The role of the nucleoporin nup93 sub complex in regulating hoxa gene expression

Abstract

The nuclear pore complex NPCs is required for the regulated import and export of RNA and proteins NPC is a megadalton multiprotein channel composed of 30 nucleoporins Nups In addition to transport nucleoporins are involved in the regulation of chromatin organization and gene expression Here we investigated the role of nucleoporin Nup93 in the regulation of HOXA gene expression HOXA expression is restricted to early stages of development and differentiation while its aberrant expression in differentiated cells is associated with cancers We showed that Nup93 is associated with HOXA1 HOXA3 and HOXA5 promoters and represses HOXA expression in a manner assisted by its interacting partners Nup188 and Nup205 Single cell imaging by 3D Fluorescence in situ hybridization 3D FISH analyses revealed that the depletion of Nup93 untethers the HOXA gene locus from the nuclear periphery which we also ascertained by RNA FISH We propose a novel role for the Nup93 sub complex in repressing HOXA gene locus thereby preventing its untimely expression in differentiated cells To address the genome wide role of Nup93 in gene regulation we performed Chromatin Immunoprecipitation ChIP of Nup93 followed by whole genome sequencing Analyses of Nup93 ChIP seq data shows that Nup93 specifically associates with genes involved in development and differentiation Furthermore Nup93 associates with genomic regions similar to the repressive histone mark H3K27me3 suggesting a repressive role of Nup93 in gene regulation In addition Nup93 enriched regions also overlap with CTCF a major genome organizer suggesting a crosstalk between Nup93 and CTCF in gene regulation To further understand the role of Nup93 and CTCF during differentiation we performed Retinoic acid mediated differentiation of NT2 D1 cells in the background of Nup93 and CTCF depletion We found that Nup93 depletion in NT2 D1 cells upregulates HOXA gene cluster In contrast CTCF depletion downregulates HOXA gene cluster Surprisingly we found that retinoic acid treatment in Nup93 dep