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choudharylabcpr.bsky.social @choudharylabcpr.bsky.social · 18/11/2025

Congrats to Takeo who led the work and to all the co-authors.

choudharylabcpr.bsky.social @choudharylabcpr.bsky.social · 18/11/2025

By revealing the scope of cohesin looping in gene regulation, and by disentangling CTCF´s looping-dependent and -independent roles of CTCF, the work offers a unified model of how Cohesin and CTCF impact gene expression.

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choudharylabcpr.bsky.social @choudharylabcpr.bsky.social · 18/11/2025

At the promoter of CTCF-regulated genes, CTCF functions as an activator or repressor, depending on the promoter binding position and strand orientation. As an activator, it promotes Pol2 recruitment, as a repressor it occludes Pol2 binding/elongation.

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choudharylabcpr.bsky.social @choudharylabcpr.bsky.social · 18/11/2025

The CTCF paralog CTCFL (BORIS) cannot anchor cohesin loops but can function as transcription activator to substitute for CTCF at promoter-regulated targets. This means it can disrupt 3D genome organization, but without hampering expression of CTCF-dependent essential genes.

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choudharylabcpr.bsky.social @choudharylabcpr.bsky.social · 18/11/2025

By endogenously mutating CTCF to disable cohesin anchoring, we show that promoter-proximal CTCF activates genes independently of enhancers and looping. Instead CTCF acts as an orientation-dependent transcription activator, primarily regulating essential housekeeping genes.

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choudharylabcpr.bsky.social @choudharylabcpr.bsky.social · 18/11/2025

CTCF, however behaves differently. Acute CTCF loss also alters hundreds of genes, but the pattern is mixed (both up and down) and only some require CBP/p300 dependent enhancers.

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choudharylabcpr.bsky.social @choudharylabcpr.bsky.social · 18/11/2025

We profiled the impact of acute CTCF or RAD21 removal on nascent transcription and compared it to gene regulation by CBP/p300. Cohesin is specifically important for CBP/p300-dependent enhancers, regulates hundreds of genes, but with a subtle impact previously overlooked.

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choudharylabcpr.bsky.social @choudharylabcpr.bsky.social · 18/11/2025

Cohesin-CTCF loops and TADs are extensively implicated in enhancer-promoter communication, but the transcriptional changes after acute cohesin and CTCF removal are very modest, the regulated genes show minimal overlap, and the extent of enhancer involvement remains uncertain.

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choudharylabcpr.bsky.social @choudharylabcpr.bsky.social · 18/11/2025

Cohesin and CTCF jointly fold genomes, but why do their depletion affect few genes, with minimal overlap? Do all regulated genes require looping and enhancers? In our new paper in Nature Genetics we disentangle their functions in gene regulation. www.nature.com/articles/s41...

nature.com

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choudharylabcpr.bsky.social @choudharylabcpr.bsky.social · 13/12/2024

Amazing work by Takeo (@takeo-narita.bsky.social) on these comprehensive analysis and many new insights.

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choudharylabcpr.bsky.social @choudharylabcpr.bsky.social · 13/12/2024

We propose that gene-skipping by enhancers are the exception, not the rule. Linear enhancer-promoter distance and coactivator requirement of genes can predict enhancer targets with accuracy rivalling state-of-the-art experimental approaches.

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choudharylabcpr.bsky.social @choudharylabcpr.bsky.social · 13/12/2024

Multi-way enhancer-promoter interactions in ultra-deep chromatin contact mapping analyses don't indicate co-regulation of multiple promoters. Within multi-way interacting promoters, enhancers regulate proximal promoter but not distal ones.

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choudharylabcpr.bsky.social @choudharylabcpr.bsky.social · 13/12/2024

Attributes of enhancer targets identified by mapping eRNA-PROMPT RNA interactions by RIC-seq are fundamentally different from enhancer targets identified by CRISPRi.

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choudharylabcpr.bsky.social @choudharylabcpr.bsky.social · 13/12/2024

Gene-skipping and non-skipping enhancers differ in chromatin features, target gene distance, activation strength, and coactivator requirements. High H2BNTac strongly predict functional non-skipping enhancers, while skipping enhancers show weaker regulation and higher FDRs.

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choudharylabcpr.bsky.social @choudharylabcpr.bsky.social · 13/12/2024

Gene-skipping enhancer-promoter contacts are rarely confirmed as being functional by CRISPRi screening. Conversely, CRISPRi identified gene-skipping enhancers also seldom show physical interactions.

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choudharylabcpr.bsky.social @choudharylabcpr.bsky.social · 13/12/2024

Do enhancers often skip active genes? Our other recent preprint revises current models, that enhancers frequently and by design skip active genes to activate distal targets. Instead simple rules can predict enhancer and GWAS targets. www.biorxiv.org/content/10.1...

biorxiv.org

Mammalian enhancers and GWASs act proximally and seldom skip active genes

Enhancers play a critical role in regulating transcription. Nearly 90% of human genetic variants identified in genome-wide association studies (GWAS) are located in distal regions, underscoring the im...

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choudharylabcpr.bsky.social @choudharylabcpr.bsky.social · 09/12/2024

Great effort by Takeo and the rest of the team in getting together this work.

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choudharylabcpr.bsky.social @choudharylabcpr.bsky.social · 09/12/2024

Our findings resolve several long-standing conundrums regarding the involvement of cohesin and CTCF in gene regulation, and we present a unified model for their combined and individual roles acting directly near promoters or in concert with p300/CBP-dependent enhancers.

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choudharylabcpr.bsky.social @choudharylabcpr.bsky.social · 09/12/2024

For the genes regulated by CTCF at the promoter, CTCF directly impacts DNA accessibility and downstream recruitment of PolII.

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choudharylabcpr.bsky.social @choudharylabcpr.bsky.social · 09/12/2024

The CTCF-like protein BORIS is also unable to anchor cohesin. Re-analysis of published data with this new perspective show, that unlike CTCF, BORIS has no impact on enhancer-regulated genes. In contrast, BORIS can selectively rescue expression of promoter-activated genes.

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choudharylabcpr.bsky.social @choudharylabcpr.bsky.social · 09/12/2024

Using a cohesin-loop-deficient CTCF mutant, we reveal that CTCF is a position- and orientation-dependent transcription activator at promoters. It directly activates hundreds of essential housekeeping genes—independently of cohesin and enhancers—even in plasmid reporter assays.

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choudharylabcpr.bsky.social @choudharylabcpr.bsky.social · 09/12/2024

Among diverse types of posited enhancers, cohesin seems to uniquely facilitate enhancer-mediated gene regulation through p300/CBP-dependent enhancers.

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choudharylabcpr.bsky.social @choudharylabcpr.bsky.social · 09/12/2024

Acute depletion of cohesin and CTCF dysregulate several hundreds of genes – far more than previously appreciated. Many of these are subtle, but as confirmed through several repetitions, they are consistent.

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choudharylabcpr.bsky.social @choudharylabcpr.bsky.social · 09/12/2024

How do cohesin and CTCF control gene expression and what are their links to enhancers? Our new preprint unravels their shared and unique roles: from precise enhancer targeting to direct transcriptional activator functions of CTCF! #Genomics #CTCF #Cohesin www.biorxiv.org/content/10.1...

biorxiv.org

A unified model of gene expression control by cohesin and CTCF

Cohesin and CTCF fold vertebrate genomes into loops and topologically associating domains (TADs). The genome folding by cohesin and CTCF is considered crucial for enhancer-promoter communication and g...

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