Direct visualization of replication and R-loop collision using single-molecule imaging DOI Creative Commons
Subin Kim,

Woo Hee Shin,

Yujin Kang

et al.

Nucleic Acids Research, Journal Year: 2023, Volume and Issue: 52(1), P. 259 - 273

Published: Nov. 22, 2023

Abstract R-loops are three-stranded nucleic acid structures that can cause replication stress by blocking fork progression. However, the detailed mechanism underlying collision of DNA forks and remains elusive. To investigate how induce stress, we use single-molecule fluorescence imaging to directly visualize replicating Phi29 polymerase (Phi29 DNAp), simplest system, R-loops. We demonstrate a single R-loop block replication, blockage is more pronounced when an RNA–DNA hybrid on non-template strand. show this asymmetry results from secondary structure formation strand, which impedes progression DNAp. also G-quadruplex displaced single-stranded in enhances stalling. Moreover, observe between DNAp RNA transcripts synthesized T7 (T7 RNAp). stalling because presence RNAp. Our work provides insights into impede at resolution.

Language: Английский

Transcription–replication conflicts underlie sensitivity to PARP inhibitors DOI Creative Commons
Michalis Petropoulos,

Angeliki Karamichali,

Giacomo G. Rossetti

et al.

Nature, Journal Year: 2024, Volume and Issue: 628(8007), P. 433 - 441

Published: March 20, 2024

Abstract An important advance in cancer therapy has been the development of poly(ADP-ribose) polymerase (PARP) inhibitors for treatment homologous recombination (HR)-deficient cancers 1–6 . PARP trap PARPs on DNA. The trapped are thought to block replisome progression, leading formation DNA double-strand breaks that require HR repair 7 Here we show PARP1 functions together with TIMELESS and TIPIN protect early S phase from transcription–replication conflicts. Furthermore, synthetic lethality deficiency is due an inability damage caused by conflicts, rather than PARPs. Along these lines, inhibiting transcription elongation rendered HR-deficient cells resistant depleting small-interfering RNA was lethal deficiency. Thus, enzymatic activity may suffice efficacy settings.

Language: Английский

Citations

56
Freedom to err: The expanding cellular functions of translesion DNA polymerases DOI Creative Commons
Inés Paniagua, Jacqueline J.L. Jacobs

Molecular Cell, Journal Year: 2023, Volume and Issue: 83(20), P. 3608 - 3621

Published: Aug. 24, 2023

Language: Английский

Citations

20
R-Loops in Genome Instability and Cancer DOI Open Access
Fang Li, Alyan Zafar, Liang Luo

et al.

Cancers, Journal Year: 2023, Volume and Issue: 15(20), P. 4986 - 4986

Published: Oct. 14, 2023

R-loops are unique, three-stranded nucleic acid structures that primarily form when an RNA molecule displaces one DNA strand and anneals to the complementary in a double-stranded molecule. R-loop formation can occur during natural processes, such as transcription, which nascent remains hybridized with template strand, while non-template is displaced. However, also arise due many non-natural including damage, dysregulation of degradation pathways, defects processing. Despite their prevalence throughout whole genome, predominantly found actively transcribed gene regions, enabling serve seemingly controversial roles. On hand, pathological accumulation contributes genome instability, hallmark cancer development plays role tumorigenesis, progression, therapeutic resistance. other play critical roles regulating essential expression, chromatin organization, class-switch recombination, mitochondrial replication, repair. In this review, we summarize discoveries related formation, suppression, removal influence on repair, oncogenic events. We have discussed therapeutical opportunities by targeting R-loops.

Language: Английский

Citations

18
Looping out of control: R-loops in transcription-replication conflict DOI
Charanya Kumar, Dirk Remus

Chromosoma, Journal Year: 2023, Volume and Issue: 133(1), P. 37 - 56

Published: July 7, 2023

Language: Английский

Citations

17
RNA polymerase II promotes the organization of chromatin following DNA replication DOI Creative Commons
Susanne Bandau, Vanesa Álvarez, Hao Jiang

et al.

EMBO Reports, Journal Year: 2024, Volume and Issue: 25(3), P. 1387 - 1414

Published: Feb. 12, 2024

Abstract Understanding how chromatin organisation is duplicated on the two daughter strands a central question in epigenetics. In mammals, following passage of replisome, nucleosomes lose their defined positioning and transcription contributes to re-organisation. However, whether plays greater role organization DNA replication remains unclear. Here we analysed protein re-association with newly replicated upon inhibition using iPOND coupled quantitative mass spectrometry. We show that nucleosome assembly re-establishment most histone modifications are uncoupled from transcription. RNAPII acts promote hundreds proteins via pathways not observed steady-state chromatin. These include ATP-dependent remodellers, factors methyltransferases. also identify set repair may handle transcription-replication conflicts during normal human non-transformed cells. Our study reveals post-replication than previously anticipated.

Language: Английский

Citations

6
Replication–Transcription Conflicts: A Perpetual War on the Chromosome DOI
Kaitlyn R. Browning, Houra Merrikh

Annual Review of Biochemistry, Journal Year: 2024, Volume and Issue: 93(1), P. 21 - 46

Published: April 10, 2024

DNA replication and transcription occur in all living cells across domains of life. Both essential processes simultaneously on the same template, leading to conflicts between macromolecular machines that perform these functions. Numerous studies over past few decades demonstrate this is an inevitable problem both prokaryotic eukaryotic cells. We have learned lead fork reversal, breaks DNA, R-loop formation, topological stress, mutagenesis can ultimately impact evolution. Recent also provided insight into various mechanisms mitigate, resolve, allow tolerance how result pathological consequences divergent species. In review, we summarize our current knowledge regarding outcomes encounters machineries explore clashes are dealt with

Language: Английский

Citations

6
RNA biogenesis and RNA metabolism factors as R-loop suppressors: a hidden role in genome integrity DOI Open Access
Rosa Luna, Belén Gómez‐González, Andrés Aguilera

et al.

Genes & Development, Journal Year: 2024, Volume and Issue: unknown

Published: July 10, 2024

Genome integrity relies on the accuracy of DNA metabolism, but as appreciated for more than four decades, transcription enhances mutation and recombination frequencies. More recent research provided evidence a previously unforeseen link between RNA which is often related to accumulation DNA–RNA hybrids R-loops. In addition physiological roles, R-loops interfere with replication repair, providing molecular scenario origin genome instability. Here, we review current knowledge multiple factors that prevent or resolve consequent transcription–replication conflicts thus act modulators dynamics.

Language: Английский

Citations

6
The many faces of the helicase RTEL1 at telomeres and beyond DOI

Noa Hourvitz,

Aya Awad, Yehuda Tzfati

et al.

Trends in Cell Biology, Journal Year: 2023, Volume and Issue: 34(2), P. 109 - 121

Published: July 31, 2023

Language: Английский

Citations

16
Base-pair resolution reveals clustered R-loops and DNA damage-susceptible R-loops DOI
Yaoyi Li, Yingliang Sheng,

Chao Di

et al.

Molecular Cell, Journal Year: 2025, Volume and Issue: unknown

Published: March 1, 2025

Language: Английский

Citations

0
Senataxin RNA/DNA helicase promotes replication restart at co-transcriptional R-loops to prevent MUS81-dependent fork degradation DOI Creative Commons
Satyajeet Rao, Martin Andrš,

Kaustubh Shukla

et al.

Nucleic Acids Research, Journal Year: 2024, Volume and Issue: 52(17), P. 10355 - 10369

Published: Aug. 9, 2024

Abstract Replication forks stalled at co-transcriptional R-loops can be restarted by a mechanism involving fork cleavage-religation cycles mediated MUS81 endonuclease and DNA ligase IV (LIG4), which presumably relieve the topological barrier generated transcription-replication conflict (TRC) facilitate ELL-dependent reactivation of transcription. Here, we report that restart R-loop-stalled replication via MUS81-LIG4-ELL pathway requires senataxin (SETX), helicase unwind RNA:DNA hybrids. We found SETX promotes progression preventing R-loop accumulation during S-phase. Interestingly, loss activity leads to nascent degradation upon induction R-loop-mediated stalling hydroxyurea. This phenotype is independent reversal results from DNA2-mediated resection MUS81-cleaved accumulate due defective restart. Finally, demonstrate acts in common with DEAD-box DDX17 suppress stress human cells. A possible cooperation between these RNA/DNA helicases unwinding TRC sites discussed.

Language: Английский

Citations

4