Regulatory R-loops as facilitators of gene expression and genome stability

C Niehrs, B Luke - Nature reviews Molecular cell biology, 2020 - nature.com
R-loops are three-stranded structures that harbour an RNA–DNA hybrid and frequently form
during transcription. R-loop misregulation is associated with DNA damage, transcription …

R-loops as cellular regulators and genomic threats

MP Crossley, M Bocek, KA Cimprich - Molecular cell, 2019 - cell.com
During transcription, the nascent RNA strand can base pair with its template DNA, displacing
the non-template strand as ssDNA and forming a structure called an R-loop. R-loops are …

Targeted in situ genome-wide profiling with high efficiency for low cell numbers

PJ Skene, JG Henikoff, S Henikoff - Nature protocols, 2018 - nature.com
Cleavage under targets and release using nuclease (CUT&RUN) is an epigenomic profiling
strategy in which antibody-targeted controlled cleavage by micrococcal nuclease releases …

[HTML][HTML] R loops: from physiological to pathological roles

T García-Muse, A Aguilera - Cell, 2019 - cell.com
DNA-RNA hybrids play a physiological role in cellular processes, but often, they represent
non-scheduled co-transcriptional structures with a negative impact on transcription …

R-ChIP using inactive RNase H reveals dynamic coupling of R-loops with transcriptional pausing at gene promoters

L Chen, JY Chen, X Zhang, Y Gu, R Xiao, C Shao… - Molecular cell, 2017 - cell.com
R-loop, a three-stranded RNA/DNA structure, has been linked to induced genome instability
and regulated gene expression. To enable precision analysis of R-loops in vivo, we develop …

Genome-wide mapping of G-quadruplex structures with CUT&Tag

J Lyu, R Shao, PY Kwong Yung… - Nucleic acids …, 2022 - academic.oup.com
Single-stranded genomic DNA can fold into G-quadruplex (G4) structures or form DNA: RNA
hybrids (R loops). Recent evidence suggests that such non-canonical DNA structures affect …

High-resolution, strand-specific R-loop mapping via S9. 6-based DNA–RNA immunoprecipitation and high-throughput sequencing

LA Sanz, F Chédin - Nature protocols, 2019 - nature.com
R-loops are prevalent three-stranded non-B DNA structures composed of an RNA–DNA
hybrid and a single strand of DNA. R-loops are implicated in various basic nuclear …

Replication-transcription conflicts generate R-loops that orchestrate bacterial stress survival and pathogenesis

KS Lang, AN Hall, CN Merrikh, M Ragheb, H Tabakh… - Cell, 2017 - cell.com
Replication-transcription collisions shape genomes, influence evolution, and promote
genetic diseases. Although unclear why, head-on transcription (lagging strand genes) is …

G-quadruplex–R-loop interactions and the mechanism of anticancer G-quadruplex binders

G Miglietta, M Russo, G Capranico - Nucleic acids research, 2020 - academic.oup.com
Genomic DNA and cellular RNAs can form a variety of non-B secondary structures, including
G-quadruplex (G4) and R-loops. G4s are constituted by stacked guanine tetrads held …

Transcription–replication conflicts as a source of genome instability

L Goehring, TT Huang, DJ Smith - Annual review of genetics, 2023 - annualreviews.org
Transcription and replication both require large macromolecular complexes to act on a DNA
template, yet these machineries cannot simultaneously act on the same DNA sequence …