Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX 77030, USA.
Department of Biochemistry and Molecular Biology, McGovern Medical School, University of Texas Health Science Center at Houston, Houston, TX 77030, USA; The University of Texas MD Anderson Cancer Center UTHealth Houston Graduate School of Biomedical Sciences, Houston, TX 77030, USA.
Cell Rep. 2022 Nov 1;41(5):111576. doi: 10.1016/j.celrep.2022.111576.
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.
核孔复合体（NPC）由超过 30 种核孔蛋白（NUPs）组成，是真核生物的标志。有研究表明，NUPs 在调节基因转录和三维基因组组织方面发挥着重要作用。然而，支持其直接作用的证据仍然有限。在这里，我们通过 Cut&Run 发现，核心 NUPs 在人类细胞中与活性启动子和增强子广泛但也具有细胞类型特异性的关联。通过生长素介导的两种 NUPs 的快速耗竭，证明 NUP93 而不是 NUP35 直接且特异性地控制基因转录。NUP93 通过促进 BRD4 充分募集到其活性增强子，直接激活 RNA 聚合酶 II 加载水平高和转录延伸的基因。基于 dCas9 的系链证实了 NUP93 在基因转录激活中的直接和因果作用。出乎意料的是，急性 NUP93 耗竭后的原位 Hi-C 和 H3K27ac 或 H3K4me1 HiChIP 结果显示，三维基因组组织的变化很小，从 A/B 区室和拓扑关联域（TADs）到增强子-启动子接触都没有变化。
