CTCF boundary remodels chromatin domain and drives aberrant HOX gene transcription in acute myeloid leukemia. CTCF boundary remodels chromatin domain and drives aberrant HOX gene transcription in acute myeloid leukemia

We analyzed RNA-seq, ATAC-seq, ChIP-seq and 4C-seq data to find that CTCF binding site located between HOXA7 and HOXA9 genes (CBS7/9) is critical for establishing and maintaining aberrant HOXA9-HOXA13 gene expression in AML. Disruption of the CBS7/9 boundary resulted in spreading of repressive H3K27me3 into the posterior active HOXA chromatin domain that subsequently impaired enhancer/promoter chromatin accessibility and disrupted ectopic long-range interactions among the posterior HOXA genes. Consistent with the role of the CBS7/9 boundary in HOXA locus chromatin organization, attenuation of the CBS7/9 boundary function reduced posterior HOTTIP lincRNA and HOXA gene expression and altered myeloid specific transcriptome profiles important for pathogenesis of myeloid malignancies. Overall design: We have submitted our RAW sequence datasets into SRA database (SRP115103 and Bioproject: PRJNA396046), including RNA-SEQ, ATAC-seq, ChIP-seq and 4C-seq for WT and CBS7/9KO MOLM13 leukemia cells

本研究通过对RNA测序（RNA-seq）、转座酶可及性测序（ATAC-seq）、染色质免疫沉淀测序（ChIP-seq）及染色体构象捕获测序（4C-seq）数据进行分析，发现位于同源框基因HOXA7与HOXA9之间的CCCTC结合因子（CTCF）结合位点（CBS7/9），在急性髓系白血病（AML）中对建立并维持HOXA9-HOXA13基因的异常表达至关重要。破坏CBS7/9边界元件可导致抑制性组蛋白修饰H3K27me3扩散至后部活性HOXA染色质结构域，进而削弱增强子与启动子的染色质可及性，并破坏后部HOXA基因间的异位远程相互作用。这一结果与CBS7/9边界元件在HOXA基因座染色质组织中的功能一致：当CBS7/9边界元件的功能减弱时，后部HOTTIP长链基因间非编码RNA（HOTTIP lincRNA）与HOXA基因的表达水平会降低，同时会改变与髓系恶性肿瘤致病机制密切相关的髓系特异性转录组特征。实验设计概述：本研究已将原始测序数据集提交至序列读取存档数据库（SRA database），登录号为SRP115103，生物项目编号为PRJNA396046，数据集涵盖野生型（WT）与CBS7/9基因敲除（CBS7/9KO）的MOLM13白血病细胞的RNA-seq、ATAC-seq、ChIP-seq及4C-seq数据。