Nucleoporin 153 links nuclear pore complex to chromatin architecture by mediating CTCF and cohesin binding

Shinichi Kadota,Eda Yildirim,Yuming Shi,Jeannie T Lee,Jiayu Sun,Jianhong Ou

doi:10.1038/s41467-020-16394-3

Abstract

Nucleoporin proteins (Nups) have been proposed to mediate spatial and temporal chromatin organization during gene regulation. Nevertheless, the molecular mechanisms in mammalian cells are not well understood. Here, we report that Nucleoporin 153 (NUP153) interacts with the chromatin architectural proteins, CTCF and cohesin, and mediates their binding across cis-regulatory elements and TAD boundaries in mouse embryonic stem (ES) cells. NUP153 depletion results in altered CTCF and cohesin binding and differential gene expression — specifically at the bivalent developmental genes. To investigate the molecular mechanism, we utilize epidermal growth factor (EGF)-inducible immediate early genes (IEGs). We find that NUP153 controls CTCF and cohesin binding at the cis-regulatory elements and POL II pausing during the basal state. Furthermore, efficient IEG transcription relies on NUP153. We propose that NUP153 links the nuclear pore complex (NPC) to chromatin architecture allowing genes that are poised to respond rapidly to developmental cues to be properly modulated.

Highlights

Nucleoporin proteins (Nups) have been proposed to mediate spatial and temporal chromatin organization during gene regulation
We performed FLAG-Nucleoporin 153 (NUP153) IP followed by western blotting and determined that NUP153 interacts with CTCF and cohesin subunits (Fig. 1b)
We aimed to provide a mechanistic understanding on how NUP153 mediates chromatin structure and influences transcription

Summary

Introduction

Nucleoporin proteins (Nups) have been proposed to mediate spatial and temporal chromatin organization during gene regulation. We report that Nucleoporin 153 (NUP153) interacts with the chromatin architectural proteins, CTCF and cohesin, and mediates their binding across cis-regulatory elements and TAD boundaries in mouse embryonic stem (ES) cells. Inducible genes including GAL, INO1, and HXK1 localize to the NPC upon transcription activation — a process that has been proposed to be critical for the establishment of transcription memory[10,11,12] For several of these loci, NPC association facilitates chromatin looping between distal regulatory elements and promoters[13,14]. NUP98 has been shown to interact with several chromatin architectural proteins, including the CCCTC-binding factor, CTCF These findings collectively suggest that Nups can facilitate chromatin structure in a direct manner by regulating transcription and in an indirect manner whereby Nup-mediated gene regulation relies on architectural proteins. Long-range loops of preferential chromatin interactions, referred to as “topologically associating domains”

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