RTEL1 Regulates G4/R-Loops to Avert Replication-Transcription Collisions

Panagiotis Kotsantis,Sandra Segura-Bayona,Pol Margalef,Paulina Marzec,Phil Ruis,Graeme Hewitt,Roberto Bellelli,Harshil Patel,Robert Goldstone,Anna R Poetsch,Simon J Boulton

doi:10.1016/j.celrep.2020.108546

Panagiotis Kotsantis, Sandra Segura-Bayona + Show 9 more

Open Access

https://doi.org/10.1016/j.celrep.2020.108546

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Abstract

SummaryRegulator of telomere length 1 (RTEL1) is an essential helicase that maintains telomere integrity and facilitates DNA replication. The source of replication stress in Rtel1-deficient cells remains unclear. Here, we report that loss of RTEL1 confers extensive transcriptional changes independent of its roles at telomeres. The majority of affected genes in Rtel1−/− cells possess G-quadruplex (G4)-DNA-forming sequences in their promoters and are similarly altered at a transcriptional level in wild-type cells treated with the G4-DNA stabilizer TMPyP4 (5,10,15,20-Tetrakis-(N-methyl-4-pyridyl)porphine). Failure to resolve G4-DNAs formed in the displaced strand of RNA-DNA hybrids in Rtel1−/− cells is suggested by increased R-loops and elevated transcription-replication collisions (TRCs). Moreover, removal of R-loops by RNaseH1 overexpression suppresses TRCs and alleviates the global replication defects observed in Rtel1−/− and Rtel1PIP_box knockin cells and in wild-type cells treated with TMPyP4. We propose that RTEL1 unwinds G4-DNA/R-loops to avert TRCs, which is important to prevent global deregulation in both transcription and DNA replication.

Highlights

Maintenance of genome stability is essential for organismal development and tumor avoidance
We show that Rtel1-deficient cells exhibit profound changes in transcription with the majority of affected genes possessing G4-DNA-forming sequences in their promoters and many corresponding to chromosomal fragile sites
Consistent with studies showing that G4-DNA structures can assemble in the displaced strand formed by R-loops (Duquette et al, 2004; Yadav et al, 2016), we found that loss of Regulator of telomere length 1 (RTEL1) results in increased R-loop levels and elevated transcription-replication conflicts (TRCs)

Summary

Introduction

Maintenance of genome stability is essential for organismal development and tumor avoidance. Evidence for the interdependence between G4-DNA and R-loops comes from observations that R-loops are enriched in sequences harboring G4-DNA motifs in the non-template DNA strand and that R-loop-specific DNA damage is induced by long tandem G-rich repeats and G4-stabilizing ligands (Chen et al, 2019; De Magis et al, 2019; Ginno et al, 2012; Nguyen et al, 2017a). These G-rich promoter sequences can harbor G4-DNAs that can affect gene regulation and mRNA translation (Varshney et al, 2020). Cells require mechanisms to tolerate, prevent, and resolve TRCs caused by persistent G4/R-loops, most of which remain poorly understood

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