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Cell Rep. 2019 Mar 12;26(11):2890-2903.e3. doi: 10.1016/j.celrep.2019.01.116.

Condensin II Counteracts Cohesin and RNA Polymerase II in the Establishment of 3D Chromatin Organization.

Author information

1
Department of Biology, Emory University, 1510 Clifton Road NE, Atlanta, GA 30322, USA.
2
Department of Molecular and Systems Biology, Geisel School of Medicine at Dartmouth, Hanover, NH, USA.
3
Department of Biology, Emory University, 1510 Clifton Road NE, Atlanta, GA 30322, USA. Electronic address: vgcorces@gmail.com.

Abstract

Interaction domains in Drosophila chromosomes form by segregation of active and inactive chromatin in the absence of CTCF loops, but the role of transcription versus other architectural proteins in chromatin organization is unclear. Here, we find that positioning of RNAPII via transcription elongation is essential in the formation of gene loops, which in turn interact to form compartmental domains. Inhibition of transcription elongation or depletion of cohesin decreases gene looping and formation of active compartmental domains. In contrast, depletion of condensin II, which also localizes to active chromatin, causes increased gene looping, formation of compartmental domains, and stronger intra-chromosomal compartmental interactions. Condensin II has a similar role in maintaining inter-chromosomal interactions responsible for pairing between homologous chromosomes, whereas inhibition of transcription elongation or cohesin depletion has little effect on homolog pairing. The results suggest distinct roles for cohesin and condensin II in the establishment of 3D nuclear organization in Drosophila.

KEYWORDS:

CTCF; Hi-C; HiChIP; TAD; compartment; loop; pairing; transcription; transvection

PMID:
30865881
DOI:
10.1016/j.celrep.2019.01.116
Free PMC Article

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