RNA polymerase II stalls on oxidative DNA damage via a torsion-latch mechanism involving lone pair–π and CH–π interactions

Abstract

Oxidation of guanine generates several types of DNA lesions, such as 8-oxoguanine (8OG), 5-guanidinohydantoin (Gh), and spiroiminodihydantoin (Sp). These guanine-derived oxidative DNA lesions interfere with both replication and transcription. However, the molecular mechanism of transcription processing of Gh and Sp remains unknown. In this study, by combining biochemical and structural analysis, we revealed distinct transcriptional processing of these chemically related oxidized lesions: 8OG allows both error-free and error-prone bypass, whereas Gh or Sp causes strong stalling and only allows slow error-prone incorporation of purines. Our structural studies provide snapshots of how polymerase II (Pol II) is stalled by a nonbulky Gh lesion in a stepwise manner, including the initial lesion encounter, ATP binding, ATP incorporation, jammed translocation, and arrested states. We show that while Gh can form hydrogen bonds with adenosine monophosphate (AMP) during incorporation, this base pair hydrogen bonding is not sufficient to hold an ATP substrate in the addition site and is not stable during Pol II translocation after the chemistry step. Intriguingly, we reveal a unique structural reconfiguration of the Gh lesion in which the hydantoin ring rotates ∼90° and is perpendicular to the upstream base pair planes. The perpendicular hydantoin ring of Gh is stabilized by noncanonical lone pair–π and CH–π interactions, as well as hydrogen bonds. As a result, the Gh lesion, as a functional mimic of a 1,2-intrastrand crosslink, occupies canonical −1 and +1 template positions and compromises the loading of the downstream template base. Furthermore, we suggest Gh and Sp lesions are potential targets of transcription-coupled repair.

Oxidative lesions modulate G-quadruplex stability and structure in the human BCL2 promoter

“…Guanine oxidation sites were found to be enriched in open chromatin regions and regulatory elements ( 19 ). In coding regions oxo G and its derivatives cause mutations and transcription stalling ( 20 ). In promoter regions oxo G was suggested to regulate transcription through changing structural properties and stability of G-quadruplex DNA ( 21 , 22 ).…”

Transcriptional processing of an unnatural base pair by eukaryotic RNA polymerase II

“…Pol II has high transcriptional fidelity with an error rate of about 10 −5 to 10 −6 18 . The impacts of various DNA lesions on Pol II transcription have been well-documented 19 – 24 . By contrast, it is not known how Pol II recognizes and processes UBPs.…”

HSFs drive stress type-specific transcription of genes and enhancers

“…Unlike heat-inducible genes, a large fraction of oxidative stress-inducible genes displayed elongating Pol II only within the early gene body (0-2 kb from TSS). This could be due to oxidative DNA damage, which has been shown to cause stalling of elongating Pol II (29). Other possible explanations are a slower movement speed of Pol II and a failure in the chromatin remodeling in front of elongating Pol II during oxidative stress.…”