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Loop extrusion dynamics and cooperative activation independently regulate enhancer-driven transcription

ABSTRACT: How enhancers transmit their activation signals to target promoters is a fundamental unanswered question. Gene activation by distal enhancers is affected by the three-dimensional organisation of chromatin driven by cohesin-mediated loop extrusion, but how the dynamic loop extrusion cycle shapes transcriptional outcomes is not fully understood. In addition, genes are typically regulated by multiple enhancers and cases of cooperativity between enhancers have been observed that depend on the relative position of enhancers and gene. The reason for such context-dependent cooperativity is unknown, and whether it is linked to loop extrusion has not been explored. Here, we use synthetic gene activation to show that NIPBL depletion, which decreases loop extrusion rate, reduces long-range activation in a dose-dependent manner. In contrast, WAPL depletion, which reduces cohesin turnover, can both increase and decrease distal gene activation depending on the presence of adjacent CTCF binding sites. These effects on gene activation correlate with the impact on chromatin contacts. Depletion of the co-activator BRD4 also affects long-range activation, but not by changing chromatin contacts. Synthetic activation from two locations results in super-additive responses, which can be predicted by an independently determined response model. These predictions hold for dual activation from proximal and/or distal sites, and with perturbed NIPBL, WAPL, or BRD4. Distal activation therefore appears to be equivalent in nature to proximal activation, and context-dependent cooperativity can arise simply from different level of activation inputs operating on a non-linear response function.

ORGANISM(S): Mus musculus

PROVIDER: GSE329685 | GEO | 2026/05/06

REPOSITORIES: GEO

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Project description:Cohesin organizes mammalian interphase chromosomes by reeling chromatin fibers into dynamic loops. "Loop extrusion" is obstructed when cohesin encounters a properly oriented CTCF protein. It has been proposed that transcription relocalizes or interferes with cohesin, and that active transcription start sites function as cohesin loading sites, but how these effects, and transcription in general, shape chromatin is unknown. To determine whether transcription can modulate loop extrusion, we studied cells in which the primary extrusion barriers could be removed by CTCF depletion and cohesin’s residence time and abundance on chromatin could be increased by Wapl knockout. We found evidence that transcription directly interacts with loop extrusion through a novel "moving barrier" mechanism, but not by loading cohesin at active promoters. Hi-C experiments showed intricate, cohesin-dependent genomic contact patterns near actively transcribed genes, and in CTCF-Wapl double knockout (DKO) cells, genomic contacts were enriched between sites of transcription-driven cohesin localization ("cohesin islands"). Similar patterns also emerged in polymer simulations in which transcribing RNA polymerases (RNAPs) acted as "moving barriers" by impeding, slowing, or pushing loop-extruding cohesins. The model predicts that cohesin does not load preferentially at promoters and instead accumulates at TSSs due to the barrier function of RNAPs. We tested this prediction by new ChIP-seq experiments, which revealed that the "cohesin loader" Nipbl co-localizes with cohesin, but, unlike in previous reports, Nipbl did not accumulate at active promoters. We propose that RNAP acts as a new type of barrier to loop extrusion that, unlike CTCF, is not stationary in its precise genomic position, but is itself dynamically translocating and relocalizes cohesin along DNA. In this way, loop extrusion could enable translocating RNAPs to maintain contacts with distal regulatory elements, allowing transcriptional activity to shape genomic functional organization.

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Loop extrusion dynamics and cooperative activation independently regulate enhancer-driven transcription

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