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TitleCTCF and R-loops are boundaries of cohesin-mediated DNA looping.
Journal, issue, pagesMol Cell, Vol. 83, Issue 16, Page 2856-22871.e8, Year 2023
Publish dateAug 17, 2023
AuthorsHongshan Zhang / Zhubing Shi / Edward J Banigan / Yoori Kim / Hongtao Yu / Xiao-Chen Bai / Ilya J Finkelstein /
PubMed AbstractCohesin and CCCTC-binding factor (CTCF) are key regulatory proteins of three-dimensional (3D) genome organization. Cohesin extrudes DNA loops that are anchored by CTCF in a polar orientation. Here, ...Cohesin and CCCTC-binding factor (CTCF) are key regulatory proteins of three-dimensional (3D) genome organization. Cohesin extrudes DNA loops that are anchored by CTCF in a polar orientation. Here, we present direct evidence that CTCF binding polarity controls cohesin-mediated DNA looping. Using single-molecule imaging, we demonstrate that a critical N-terminal motif of CTCF blocks cohesin translocation and DNA looping. The cryo-EM structure of the cohesin-CTCF complex reveals that this CTCF motif ahead of zinc fingers can only reach its binding site on the STAG1 cohesin subunit when the N terminus of CTCF faces cohesin. Remarkably, a C-terminally oriented CTCF accelerates DNA compaction by cohesin. DNA-bound Cas9 and Cas12a ribonucleoproteins are also polar cohesin barriers, indicating that stalling may be intrinsic to cohesin itself. Finally, we show that RNA-DNA hybrids (R-loops) block cohesin-mediated DNA compaction in vitro and are enriched with cohesin subunits in vivo, likely forming TAD boundaries.
External linksMol Cell / PubMed:37536339
MethodsEM (single particle)
Resolution6.5 Å
Structure data

32252

7w1m

EMDB-32252, PDB-7w1m:
Cryo-EM structure of human cohesin-CTCF-DNA complex
Method: EM (single particle) / Resolution: 6.5 Å

Chemicals

ChemComp-ADP:
ADENOSINE-5'-DIPHOSPHATE / ADP, energy-carrying molecule*YM

ChemComp-BEF:
BERYLLIUM TRIFLUORIDE ION

ChemComp-ZN:
Unknown entry

Source
  • homo sapiens (human)
KeywordsDNA BINDING PROTEIN/DNA / Cohesin / NIPBL / CTCF / DNA / chromosome folding / topologically associating domain / chromatin loops / DNA loop extrusion / sister chromatid cohesion / complex / ATPase / HEAT repeat protein / DNA BINDING PROTEIN / DNA BINDING PROTEIN-DNA complex

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