Existence, relative abundance, and putative function of guanine quadruplexes in the model species Danio rerio

EZEQUIEL MARGARIT; PABLO ARMAS; NORA B CALCATERRA

Rosario

Congreso; IV Argentinean Conference on Computational Biology and Bioinformatics & IV Conference of the Iberoamerican Society for Bioinformatics; 2013

Asociación Argentina de Bioinformática y Biología Computacional (A2B2C) y Sociedad Iberoamericana de Bioinformática (SoIBio)

Background Guanine quadruplexes (G4) are secondary structures of single-stranded DNA or RNA formed by the stacking of planar layers of four guanines (tetrads) interacting by Hoogsteen hydrogen bonds. G4 were characterized in several species and related to specific biological functions, such as gene expression regulation and chromatin structure modification. Albeit the widespread use of Danio rerio for the study of vertebrate gene function, genome-wide studies regarding these structures have not been performed yet. Methods and Results In this work, we performed and exhaustive analysis of zebrafish genomic, gene, and promoter sequences searching for putative G4 sequences (PQS). Sequences were downloaded from Ensembl (www.ensembl.org) and scanned for PQS formed by the stacking of two (G4-2) or three (G4-3) guanine tetrads using Quadparser (www.quadruplex.org). We found 55,109 G4-3s and 17,137,202 G4-2s in the zebrafish genome. Most of the G4-3s (46%) were found within transcriptional units, contained either in mature mRNAs (5.6%) or intronic sequences (94.4%). Furthermore, 79 and 702 G4-3s were detected in 5´- and 3´-UTRs, respectively. Scanning of promoter regions revealed the existence of 1,023 G4-3s (1.8%) in 918 genes. Regarding G4-2s, 819,495 (4.8%) were found in 26,426 transcriptional units, mainly in intronic sequences (98.6%). G4 density was calculated and compared to the whole genome value. As expected, G4 density was lower than in warm-blood animals, likely due to the lower GC content of zebrafish genome. G4-2s were enriched in coding sequences and 5´-UTRs, while lower in 3´-UTRs. No significant differences in G4-3s densities were found among either coding sequences or 3´-UTR, while an impoverishment in G4-3s was detected in 5-´UTRs. Furthermore, an enrichment of G4-3s was detected in transcription template DNA strands. Promoters and mRNAs enriched in PQS were classified according Gene Ontology (GO) terms using Cytoscape (www.cytoscape.org). mRNAs grouped in development, differentiation and embryo morphogenesis, while promoters grouped in regulation of gene expression, embryo development and morphogenesis. Finally, PQS-containing promoters from zebrafish, mouse and human were compared resulting in a total of 104 conserved genes grouped in development and gene expression regulation GO terms. Conclusions: This study presents a first draft of the distribution and potential function of G4 in zebrafish genome and establishes a starting point concerning their role in vertebrate development and evolution. Although not highly represented in zebrafish genome, we speculate that PQS in developmental genes have been positively selected during natural evolution.