Labade Ajay S, Karmodiya Krishanpal, Sengupta Kundan
Biology, Indian Institute of Science Education and Research (IISER), Dr. Homi Bhabha Road, Pashan, Pune, Maharashtra 411008 India.
Epigenetics Chromatin. 2016 Dec 3;9:54. doi: 10.1186/s13072-016-0106-0. eCollection 2016.
The nuclear pore complex (NPC) mediates nuclear transport of RNA and proteins into and out of the nucleus. Certain nucleoporins have additional functions in chromatin organization and transcription regulation. Nup93 is a scaffold nucleoporin at the nuclear pore complex which is associated with human chromosomes 5, 7 and 16 and with the promoters of the HOXA gene as revealed by ChIP-on-chip studies using tiling microarrays for these chromosomes. However, the functional consequences of the association of Nup93 with HOXA is unknown.
Here, we examined the association of Nup93 with the HOXA gene cluster and its consequences on HOXA gene expression in diploid colorectal cancer cells (DLD1). Nup93 showed a specific enrichment ~1 Kb upstream of the transcription start site of each of the HOXA1, HOXA3 and HOXA5 promoters, respectively. Furthermore, the association of Nup93 with HOXA was assisted by its interacting partners Nup188 and Nup205. The depletion of the Nup93 sub-complex significantly upregulated HOXA gene expression levels. However, expression levels of a control gene locus (GLCCI1) on human chromosome 7 were unaffected. Three-dimensional fluorescence in situ hybridization (3D-FISH) analyses revealed that the depletion of the Nup93 sub-complex (but not Nup98) disengages the HOXA gene locus from the nuclear periphery, suggesting a potential role for Nup93 in tethering and repressing the HOXA gene cluster. Consistently, Nup93 knockdown increased active histone marks (H3K9ac), decreased repressive histone marks (H3K27me3) on the HOXA1 promoter and increased transcription elongation marks (H3K36me3) within the HOXA1 gene. Moreover, the combined depletion of Nup93 and CTCF (a known organizer of HOXA gene cluster) but not Nup93 alone, significantly increased GLCCI1 gene expression levels. Taken together, this suggests a novel role for Nup93 and its interactors in repressing the HOXA gene cluster.
This study reveals that the nucleoporin Nup93 assisted by its interactors Nup188 and Nup205 mediates the repression of HOXA gene expression.
核孔复合体（NPC）介导RNA和蛋白质进出细胞核的运输。某些核孔蛋白在染色质组织和转录调控中具有额外功能。芯片上染色质免疫沉淀（ChIP-on-chip）研究使用这些染色体的平铺微阵列揭示，Nup93是核孔复合体中的一种支架核孔蛋白，与人类5号、7号和16号染色体以及HOXA基因的启动子相关。然而，Nup93与HOXA关联的功能后果尚不清楚。
在此，我们研究了Nup93与HOXA基因簇的关联及其对二倍体结肠癌细胞（DLD1）中HOXA基因表达的影响。Nup93分别在HOXA1、HOXA3和HOXA5启动子转录起始位点上游约1 kb处显示出特异性富集。此外，Nup93与其相互作用伙伴Nup188和Nup205共同参与了与HOXA的关联。Nup93亚复合体的缺失显著上调了HOXA基因表达水平。然而，人类7号染色体上一个对照基因座（GLCCI1）的表达水平未受影响。三维荧光原位杂交（3D-FISH）分析显示，Nup93亚复合体（而非Nup98）的缺失使HOXA基因座与核周边脱离，提示Nup93在锚定和抑制HOXA基因簇方面可能发挥作用。一致的是，Nup93敲低增加了HOXA1启动子上的活性组蛋白标记（H3K9ac），减少了抑制性组蛋白标记（H3K27me3），并增加了HOXA1基因内的转录延伸标记（H3K36me3）。此外，Nup93和CTCF（一种已知的HOXA基因簇组织者）的联合缺失而非单独的Nup93缺失，显著增加了GLCCI1基因表达水平。综上所述，这表明Nup93及其相互作用蛋白在抑制HOXA基因簇方面具有新的作用。
本研究揭示，在其相互作用伙伴Nup188和Nup205的协助下，核孔蛋白Nup93介导了HOXA基因表达的抑制。
