Transcriptional regulation and chromatin architecture maintenance are decoupled functions at the Sox2 locus.

Genes & development 2022 Jun 01

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How distal regulatory elements control gene transcription and chromatin topology is not clearly defined, yet these processes are closely linked in lineage specification during development. Through allele-specific genome editing and chromatin interaction analyses of the Sox2 locus in mouse embryonic stem cells, we found a striking disconnection between transcriptional control and chromatin architecture. We traced nearly all Sox2 transcriptional activation to a small number of key transcription factor binding sites, whose deletions have no effect on promoter-enhancer interaction frequencies or topological domain organization. Local chromatin architecture maintenance, including at the topologically associating domain (TAD) boundary downstream from the Sox2 enhancer, is widely distributed over multiple transcription factor-bound regions and maintained in a CTCF-independent manner. Furthermore, partial disruption of promoter-enhancer interactions by ectopic chromatin loop formation has no effect on Sox2 transcription. These findings indicate that many transcription factors are involved in modulating chromatin architecture independently of CTCF. © 2022 Taylor et al.; Published by Cold Spring Harbor Laboratory Press.

Citation

Tiegh Taylor, Natalia Sikorska, Virlana M Shchuka, Sanjay Chahar, Chenfan Ji, Neil N Macpherson, Sakthi D Moorthy, Marit A C de Kort, Shanelle Mullany, Nawrah Khader, Zoe E Gillespie, Lida Langroudi, Ian C Tobias, Tineke L Lenstra, Jennifer A Mitchell, Tom Sexton. Transcriptional regulation and chromatin architecture maintenance are decoupled functions at the Sox2 locus. Genes & development. 2022 Jun 01;36(11-12):699-717