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

Woo Hee Shin,

Yujin Kang

и другие.

Nucleic Acids Research, Год журнала: 2023, Номер 52(1), С. 259 - 273

Опубликована: Ноя. 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.

Язык: Английский

Distinct Mechanisms of Recognition of Phosphorylated RNAPII C-Terminal Domain by BRCT Repeats of the BRCA1-BARD1 Complex: Insights from Structural and Functional Analyses DOI Creative Commons
Veronika Klapstova,

Kateřina Šedová,

Josef Houser

и другие.

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2025, Номер unknown

Опубликована: Янв. 22, 2025

Abstract Transcription competes with other DNA-dependent processes, such as DNA repair, for access to its substrate, DNA. However, the principles governing interplay between these processes remain poorly understood. Evidence suggests that BRCA1-BARD1 complex, a key player in damage response, may act mediator of this crosstalk. In study, we investigated molecular mechanism underpinning interaction RNA polymerase II (RNAPII) and well functional implications. Our findings reveal BRCT repeat BRCA1 binds Ser5-phosphorylated CTD RNAPII, utilising previously established ligands. Furthermore, demonstrate is critical organisation RNAPII into condensates liquid-like properties. Analysis disease-associated variants within repeats further supports biological relevance condensation. Collectively, our results suggest complex coordinate transcription repair by facilitating factories.

Язык: Английский

Процитировано

0
Deaminase-Driven Reverse Transcription Mutagenesis in Oncogenesis: Critical Analysis of Transcriptional Strand Asymmetries of Single Base Substitution Signatures DOI Open Access
Edward J. Steele, Robyn A. Lindley

International Journal of Molecular Sciences, Год журнала: 2025, Номер 26(3), С. 989 - 989

Опубликована: Янв. 24, 2025

This paper provides a critical analysis of the molecular mechanisms presently used to explain transcriptional strand asymmetries single base substitution (SBS) signatures observed in cancer genomes curated at Catalogue Somatic Mutations Cancer (COSMIC) database (Wellcome Trust Sanger Institute). The is based on deaminase-driven reverse transcriptase (DRT) mutagenesis model oncogenesis involving both cytosine (AID/APOBEC) and adenosine (ADAR) mutagenic deaminases. In this we apply what known, or can reasonably be inferred, immunoglobulin somatic hypermutation (Ig SHM) mechanism stand COSMIC SBS that are genomes. underlying assumption mutations arising driven by dysregulated off-target Ig SHM-like processes non-Ig loci. It reasoned most whether “unknown etiology” assigned-molecular causation, readily understood terms DRT-paradigm. These include major age-related “clock-like” SBS5 signature all sequenced many other common subset including SBS1, SBS3, SBS2/13, SBS6, SBS12, SBS16, SBS17a/17b, SBS19, SBS21, as well clearly from exogenous causation. We conclude DRT-model plausible framework augments our current understanding immunogenetic driving oncogenesis. accommodates known about AID/APOBEC ADAR mutation fully integrated into origins signatures. DRT-paradigm thus scientists clinicians with additional insights causal links between deaminase-associated genomic oncogenic processes.

Язык: Английский

Процитировано

0
The emerging regulatory interface between DNA repair and steroid hormone receptors in cancer DOI

Bim de Klein,

Nils Eickhoff, Wilbert Zwart

и другие.

Trends in Molecular Medicine, Год журнала: 2025, Номер unknown

Опубликована: Фев. 1, 2025

Язык: Английский

Процитировано

0
Transcription-replication conflicts drive R-loop-dependent nucleosome eviction and require DOT1L activity for transcription recovery DOI Creative Commons
Marcel Werner, Michael Trauner, Tamás Schauer

и другие.

Nucleic Acids Research, Год журнала: 2025, Номер 53(4)

Опубликована: Фев. 8, 2025

Progressing transcription and replication machineries profoundly impact their underlying chromatin template. Consequently, transcription-replication conflict (TRC) sites are vulnerable to epigenome alterations, provoking genome instability. Here, we engineered an inducible TRC reporter system using a genome-integrated R-loop-prone sequence characterized the dynamic changes of local structure inflicted by TRCs, leading reduced nucleosome occupancy fork blockage. Strikingly, inducing small number TRCs on results in measurable global stress response. Furthermore, find TRC-dependent increase H3K79 methylation specifically at R-loop forming site. Accordingly, inhibition methyltransferase DOT1L leads transcriptional output exacerbated DNA damage response, suggesting that deposition this mark is required for effective recovery resolution TRCs. Our work shows molecular dynamics reveals specific epigenetic modifier bookmarking sites, relevant cancer other diseases.

Язык: Английский

Процитировано

0
Mechanisms underlining R-loop biology and implications for human disease DOI Creative Commons
Junzhe Liu,

Fengze Li,

Yulong Cao

и другие.

Frontiers in Cell and Developmental Biology, Год журнала: 2025, Номер 13

Опубликована: Фев. 21, 2025

R-loops are three-stranded non-canonical nucleic acid structures composed of nascent RNA hybridized with the template DNA strand, leaving non-template strand displaced. These play crucial roles in regulating gene expression, replication, and transcription processes. However, have also been increasingly described as highly deleterious, causing genomic instability damage. To maintain at a relatively safe level, complex regulatory mechanisms exist to prevent their excessive formation. The growing understanding R-loop functions has provided valuable insights into structure potential clinical applications. Emerging research indicates that contribute pathogenesis various disorders, including neurodegenerative, immune-related, neoplastic diseases. This review summarizes metabolism its significance etiology associated disorders. By elucidating governing R-loops, we aim establish theoretical foundation for disease exploring novel therapeutic strategies targeting these hybrid structures.

Язык: Английский

Процитировано

0
R-loop homeostasis in genome dynamics, gene expression and development DOI
Paula Aguilera, Andrés Aguilera

Current Opinion in Genetics & Development, Год журнала: 2025, Номер 92, С. 102325 - 102325

Опубликована: Март 4, 2025

Язык: Английский

Процитировано

0
DNA lesions can frequently precede DNA:RNA hybrid accumulation DOI Creative Commons
Raphaël M. Mangione, Steven Pierce, Myriam Zheng

и другие.

Nature Communications, Год журнала: 2025, Номер 16(1)

Опубликована: Март 10, 2025

Abstract While DNA:RNA hybrids contribute to multiple genomic transactions, their unscheduled formation is a recognized source of DNA lesions. Here, through suite systematic screens, we rather observed that wide range yeast mutant situations primarily triggering damage actually leads hybrid accumulation. Focusing on Okazaki fragment processing, establish genic can form as consequence replication-born discontinuities such unprocessed flaps or unligated fragments. Strikingly, “post-lesion” neither detectably genetic instability, nor disturb gene expression, opposed “pre-lesion” formed upon defective mRNA biogenesis, e.g ., in THO complex mutants. Post-lesion similarly arise distinct instability situations, triggered by pharmacological manipulation DNA-dependent processes, both and human cells. Altogether, our data the accumulation transcription-born occur various types natural pathological lesions, yet do not necessarily aggravate genotoxicity.

Язык: Английский

Процитировано

0
RNase H2 degrades toxic RNA:DNA hybrids behind stalled forks to promote replication restart DOI
Jonathan Heuzé, Samira Kemiha,

Antoine Barthe

и другие.

The EMBO Journal, Год журнала: 2023, Номер 42(23)

Опубликована: Окт. 19, 2023

Язык: Английский

Процитировано

10
WRNIP1 prevents transcription-associated genomic instability DOI Creative Commons
Pasquale Valenzisi, Veronica Marabitti, Pietro Pichierri

и другие.

eLife, Год журнала: 2024, Номер 12

Опубликована: Март 15, 2024

R-loops are non-canonical DNA structures that form during transcription and play diverse roles in various physiological processes. Disruption of R-loop homeostasis can lead to genomic instability replication impairment, contributing several human diseases, including cancer. Although the molecular mechanisms protect cells against such events not fully understood, recent research has identified fork protection factors damage response proteins as regulators dynamics. In this study, we identify Werner helicase-interacting protein 1 (WRNIP1) a novel factor counteracts transcription-associated upon perturbation. Loss WRNIP1 leads accumulation, resulting collisions between replisome machinery. We observe co-localization with transcription/replication complexes after perturbation, suggesting its involvement resolving transcription-replication conflicts. Moreover, WRNIP1-deficient show impaired restart from transcription-induced stalling. Notably, inhibition RNase H1 overexpression rescue all defects caused by loss WRNIP1. Importantly, our findings highlight critical role ubiquitin-binding zinc finger (UBZ) domain preventing pathological persistence limiting damage, thereby safeguarding genome integrity.

Язык: Английский

Процитировано

3
A rewiring of DNA replication mediated by MRE11 exonuclease underlies primed-to-naive cell de-differentiation DOI Creative Commons
Patricia Ubieto‐Capella, Pilar Ximénez‐Embún, Daniel Giménez-Llorente

и другие.

Cell Reports, Год журнала: 2024, Номер 43(4), С. 114024 - 114024

Опубликована: Апрель 1, 2024

Mouse embryonic stem cells (mESCs) in the primed pluripotency state, which resembles post-implantation epiblast, can be de-differentiated culture to a naive state that pre-implantation inner cell mass. We report primed-to-naive mESC transition entails significant slowdown of DNA replication forks and compensatory activation dormant origins. Using isolation proteins on nascent coupled mass spectrometry, we identify key changes replisome composition are responsible for these effects. Naive enriched MRE11 nuclease other repair proteins. is recruited newly synthesized response transcription-replication conflicts, its inhibition or genetic downregulation mESCs sufficient restore fork rate cells. Transcriptomic analyses indicate exonuclease activity required complete transition, demonstrating direct link between dynamics de-differentiation process.

Язык: Английский

Процитировано

3