Oncogenic Notch promotes long-range regulatory interactions within hyperconnected 3D cliques [MB157_ChIP-seq]. Oncogenic Notch promotes long-range regulatory interactions within hyperconnected 3D cliques [MB157_ChIP-seq]

Purpose: To investigate the impact of oncogenic Notch on the 3D genome organization of cancer cells. Methods: We generated cohesin HiChIP and 1D epigenomic data sets in two different Notch-dependent cancer cell types, triple-negative breast cancer (TNBC) and mantle cell lymphoma (MCL), in the Notch-on and -off states. Results: We report here that Notch transcription complexes control their direct target genes through two distinct regulatory modes: either through existing loops or by facilitating new long-range regulatory interactions. This combination of pre-existing and Notch-promoted loops coalesce enhancers and promoters to form highly interacting clusters, termed “3D cliques”. Notch preferentially activates enhancers and promotes looping interactions within highly connected 3D cliques that regulate key oncogenes. Conclusions: These observations suggest a general mechanism that oncogenic transcription factors can exploit to regulate the transcriptional outputs of cancer cells. Overall design: ChIP-seq, RNA-seq and HiChIP in Notch-on, -off, -recovery conditions in TNBC and MCL cell lines to profile Notch transcriptional complex binding, histone modification, Notch target genes and contact between regulatory elements.

研究目的：探究致癌Notch信号对癌细胞三维基因组组织的影响。
实验方法：我们在两种Notch依赖性癌细胞类型——三阴性乳腺癌（triple-negative breast cancer, TNBC）与套细胞淋巴瘤（mantle cell lymphoma, MCL）——的Notch激活（Notch-on）与失活（Notch-off）状态下，生成了黏连蛋白（cohesin）HiChIP及一维表观基因组数据集。
实验结果：本研究发现，Notch转录复合物可通过两种截然不同的调控模式直接调控其靶基因：一是借助已存在的染色质环，二是促进新型远距离调控相互作用。这种预存染色质环与Notch诱导的环的组合，会将增强子与启动子凝聚为高度互作的簇状结构，我们将其命名为“三维clique（3D cliques）”。Notch优先激活增强子，并在调控关键致癌基因的高度连接的三维clique内促进环化相互作用。
研究结论：上述观测结果提示，致癌转录因子可通过一种通用机制调控癌细胞的转录输出。
整体实验设计：在三阴性乳腺癌和套细胞淋巴瘤细胞系的Notch激活、失活及恢复条件下，开展ChIP-seq、RNA-seq及HiChIP实验，以分析Notch转录复合物结合情况、组蛋白修饰、Notch靶基因及调控元件间的相互接触。