#20 · Epigenomics

Computational checks expose DNA off-targeting artifacts and novel intronic polyadenylation

The common thread is scrutiny of what computational RNA processing analyses actually measure. A meta-analysis of RNA-chromatin occupancy datasets finds that many lncRNA-bound regions are artifacts of probe-complementary DNA off-targeting, a confound that limits interpretation of these assays. IPScan addresses intronic polyadenylation from RNA-seq, detecting, quantifying, and visualizing novel events with benchmarking on simulated data. An integrative analysis of RNA-binding proteins identifies DDX55 as a regulator of 3'UTR isoform diversity. Taken together, the items emphasize specificity and validation in pipelines that infer RNA processing events from sequencing data. What is new is the systematic quantification of off-target contamination in existing RNA-chromatin datasets and a benchmarked tool for intronic polyadenylation events.