The BAF chromatin remodeler synergizes with RNA polymerase II and transcription factors to evict nucleosomes

Nature Genetics, Journal Year: 2023, Volume and Issue: 56(1), P. 100 - 111

Published: Dec. 4, 2023

Abstract Chromatin accessibility is a hallmark of active transcription and entails ATP-dependent nucleosome remodeling, which carried out by complexes such as Brahma-associated factor (BAF). However, the mechanistic links between transcription, remodeling chromatin are unclear. Here, we used chemical–genetic approach coupled with time-resolved profiling to dissect interplay RNA Polymerase II (RNAPII), BAF DNA-sequence-specific factors in mouse embryonic stem cells. We show that dynamically unwraps evicts nucleosomes at accessible regions, while RNAPII promoter-proximal pausing stabilizes occupancy enhances eviction BAF. find although probe both transcriptionally Polycomb-repressed genomic pluripotency binding confers locus specificity for productive Our study suggests paradigm how functional synergy acting regulates locus-specific organization accessibility.

Language: Английский

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Safeguarding the epigenome through the cell cycle: a multitasking game

Current Opinion in Genetics & Development, Journal Year: 2024, Volume and Issue: 85, P. 102161 - 102161

Published: March 5, 2024

Sustaining cell identity and function across division is germane to human development, healthspan, cancer avoidance. This relies significantly on propagation of chromatin organization between generations, as presents a barrier fate state conversions. Inheritance states the many divisions required for development tissue homeostasis represents major challenge, especially because disrupted allow passage DNA replication fork synthesize two daughter strands. process also leads twofold dilution epigenetic information in histones, which needs be accurately restored faithful divisions. Recent research has identified distinct multilayered mechanisms acting propagate Here, we summarize key principles how parental histones transferred new robustly acquire same postreplication, representing core component memory.

Language: Английский

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RNA polymerase II promotes the organization of chromatin following DNA replication

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

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Epigenetic control and manipulation of neuronal maturation timing

Current Opinion in Genetics & Development, Journal Year: 2024, Volume and Issue: 85, P. 102164 - 102164

Published: Feb. 27, 2024

During brain development, the sequence of developmental steps and underlying transcriptional regulatory logic are largely conserved across species. However, temporal unfolding programs varies dramatically species within a given regions cell identities. The maturation neurons in human cerebral cortex is particularly slow lasts for many years compared with only few weeks corresponding mouse neurons. mechanisms setting 'schedule' neuronal remain unclear but appear to be linked cell-intrinsic 'clock'. Here, we discuss recent findings that highlight role epigenetic factors timing maturation. Manipulations those stem cell-based models can override intrinsic pace maturation, including its protracted nature cortical We then contextualize regulation from other model systems propose potential interactions between pathways drivers rates.

Language: Английский

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Replication-transcription symbiosis in the mammalian nucleus: The art of living together

Current Opinion in Cell Biology, Journal Year: 2025, Volume and Issue: 93, P. 102479 - 102479

Published: Feb. 11, 2025

Similarly to life in our planet, where thousands of species inhabit the same ecosystem, cell nucleus hosts different essential processes that share territory, making interaction between them unavoidable. DNA replication and transcription are copy decode information contained genomes, sharing -and competing for- chromatin template. Both activities executed by large macromolecular machines with similar requirements access DNA, remodel nucleosomes ahead reassemble make-up behind. Mechanistically, both cannot simultaneously act on sequence, but emerging evidence shows they frequently interact. Here we revise recent data how occur highlighting symbiotic relationship processes, which might help explain their contribute shape structure function mammalian genome.

Language: Английский

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Transcription-replication conflicts drive R-loop-dependent nucleosome eviction and require DOT1L activity for transcription recovery

Nucleic Acids Research, Journal Year: 2025, Volume and Issue: 53(4)

Published: Feb. 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.

Language: Английский

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Increased levels of lagging strand polymerase α in an adult stem cell lineage affect replication-coupled histone incorporation

Science Advances, Journal Year: 2025, Volume and Issue: 11(9)

Published: Feb. 28, 2025

Stem cells display asymmetric histone inheritance, while nonstem progenitor exhibit symmetric patterns in the Drosophila male germ line. Here, we report that components involved lagging strand synthesis, DNA polymerases α and δ, have substantially reduced levels stem compared to cells, this promotes local asymmetry of parental incorporation at replication fork. Compromising Polα genetically induces replication-coupled pattern resemble seen by both nuclear localization chromatin fibers. This is recapitulated using a inhibitor concentration-dependent manner. The old versus new comparable between S phase M phase. Together, these results indicate developmentally programmed expression key important shape cell chromatin. Furthermore, manipulating one crucial component can induce dynamics those cells.

Language: Английский

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Calcium Handling Machinery and Sarcomere Assembly are Impaired Through Multipronged Mechanisms in Cancer Cytokine‐Induced Cachexia

Journal of Cachexia Sarcopenia and Muscle, Journal Year: 2025, Volume and Issue: 16(2)

Published: April 1, 2025

Abstract Background Cachexia is a severe form of muscle wasting disorder particularly observed in patients with advanced cancer. The absence effective strategies to ameliorate cachexia indicates our poor understanding the mechanisms cachexia. By employing system‐wide approaches, we investigated molecular underlying cancer secreted pro‐inflammatory cytokine‐induced (CIC). Methods As cellular model systems, employed mouse satellite stem cell‐derived primary cells, C2C12 myoblast progenitor myotubes, and neonatal rat cardiomyocytes. We induced CIC by incubating striated cells cytokines TNF‐α IFN‐γ. To understand physiological effects CIC, probed contractile properties following electrical stimulation measured intracellular calcium transients. Effects on sarcomere organization were monitored confocal microscopy. Large‐scale quantitative proteomics RNA sequencing assays enabled us examine CIC. Using chromatin immunoprecipitation experiments, signalling modulation epigenetic marks muscle‐specific genes investigated. Results Here, drastic loss cell contraction primarily, due acutely disorganized structures impeded handling process. In transients, extent (Ca 2+ ) release, as indicated amplitude during excitation–contraction coupling (ECC) process, was reduced (19.6 ± 2.35% control 8.6 1.52% p = 4.8 * 10 −11 ). Kinetics i.e., Ca release rate (26 0.5 ms 29 5.1 median 0.014), re‐uptake (137 13 185 24 0.032) both prolonged. Proteomic analysis showed altered proteostasis related sarcoplasmic reticulum (SR). Transcriptomic unravelled upstream deregulation global transcriptional events for sarcomeric SR genes. Mechanistically, loading transcriptionally active Polymerase II genes, including Myh1 Atp2a1 , impeded. This diminished H3K4 trimethylation resulted lower activity these ultimately MyHC‐IId motor protein SERCA1 levels. Conclusions Our top‐down approach elucidated that mechanism proteomic state perturbed functionally machinery responsible Knowledge cause mass compromised function key developing therapeutic solutions cachectic conditions.

Language: Английский

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Mechanism of SETX-BRCA1-BARD1 complex in resolution of R-loops and transcription-replication conflicts

Research Square (Research Square), Journal Year: 2024, Volume and Issue: unknown

Published: Jan. 15, 2024

Abstract Senataxin (SETX), a putative RNA-DNA helicase, is recruited to transcription pause sites via the tumor suppressor BRCA1. Here, we define mechanism by which SETX-BRCA1 resolves transcription-associated R-loops prevent deleterious outcomes. Specifically, show that SETX unwinds R-loops, and complex of BRCA1 its obligatory partner BARD1 binds stimulates R-loop unwinding SETX. Importantly, BRCA1-BARD1 alleviates inhibitory effect RAD52 on SETX-mediated unwinding. We also demonstrate phosphorylation Ser642 in promotes interaction with tandem BRCT domain latter. Accordingly, mutations catalytic or lead accumulation, transcription-replication conflicts, replication fork stalling, DNA double strand breaks human cells. Our results thus establish molecular basis for functional synergy between resolution mitigation conflicts preserve genome integrity.

Language: Английский

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RNA polymerase collisions and their role in transcription

Transcription, Journal Year: 2024, Volume and Issue: 15(1-2), P. 38 - 47

Published: Feb. 15, 2024

RNA polymerases are the central enzymes of gene expression and function frequently in either a head-on or co-directional manner on busy DNA track. Whether how these collisions between contribute to transcriptional regulation is mysterious. Increasing evidence from biochemical single-molecule studies suggests that polymerase as an important regulator fine-tune transcription, rather than creating deleterious "traffic jams". This review summarizes recent progress elucidating consequences during transcription highlights significance cooperation coordination polymerases.

Language: Английский

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