Screening for target genes of a nucleic acid chaperone essential for craniofacial development

ARMAS, P.; MARGARIT, E.; ALLENDE, M. L.; CALCATERRA, N. B.

Puerto Madryn, Chubut, Argentina.

Congreso; XLVI Annual Meeting of the Argentine Society for Biochemestry and Molecular Biology Research.; 2010

Sociedad Argentina de Investigación en Bioquímica y Biología Molecular

Cellular nucleic acid binding protein (CNBP) is a highly conserved single-stranded nucleic acid binding protein required for craniofacial development. CNBP acts as nucleic acid chaperonerearranging the secondary structure of its targets and promoting the formation of G-quadruplexes (G4), stable nucleic acid structures described as novel elements for gene expression regulation. So far, the direct target genes regulated by CNBP remain unknown. Here, we performed a genome-wide screening for zebrafish CNBP binding sites using inverse one-hybrid strategy on genomic zebrafish and mouse libraries cloned in yeast. We obtained 76 and more than 170 clones from zebrafish and mouse libraries, respectively. Many of them were repeated, and 50% were chimeras consisting of unrelated genomic fragments cloned in tandem. Sequences were in silico mapped to the zebrafish and mouse genomes to define their location in or nearby annotated genes and putative promoter regions likely related to CNBP function. Forty % matched to annotated genes with variable functions, while 60% to intergenic regions. Several sequences were nearby clusters of small non-coding RNA genes (snRNA, rRNA, miRNA). Moreover, morethan 80% of the sequences contained putative G4 formed by 2 tetrads. This is a 2-fold higher frequency than average in the analyzed genomes, meaning that CNBP prefers sequences with G4formation potential.