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

Karol Szlachta,Yuh-Hwa Wang,Naomi D Atkin,Levi C T Pierce,Stefan Bekiranov,Ryan G Thys

doi:10.1186/s13059-018-1463-8

Karol Szlachta, Yuh-Hwa Wang + Show 4 more

Open Access

https://doi.org/10.1186/s13059-018-1463-8

Copy DOI

Abstract

BackgroundAlternative 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.ResultsThe 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 highly stable secondary structure is likely to form about 10–50 nucleotides upstream of a Pol II pausing site. Structure probing data confirm the existence of DNA secondary structures enriched at the promoter-proximal regions of paused genes in human cells. Using an in vitro transcription assay, we demonstrate that Pol II pausing at HSPA1B, a human heat shock gene, is affected by manipulating DNA secondary structure upstream of the pausing site.ConclusionsOur results indicate alternative DNA secondary structure formation as a mechanism for how GC-rich sequences regulate RNA Pol II promoter-proximal pausing genome-wide.

Highlights

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
These results demonstrate that predicted DNA secondary structure formation is widespread across the human genome, and the location of potential highly stable DNA secondary structure regions suggests that these structures could participate in gene transcription
Using our genome-wide Mfold data, we found that the region proximal to the transcription start site (TSS) (250 nt upstream to 250 nt downstream) of paused genes displays a significantly lower ΔG than non-paused genes or genes without polymerase II (Pol II) bound in all investigated cell lines (Additional file 1: Figure S2B and Table S4), further suggesting the potential for alternative DNA secondary structures to contribute to Pol II pausing in human cells

Summary

Introduction

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. While DNA is typically found in the B-DNA conformation, it has the ability to form a variety of non-B DNA secondary structures, including hairpins and quadruplexes. During DNA processes like replication and transcription, the duplex DNA is unwound, potentially allowing single-stranded DNA to form stable secondary structures, including stem-loop structures. Once formed, DNA secondary structures can play a role in many processes, including replication, transcription, and DNA repair [1]. A variety of DNA structures formed in gene promoter regions have been suggested to block gene expression for a number of genes [8,9,10,11,12,13,14]. DNA secondary structure can promote transcription by altering transcription factor binding sites [15]

Methods

Results

Discussion

Conclusion