RegCFinder: targeted discovery of genomic subregions with differential read density.

Motivation: To date, no methods are available for the targeted identification of genomic subregions with differences in sequencing read distributions between two conditions. Existing approaches either only determine absolute read number changes, require predefined subdivisions of input windows or average across multiple genes.

Results: Here, we present RegCFinder, which automatically identifies subregions of input windows with differences in read density between two conditions.

HSV-1 Infection Induces a Downstream Shift of Promoter-Proximal Pausing for Host Genes.

Herpes simplex virus 1 (HSV-1) infection exerts a profound shutoff of host gene expression at multiple levels. Recently, HSV-1 infection was reported to also impact promoter-proximal RNA polymerase II (Pol II) pausing, a key step in the eukaryotic transcription cycle, with decreased and increased Pol II pausing observed for activated and repressed genes, respectively. Here, we demonstrate that HSV-1 infection induces more complex alterations in promoter-proximal pausing than previously suspected for the vast majority of cellular genes.

CDK11 regulates pre-mRNA splicing by phosphorylation of SF3B1.

RNA splicing, the process of intron removal from pre-mRNA, is essential for the regulation of gene expression. It is controlled by the spliceosome, a megadalton RNA-protein complex that assembles de novo on each pre-mRNA intron through an ordered assembly of intermediate complexes. Spliceosome activation is a major control step that requires substantial protein and RNA rearrangements leading to a catalytically active complex.