Transcription shapes 3D chromatin organization by interacting with loop extrusion

Proceedings of the National Academy of Sciences, Год журнала: 2023, Номер 120(11)

Опубликована: Март 10, 2023

Cohesin folds mammalian interphase chromosomes by extruding the chromatin fiber into numerous loops. "Loop extrusion" can be impeded chromatin-bound factors, such as CTCF, which generates characteristic and functional organization patterns. It has been proposed that transcription relocalizes or interferes with cohesin active promoters are loading sites. However, effects of on have not reconciled observations extrusion cohesin. To determine how modulates extrusion, we studied mouse cells in could alter abundance, dynamics, localization genetic "knockouts" regulators CTCF Wapl. Through Hi-C experiments, discovered intricate, cohesin-dependent contact patterns near genes. Chromatin around genes exhibited hallmarks interactions between transcribing RNA polymerases (RNAPs) cohesins. These reproduced polymer simulations RNAPs were moving barriers to obstructed, slowed, pushed The predicted preferential at is inconsistent our experimental data. Additional ChIP-seq experiments showed putative loader Nipbl predominantly enriched promoters. Therefore, propose preferentially loaded barrier function RNAP accounts for accumulation Altogether, find an stationary, but rather, translocates Loop might interact dynamically generate maintain gene regulatory elements shape genomic organization.

Язык: Английский

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Enhancer–promoter interactions can bypass CTCF-mediated boundaries and contribute to phenotypic robustness

Nature Genetics, Год журнала: 2023, Номер 55(2), С. 280 - 290

Опубликована: Янв. 30, 2023

Язык: Английский

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New insights into genome folding by loop extrusion from inducible degron technologies

Nature Reviews Genetics, Год журнала: 2022, Номер 24(2), С. 73 - 85

Опубликована: Сен. 30, 2022

Язык: Английский

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Transcription shapes 3D chromatin organization by interacting with loop extrusion

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2022, Номер unknown

Опубликована: Янв. 8, 2022

Abstract Cohesin folds mammalian interphase chromosomes by extruding the chromatin fiber into numerous loops. “Loop extrusion” can be impeded chromatin-bound factors, such as CTCF, which generates characteristic and functional organization patterns. It has been proposed that transcription relocalizes or interferes with cohesin, active promoters are cohesin loading sites. However, effects of on have not reconciled observations extrusion cohesin. To determine how modulates extrusion, we studied mouse cells in could alter abundance, dynamics, localization genetic ‘knockouts’ regulators CTCF Wapl. Through Hi-C experiments, discovered intricate, cohesin-dependent contact patterns near genes. Chromatin around genes exhibited hallmarks interactions between transcribing RNA polymerases (RNAPs) cohesins. These reproduced polymer simulations RNAPs were “moving barriers” to obstructed, slowed, pushed The predicted preferential at is inconsistent our experimental data. Additional ChIP-seq experiments showed putative loader Nipbl predominantly enriched promoters. Therefore, propose preferentially loaded barrier function RNAP accounts for accumulation Altogether, find a new type stationary, but rather, translocates Loop might interact dynamically generate maintain gene regulatory elements shape genomic organization. Significance Statement critical folding genome Extrusion halted proteins bound specific loci, chromosomal domains regulate expression. process itself modulate thus refolding simulations, show act loop-extruding Unlike stationary barriers, actively relocalize cohesins, spatial Our model predicts explain why accumulates provides mechanism clustering transcription-extrusion interactions, contacts.

Язык: Английский

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Region Capture Micro-C reveals coalescence of enhancers and promoters into nested microcompartments

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2022, Номер unknown

Опубликована: Июль 14, 2022

Although enhancers are central to the regulation of mammalian gene expression, mechanisms underlying Enhancer-Promoter (E-P) interactions remain unclear. Chromosome conformation capture (3C) methods effectively large-scale 3D genome structure but struggle achieve depth necessary resolve fine-scale E-P interactions. Here, we develop Region Capture Micro-C (RCMC) by combining MNase-based 3C with a tiling region-capture approach and generate deepest maps reported thus far only modest sequencing. By applying RCMC in mouse embryonic stem cells reaching genome-wide equivalent ∼200 billion unique contacts, reveals previously unresolvable patterns highly nested focal interactions, which term microcompartments. Microcompartments frequently connect promoters largely robust loss loop extrusion inhibition transcription. We therefore propose that many form through compartmentalization mechanism, may explain why acute cohesin depletion modestly affects global expression.

Язык: Английский

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Three-dimensional genome organization in immune cell fate and function

Nature reviews. Immunology, Год журнала: 2022, Номер 23(4), С. 206 - 221

Опубликована: Сен. 20, 2022

Язык: Английский

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Cohesin regulates promoter-proximal pausing of RNA Polymerase II by limiting recruitment of super elongation complex

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2024, Номер unknown

Опубликована: Март 16, 2024

Abstract Cohesin is a ring-shaped complex, responsible for establishing sister chromatid cohesion and forming topologically associating domains (TADs) chromatin loops. Loss-of-function mutations in cohesin subunits its regulatory factors can cause Cornelia de Lange syndrome (CdLS). Because dysregulated gene expression was observed CdLS, it has long been thought that plays role transcription. Here, we investigated the effect of acute depletion on transcription small number genes exhibited differential expression. Analysis RNA polymerase II (Pol II) distribution revealed reduced Pol promoter binding pausing simultaneously at majority genes. This implies most genes, two decreases counterbalance each other, resulting unchanged Additionally, find loss increased super elongation complex (SEC), which mediates release from paused state. Moreover, reduction caused by no longer when SEC inhibited. These observations suggest regulates restricting recruitment to promoters. Together, our study demonstrates involvement transcriptional regulation, particularly pause release.

Язык: Английский

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RNA polymerase II and PARP1 shape enhancer-promoter contacts

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2022, Номер unknown

Опубликована: Июль 8, 2022

Abstract How enhancers control target gene expression over long genomic distances remains an important unsolved problem. Here we studied enhancer-promoter contact architecture and communication by integrating data from nucleosome-resolution maps, nascent transcription, perturbations to transcription-associated proteins thousands of candidate enhancers. Contact frequency between functionally validated pairs was most enriched near the +1 +2 nucleosomes at promoters, indicating that functional spend time in close physical proximity. Blocking RNA polymerase II (Pol II) caused major disruptions contacts. Paused Pol occupancy enzymatic activity poly (ADP-ribose) 1 (PARP1) stabilized Based on our findings, propose updated model couples transcriptional dynamics communication.

Язык: Английский

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A genome-wide nucleosome-resolution map of promoter-centered interactions in human cells corroborates the enhancer-promoter looping model

Опубликована: Дек. 18, 2023

The enhancer-promoter looping model, in which enhancers activate their target genes via physical contact, has long dominated the field of gene regulation. However, ubiquity this model been questioned due to evidence alternative mechanisms and lack its systematic validation, primarily owing absence suitable experimental techniques. In study, we present a new MNase-based proximity ligation method called MChIP-C, allowing for measurement protein-mediated chromatin interactions at single-nucleosome resolution on genome-wide scale. By applying MChIP-C study H3K4me3 promoter-centered K562 cells, found that it had greatly improved sensitivity compared restriction endonuclease-based C-methods. This allowed us identify EP300 histone acetyltransferase SWI/SNF remodeling complex as potential candidates establishing and/or maintaining interactions. Finally, leveraging data from published CRISPRi screens, most functionally-verified do physically interact with cognate promoters, supporting model.

Язык: Английский

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Transcription regulates bleb formation and stability independent of nuclear rigidity

bioRxiv (Cold Spring Harbor Laboratory), Год журнала: 2022, Номер unknown

Опубликована: Ноя. 15, 2022

Abstract Chromatin is an essential component of nuclear mechanical response and shape that maintains compartmentalization function. The biophysical properties chromatin alter stability, but little known about whether or how major genomic functions can impact the integrity nucleus. We hypothesized transcription might affect cell rupture through its effects on structure dynamics. To test this idea, we inhibited with RNA polymerase II inhibitor alpha-amanitin in wild type cells perturbed present increased blebbing. Transcription inhibition suppresses blebbing for several types, perturbations, inhibitors. Furthermore, necessary robust bleb formation, stabilization, bleb-based ruptures. These morphological appear to occur a novel pathway, since does not either histone modification state rigidity, which typically control find active/phosphorylated pol Ser5, marking initiation, enriched blebs relative DNA. Thus, initiation hallmark blebs. Polymer simulations suggest motor activity within chromatin, such as II, generate active forces deform periphery, deformations depend Our data provide evidence function impacts suggests mechanism, separate distinct from regulating large-scale

Язык: Английский

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