Genome-wide quantification of microRNA processing efficiency from RNA-seq data

ABSTRACT: We perform polyA independent deep sequencing of chromatin associated primary transcripts across three different cell lines to obtain a global view on in vivo microRNA processing. We use these data to define a MicroProcessing Index (MPI), to quantify the cleavage efficiency of the Microprocessor complex. Hallmarks of efficient Drosha-mediated processing are confirmed by means of deep sequencing of chromatin-associated transcripts upon Drosha knockdown. Our results suggest that both sequence features and thermodynamic properties, e.g. secondary structure of the regions flanking the pre-miRNA hairpins are determinants for efficient processing. Our data furthermore enables us to observe endogenous microprocessor cleavage sites at nucleotide resolution. This analysis reveals the presence of non

ORGANISM(S): Homo sapiens

SUBMITTER: Annalisa Marsico 

PROVIDER: E-GEOD-56862 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress