How does cohesin organize the 3D genome?

Abstract

Cohesin and CCCTC-binding factor (CTCF) are key regulatory proteins of three-dimensional (3D) genome organization. I will present direct evidence that cohesin extrudes DNA loops that are anchored by CTCF proteins in specific orientations. CTCF binding polarity controls cohesin-mediated DNA looping. Using single-molecule imaging of CTCF-cohesin collisions, we demonstrate that the N-terminus of CTCF must be oriented towards cohesin to block its ability to compact DNA. C-terminally oriented CTCF accelerates DNA compaction by cohesin. Oriented inactive Cas9 and Cas12a ribonucleoproteins exhibit similar polar effects on DNA compaction by cohesin. RNA-DNA hybrids (R-loops), such as those that occur at highly transcribed genes, efficiently block cohesin-mediated DNA compaction. Our results explain long-standing puzzles regarding how CTCF and transcription shape the 3D genome. © FASEB.