGARIT; PABLO ARMAS; NORA B CALCATERRA

Potrero de los Funes - San Luis

Congreso; 47th Annual Meeting Argentine Society for Biochemistry and Molecular Biology; 2011

SAIB - Sociedad Argentina de Investigación en Bioquímica y Biología Molecular

Guanine quadruplexes (G4) are secondary structures of single-stranded DNA or RNA constituted by the stacking of planar layers of four guanines interacting by Hoogsteen hydrogen bonding. G4 were characterized in several species and related to specific biological functions, such as gene expression regulation and chromatin structure modification. Until now, genome-wide screening of G4 in zebrafish (Danio rerio) had not been performed. Here, zebrafish genomic, gene, and promoter sequences were downloaded from Ensembl (version ZV9; www.ensembl.org) and searched for putative G4 (PG4) sequences using the Quadparser software (www.quadruplex.org). We found 55,109 PG4 in the zebrafish genome. Among them, 25,602 corresponded to 9,517 genes. The 4.3% (1,093 PG4) were found in mRNAs synthesized from 674 genes. Moreover, we found 1,023 PG4 in the promoters of 918 genes (2.9%). Gene ontology categories enrichment in G4 containing sequences were measured with the Cytoscape software (www.cytoscape.org). Interestingly, developmental categories were significatively enriched among the identified sequences. This study presents a first draft of the distribution and potential function of G4 sequences in zebrafish and establishes a starting point concerning their role in development and disease.