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

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-canonical processing events occurring one helical turn distal of most efficiently cleaved miRNA precursors. We performed polyA independent deep sequencing of the chromatin-isolated RNA fraction for 5 samples: 2 replicates in HeLa cells, 1 Drosha knock down in HeLa cells, 1 sample for A549 cells and 1 sample for HEK293 cells. We also performed deep sequencing of the small RNA fraction in the same cell lines.