Mechanisms of lncRNA biogenesis as revealed by nascent transcriptomics

T Nojima, NJ Proudfoot - Nature reviews Molecular cell biology, 2022 - nature.com
Mammalian genomes express two principal gene categories through RNA polymerase II-
mediated transcription: protein-coding transcription units and non-coding RNA transcription …

Walking a tightrope: the complex balancing act of R-loops in genome stability

JR Brickner, JL Garzon, KA Cimprich - Molecular cell, 2022 - cell.com
Although transcription is an essential cellular process, it is paradoxically also a well-
recognized cause of genomic instability. R-loops, non-B DNA structures formed when …

Intertwining roles of R-loops and G-quadruplexes in DNA repair, transcription and genome organization

P Wulfridge, K Sarma - Nature Cell Biology, 2024 - nature.com
R-loops are three-stranded nucleic acid structures that are abundant and widespread across
the genome and that have important physiological roles in many nuclear processes. Their …

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 …

METTL3 and N6-methyladenosine promote homologous recombination-mediated repair of DSBs by modulating DNA-RNA hybrid accumulation

C Zhang, L Chen, D Peng, A Jiang, Y He, Y Zeng… - Molecular cell, 2020 - cell.com
Double-strand breaks (DSBs) are the most deleterious DNA lesions, which, if left unrepaired,
may lead to genome instability or cell death. Here, we report that, in response to DSBs, the …

R-loops as Janus-faced modulators of DNA repair

A Marnef, G Legube - Nature cell biology, 2021 - nature.com
R-loops are non-B DNA structures with intriguing dual consequences for gene expression
and genome stability. In addition to their recognized roles in triggering DNA double-strand …

Human Rad52 promotes XPG-mediated R-loop processing to initiate transcription-associated homologous recombination repair

T Yasuhara, R Kato, Y Hagiwara, B Shiotani… - Cell, 2018 - cell.com
Given that genomic DNA exerts its function by being transcribed, it is critical for the
maintenance of homeostasis that DNA damage, such as double-strand breaks (DSBs) …

Functional transcription promoters at DNA double-strand breaks mediate RNA-driven phase separation of damage-response factors

F Pessina, F Giavazzi, Y Yin, U Gioia, V Vitelli… - Nature cell …, 2019 - nature.com
Damage-induced long non-coding RNAs (dilncRNA) synthesized at DNA double-strand
breaks (DSBs) by RNA polymerase II are necessary for DNA-damage-response (DDR) focus …

Mechanisms of nuclear content loading to exosomes

A Yokoi, A Villar-Prados, PA Oliphint, J Zhang… - Science …, 2019 - science.org
Exosome cargoes are highly varied and include proteins, small RNAs, and genomic DNA
(gDNA). The presence of gDNA suggests that different intracellular compartments contribute …

BRCA2 controls DNA: RNA hybrid level at DSBs by mediating RNase H2 recruitment

G D'Alessandro, DR Whelan, SM Howard… - Nature …, 2018 - nature.com
DNA double-strand breaks (DSBs) are toxic DNA lesions, which, if not properly repaired,
may lead to genomic instability, cell death and senescence. Damage-induced long non …