Transcription shapes 3D chromatin organization by interacting with loop extrusion

Area of Science:

• Genomics
• Molecular Biology
• Chromatin Organization

Background:

• Cohesin mediates chromosome folding via loop extrusion, influenced by factors like CTCF.
• The interplay between transcription and cohesin's extrusion activity remains incompletely understood, with conflicting models.
• Previous hypotheses suggested transcription interferes with cohesin or that promoters are key loading sites.

Purpose of the Study:

• To investigate how transcription modulates cohesin-mediated loop extrusion.
• To reconcile the observed active extrusion by cohesin with the effects of transcription.
• To elucidate the precise role of transcribing RNA polymerases (RNAPs) in chromatin organization.

Main Methods:

• Genetic manipulation of cohesin regulators (CTCF, Wapl) in mouse cells.
• High-throughput chromosome conformation capture (Hi-C) to analyze chromatin contacts.
• Polymer simulations modeling RNAP-cohesin interactions during extrusion.
• Chromatin immunoprecipitation sequencing (ChIP-seq) to assess protein localization.

Main Results:

• Cohesin-dependent contact patterns near active genes suggest interactions between transcribing RNAPs and cohesin.
• Polymer simulations demonstrated RNAPs act as mobile barriers, obstructing and redirecting cohesin extrusion.
• Experimental data contradicted preferential cohesin loading at promoters; RNAP barrier function explained promoter accumulation.
• Nipbl, a putative cohesin loader, showed no predominant enrichment at active promoters.

Conclusions:

• Transcribing RNAPs function as dynamic extrusion barriers, not stationary obstacles.
• Cohesin is likely not preferentially loaded at promoters; RNAP barrier activity drives promoter localization.
• The interaction between RNAP-mediated extrusion barriers and loop extrusion dynamically shapes genome organization and gene regulation.