Alternative DNA secondary structure formation affects RNA polymerase II promoter-proximal pausing in human.

ABSTRACT:

Background

Alternative DNA secondary structures can arise from single-stranded DNA when duplex DNA is unwound during DNA processes such as transcription, resulting in the regulation or perturbation of these processes. We identify sites of high propensity to form stable DNA secondary structure across the human genome using Mfold and ViennaRNA programs with parameters for analyzing DNA.

Results

The promoter-proximal regions of genes with paused transcription are significantly and energetically more favorable to form DNA secondary structure than non-paused genes or genes without RNA polymerase II (Pol II) binding. Using Pol II ChIP-seq, GRO-seq, NET-seq, and mNET-seq data, we arrive at a robust set of criteria for Pol II pausing, independent of annotation, and find that a highl

SUBMITTER: Szlachta K 

PROVIDER: S-EPMC6042338 | biostudies-literature | 2018 Jul

REPOSITORIES: biostudies-literature