Transcriptional coregulation in cis around a contact insulation site revealed by single-molecule microscopy

Published: May 16, 2025

Abstract Chromosome conformation in mammals is closely related to gene regulation. Within topologically associating domains, where genomic contacts are enriched, genes tend show correlated expression across tissues and conditions, suggesting domain-wide mechanisms coregulating multiple genes, such as enhancer sharing or local histone mark spreading. At the single-cell level, transcription occurs sporadic bursts, transcriptional coordination has been observed between proximal but how folding of mammalian chromosomes influences coregulation cis at individual alleles remains unclear. Using single-molecule microscopy, we imaged nascent from three adjacent located around a strong contact insulation site FOS locus, during estrogen response human breast cancer cells. To interpret this data, developed two new analysis approaches dissect sources (co)variation activities: one separate allele-extrinsic, allele-intrinsic, gene-autonomous components; another quantify contributions burst co-occurrence size correlations. We find that variability largely gene-autonomous, yet correlations display distinct patterns occur almost exclusively cis. Correlations stronger less insulated genes. However, unexpectedly, substantial also and, under certain on same side can exhibit uncorrelated occurrences. By disentangling correlations, reveal coregulatory influenced by chromosome folding.

Language: Английский

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Transcriptional coregulation in cis around a contact insulation site revealed by single-molecule microscopy

Published: May 16, 2025

Abstract Chromosome conformation in mammals is closely related to gene regulation. Within topologically associating domains, where genomic contacts are enriched, genes tend show correlated expression across tissues and conditions, suggesting domain-wide mechanisms coregulating multiple genes, such as enhancer sharing or local histone mark spreading. At the single-cell level, transcription occurs sporadic bursts, transcriptional coordination has been observed between proximal but how folding of mammalian chromosomes influences coregulation cis at individual alleles remains unclear. Using single-molecule microscopy, we imaged nascent from three adjacent located around a strong contact insulation site FOS locus, during estrogen response human breast cancer cells. To interpret this data, developed two new analysis approaches dissect sources (co)variation activities: one separate allele-extrinsic, allele-intrinsic, gene-autonomous components; another quantify contributions burst co-occurrence size correlations. We find that variability largely gene-autonomous, yet correlations display distinct patterns occur almost exclusively cis. Correlations stronger less insulated genes. However, unexpectedly, substantial also and, under certain on same side can exhibit uncorrelated occurrences. By disentangling correlations, reveal coregulatory influenced by chromosome folding.

Language: Английский

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Nucleosomes play a dual role in regulating transcription dynamics

Proceedings of the National Academy of Sciences, Journal Year: 2024, Volume and Issue: 121(28)

Published: July 5, 2024

Transcription has a mechanical component, as the translocation of transcription machinery or RNA polymerase (RNAP) on DNA chromatin is dynamically coupled to torsion. This posits mechanics possible regulator eukaryotic transcription, however, modes and mechanisms this regulation are elusive. Here, we first take statistical approach model torsional response topology-constrained chromatin. Our recapitulates experimentally observed weaker stiffness compared bare proposes structural transitions nucleosomes into chirally distinct states driver contrasting mechanics. Coupling with RNAP in stochastic simulations, reveal complex interplay supercoiling nucleosome dynamics governing velocity. Nucleosomes play dual role controlling dynamics. The steric barrier aspect gene body counteracts via hindering motion, whereas chiral facilitate motion driving low restoring torque upon twisting DNA. While dissociation rates typically transcriptionally repressive, highly dynamic offer less enhance elongation weakly transcribed genes buffering twist. We use predict transcription-dependent levels segments budding yeast genome that accord available experimental data. unveils paradigm supercoiling-mediated interaction between makes testable predictions will guide design.

Language: Английский

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Transcriptional noise, gene activation, and roles of SAGA and Mediator Tail measured using nucleotide recoding single-cell RNA-seq

Cell Reports, Journal Year: 2024, Volume and Issue: 43(8), P. 114593 - 114593

Published: Aug. 1, 2024

We describe a time-resolved nascent single-cell RNA sequencing (RNA-seq) approach that measures gene-specific transcriptional noise and the fraction of active genes in S. cerevisiae. Most are expressed with near-constitutive behavior, while subset show high mRNA variance suggestive transcription bursting. Transcriptional is highest cofactor/coactivator-redundant (CR) gene class (dependent on both SAGA TFIID) strongest TATA-containing CR genes. Using this approach, we also find histone switches from low-level, low-noise constitutive mode during M M/G1 to an activated state S phase shows increase promoters switch noisy bursty mode. Rapid depletion cofactors MED Tail indicates factors play important role stimulating at genes, more modest noise.

Language: Английский

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How Transcription Factors Binding Stimulates Transcriptional Bursting

The Journal of Physical Chemistry Letters, Journal Year: 2024, Volume and Issue: 15(34), P. 8781 - 8789

Published: Aug. 20, 2024

Transcription is a fundamental biological process of transferring genetic information which often occurs in stochastic bursts when periods intense activity alternate with quiescent phases. Recent experiments identified strong correlations between the association transcription factors (TFs) to gene promoters on DNA and transcriptional activity. However, underlying molecular mechanisms this phenomenon remain not well understood. Here, we present theoretical framework that allowed us investigate how binding dynamics TF influences bursting. Our minimal model incorporates most relevant physical-chemical features, including exchange among multiple sites at association/dissociation dynamics. Using analytical calculations supported by Monte Carlo computer simulations, it demonstrated bursting depends strength number sites. Stronger affinity prolongs burst duration but reduces variability, while an optimal maximizes noise, facilitating cellular adaptation. method explains available experimental observations quantitatively, confirming model's predictive accuracy. This study provides important insights into expression regulation, offering new tool for understanding complex processes.

Language: Английский

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