Acute Depletion of Human Core Nucleoporin Reveals Direct Roles in Transcription Control but Dispensability for 3d Genome Organization

Authors

Xiaoyu Zhu
Chuangye Qi
Ruoyu Wang
Joo-Hyung Lee
Jiaofang Shao
Lanxin Bei
Feng Xiong
Phuoc T Nguyen
Guojie Li
Joanna Krakowiak
Su-Pin Koh
Lukas M Simon
Leng Han
Travis I Moore
Wenbo Li

Publication Date

11-1-2022

Journal

Cell Reports

Abstract

The nuclear pore complex (NPC) comprises more than 30 nucleoporins (NUPs) and is a hallmark of eukaryotes. NUPs have been suggested to be important in regulating gene transcription and 3D genome organization. However, evidence in support of their direct roles remains limited. Here, by Cut&Run, we find that core NUPs display broad but also cell-type-specific association with active promoters and enhancers in human cells. Auxin-mediated rapid depletion of two NUPs demonstrates that NUP93, but not NUP35, directly and specifically controls gene transcription. NUP93 directly activates genes with high levels of RNA polymerase II loading and transcriptional elongation by facilitating full BRD4 recruitment to their active enhancers. dCas9-based tethering confirms a direct and causal role of NUP93 in gene transcriptional activation. Unexpectedly, in situ Hi-C and H3K27ac or H3K4me1 HiChIP results upon acute NUP93 depletion show negligible changesS2211-1247(22)01437-1 of 3D genome organization ranging from A/B compartments and topologically associating domains (TADs) to enhancer-promoter contacts.

Keywords

3D genome organization, CP: Molecular biology, Cut&Run, PRO-seq, Hi-C, HiChIP, dCas9 tethering, enhancers, nuclear pore complex, nucleoporins, transcription