RNA polymerase II and PARP1 shape enhancer-promoter contacts

Barshad, Gilad; Lewis, James J.; Chivu, Alexandra G.; Abuhashem, Abderhman; Krietenstein, Nils; Rice, Edward J.; Rando, Oliver J.; Hadjantonakis, Anna-Katerina; Danko, Charles G.

doi:10.1101/2022.07.07.499190

Cited by 19 publications

(26 citation statements)

References 99 publications

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“…First, A/B-compartments, TADs, and loops were uncovered as deeper sequencing increased the number of captured unique contacts in 3C experiments from ~8 million 3 to ~450 million 5 to ~5 billion 7 , respectively. Second, in overcoming the resolution limits imposed by Hi-C's dependence on restriction enzymes, Micro-C achieved nucleosome-scale resolution by digesting chromatin with micrococcal nuclease (MNase); this allows Micro-C to better resolve finer-scale regulatory interactions including between enhancers and promoters 8,[11][12][13]15,19,20 . Third, perturbation studies have yielded profound mechanistic insights into 3D genome structure.…”

Section: Introductionmentioning

confidence: 99%

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

Goel

Huseyin

Hansen

2022

Preprint

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

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Section: Introductionmentioning

confidence: 99%

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

Goel

Huseyin

Hansen

2022

Preprint

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“…The link between RNAPolII and looping has been debated, with conflicting results linked to low-resolution datasets or pharmacological agents with non-specific indirect effects 22,31,32,[39][40][41][42][43] .…”

Section: Discussionmentioning

confidence: 99%

“…Most recently, two studies employed a degron to achieve short-term RNAPolII degradation and uncovered a previously underappreciated effect on E-P loop maintenance 31,32 . Here, we build on these works by creating genome-wide maps of cell type-invariant and cell type-specific chromatin loops during the transitions from hiPSCs to NPCs and NPCs to post-mitotic neurons.…”

Section: Discussionmentioning

confidence: 99%

Cell type-specific loops linked to RNA polymerase II elongation in human neural differentiation

Titus,

Simandi,

Chandrashekar

et al. 2023

Preprint

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DNA is folded into higher-order structures that shape and are shaped by genome function. The role for long-range loops in the establishment of new gene expression patterns during cell fate transitions remains poorly understood. Here, we investigate the link between cell-specific loops and RNA polymerase II (RNAPolII) during neural lineage commitment. We find thousands of loops decommissioned or gainedde novoupon differentiation of human induced pluripotent stem cells (hiPSCs) to neural progenitors (NPCs) and post-mitotic neurons. During hiPSC-to-NPC and NPC-to-neuron transitions, genes changing from RNAPolII initiation to elongation are >4-fold more likely to anchor cell-specific loops than repressed genes. Elongated genes exhibit significant mRNA upregulation when connected in cell-specific promoter-enhancer loops but not invariant promoter-enhancer loops, promoter-promoter loops, or unlooped. Genes transitioning from repression to RNAPolII initiation exhibit slight mRNA increase independent of loop status. Our data link cell-specific loops and robust RNAPolII-mediated elongation during neural cell fate transitions.HighlightsThousands of loops are decommissioned and gained upon human iPSC differentiation to NPCs/neuronsGenes transitioning from initiated-to-elongated exhibit robust mRNA upregulation when connected in cell type-specific promoter-enhancer loopsGenes transitioning from repressed-to-initiated exhibit slight increases in mRNA levels independent of loop statusUpon short-term RNAPolII degradation, loops formed by elongated genes are more severely disrupted than those anchoring initiated genes

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“…We also compared MChIP-C with a recently published K562 Micro-C data (Barshad et al, 2023). Raw Micro-C sequencing reads were downloaded from GEO (GSE206131) and analyzed with the pipeline we used for MChIP-C and PLAC-seq data processing.…”

Section: Methodsmentioning

confidence: 99%

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

Golov

Гаврилов

Kaplan

et al. 2023

Preprint

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

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RNA polymerase II and PARP1 shape enhancer-promoter contacts

Cited by 19 publications

References 99 publications

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

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

Cell type-specific loops linked to RNA polymerase II elongation in human neural differentiation

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

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