In flies, the 5´ ends of both microRNAs and their miRNA* strands are more accurately defined than their 3´ termini

ABSTRACT: MicroRNAs (miRNAs) are short (∼ 21-23 nt) regulatory RNAs that guide the degradation or translational repression of their RNA targets. The miRNA “seed”—nucleotides 2 through 7—establishes miRNA target specificity, because this region is the primary determinant of RNA binding by both miRNA and small interfering RNAs. Accurate processing of the miRNA 5´ end is thought to be under strong selective pressure, as a shift by just one nucleotide in the 5´ end of a miRNA would alter its seed sequence, redefining its repertoire of targets. Animal miRNAs are produced by the sequential cleavage of partially double-stranded precursor RNAs by the RNase III endonucleases Drosha, which cleaves the primary miRNA transcript in the nucleus to release a pre-miRNA, and Dicer, which cleaves the pre-miRNA to generate a transitory intermediate comprising the mature miRNA paired with its miRNA* strand. Here, we report that in flies, the 5´ end of a miRNA is typically more precisely defined than the 3´ ends of both the miRNA and its miRNA*. Surprisingly, the 5´ end of the miRNA* sequence was also more precisely defined than the adjacent 3´ end of the miRNA. Our data imply either that many miRNA* sequences are under evolutionary pressure to maintain their seed sequences—that is, they have cellular or exogenous RNA targets—or that secondary constraints, such as the sequence requirements for loading small RNAs into functional Argonaute protein complexes narrow the range of miRNA and miRNA* 5´ ends that accumulate in flies. Keywords: microRNA deep sequencing; pyrosequencing

ORGANISM(S): Drosophila melanogaster

PROVIDER: GSE9389 | GEO | 2008/01/22

SECONDARY ACCESSION(S): PRJNA103109

REPOSITORIES: GEO