PO.MCB06.01 · 分子与细胞生物学
STAG2-cohesin 介导三维基因组动态变化，调控神经母细胞瘤中 MYCN 驱动的致癌转录组
Stag2-cohesin mediates 3d genome dynamics to regulate MYCN driven oncogenic transcriptome in neuroblastoma.
作者与单位 Authors & Affiliations
摘要 Abstract
中文摘要
神经母细胞瘤（NB）的特征是由核心调控回路（CRC）转录因子（TF）网络与细胞类型特异性增强子景观所驱动的异常转录组。神经母细胞瘤源于细胞分化缺陷，或是终末分化失败，或是回复至类多能状态。虽然已知 CRC TF 结合细胞类型特异性增强子和启动子以确定正常分化所需的转录组，但它们与三维核结构蛋白（如 cohesin，由 SMC1A、SMC3、RAD21 以及 STAG1 或 STAG2 组成）之间的功能相互作用在很大程度上仍未被探索。三维基因组组织通过促进增强子-启动子成环，在确定细胞类型特异性转录景观中发挥关键作用，而这种成环在分化过程中会经历动态重连。除了在 DNA 复制和修复中的经典作用外，cohesin 还介导增强子与启动子之间的染色质成环，从而精确调控靶基因表达。理解 CRC TF 如何与 cohesin 协作以建立和维持 NB 特异性转录程序，可能为阐明神经母细胞瘤发病机制和分化缺陷的机制提供宝贵见解。为界定 STAG1-cohesin 和 STAG2-cohesin 在 MYCN 靶基因调控中的作用，我们进行了全基因组 RNA-seq 和 ChIP-seq 分析，以揭示这些复合物在调控 NB 细胞致癌转录组中各自独特但又相互重叠的作用。STAG1 敲低（KD）对 NB 细胞增殖或转录活性的影响极小。相比之下，STAG2 KD 降低细胞增殖，并伴随 MYCN 靶基因下调和神经元分化基因上调。全基因组 ChIP-seq 分析显示，MYCN/STAG1 峰与经典 MYCN 靶基因的启动子相关。相比之下，MYCN/STAG2 峰主要与神经分化基因的启动子和增强子相关。STAG2 KD 减少了染色质结合的 MYCN，尤其是在增强子和启动子处，而 MYCN 总蛋白水平无变化。这种减少与观察到的 MYCN 靶基因下调相关。相比之下，STAG1 KD 不影响 MYCN 的染色质结合。在 MYCN 非扩增的 SHEP 细胞中异位诱导 MYCN 显著增加了 STAG2 的染色质结合，而 STAG1 的结合保持不变。相比之下，尽管 MYCN KD 导致 STAG1 和 STAG2 总蛋白水平降低，但其染色质结合水平不受影响。这些发现强调了 STAG2-cohesin 通过选择性调节 MYCN 染色质结合来维持 NB 致癌转录组的关键作用。本研究突出了 STAG2-cohesin 的功能特化，将其确立为 cohesin 动态和 NB 转录程序的关键调控因子。
查看英文原文 English abstract
Neuroblastoma(NB) is characterized by an abnormal transcriptome driven by a network of core regulatory circuitry (CRC) transcription factors (TFs) and cell type-specific enhancer landscapes. Neuroblastoma arises due to defects in cellular differentiation, either through a failure to terminally differentiate or a reversion to a pluripotent-like state. While CRC TFs are known to bind cell type-specific enhancers and promoters to define transcriptomes necessary for proper differentiation, their functional interplay with 3D nuclear architectural proteins, such as cohesin (comprising SMC1A, SMC3, RAD21, and STAG1 or STAG2), remains largely unexplored. 3D genome organization plays a critical role in defining the cell type-specific transcriptional landscape by facilitating enhancer-promoter looping, which undergoes dynamic rewiring during differentiation. Beyond their canonical roles in DNA replication and repair, cohesin mediates chromatin looping between enhancers and promoters, enabling precise regulation of target gene expression. Understanding how CRC TFs collaborate with cohesin to establish and maintain NB-specific transcriptional programs could provide valuable insights into the mechanisms underlying neuroblastoma pathogenesis and differentiation defects. To define roles of STAG1- and STAG2-cohesin in MYCN target regulation , genome-wide RNA-seq and ChIP-seq analyses were performed to uncover the distinct yet overlapping roles of these complexes in regulating the oncogenic transcriptome of NB cells. STAG1 Knockdown (KD) has minimal impact on NB cell proliferation or transcriptional activity. In contrast, STAG2 KD reduces cell proliferation, accompanied by downregulation of MYCN target genes and upregulation of neuronal differentiation genes. Genome-wide ChIP-seq analysis revealed that MYCN/STAG1 peaks are associated with promoters of canonical MYCN target genes. In contrast, MYCN/STAG2 peaks are primarily associated with promoters and enhancers of neural differentiation genes. STAG2 KD decreases chromatin-bound MYCN, particularly at enhancers and promoters, with no change in total MYCN protein levels. This reduction correlates with the observed downregulation of MYCN target genes. In contrast, STAG1 KD does not affect MYCN chromatin binding. Ectopic induction of MYCN in MYCN-nonamplified SHEP cells significantly increased STAG2 chromatin binding, whereas STAG1 binding remains unchanged. In contrast, chromatin-bound STAG1 and STAG2 levels remained unaffected by MYCN KD despite the reduction in their total protein levels. These findings underscore the critical role of STAG2-cohesin in sustaining the NB oncogenic transcriptome by selectively modulating MYCN chromatin binding. This study highlights STAG2-cohesin's functional specialization, establishing it as a pivotal regulator of cohesin dynamics and NB transcriptional programs.
利益披露 Disclosure
J. Kang, None.