TOP2B binding and enzymatic activity on promoters and introns modulates multiple oncogenes in human gliomas [ATAC-seq]. TOP2B binding and enzymatic activity on promoters and introns modulates multiple oncogenes in human gliomas [ATAC-seq]

We investigated the contribution of TOP2B to transcriptional modulation in gliomas given the variable expression of this helicase across tumors, and its emerging role in epigenetic regulation of transcription. We mapped the genomic location of TOP2B, and identified distinct sites of native binding and enzymatic activity across human glioma cell lines and human tumor specimens. TOP2B was active in a subset of promoters and introns, and its inhibition led to downregulation of these genes. We investigated the contribution of TOP2B to transcriptional modulation in gliomas given the variable expression of this helicase across tumors, and its emerging role in epigenetic regulation of transcription. We mapped the genomic location of TOP2B, and identified distinct sites of native binding and enzymatic activity across human glioma cell lines and human tumor specimens. TOP2B was active in a subset of promoters and introns, and its inhibition led to downregulation of these genes. Overall design: We performed ChIP-seq (Chromatin immunoprecipitation and sequencing) for TOP2A and TOP2B to investigate its genomic localization in proneural glioma genotypes TS543 and BT142 and two mesenchymal glioma cell lines SNB19 and 0777A. To analyze the contribution of TOP2B on gene expression we treated cells with the TOP2 inhibitor ICRF193 10Um for 5hrs followed by RNA-seq. 20 TS543 samples (10 untreated; 10 treated), 12 BT142 samples (5 untreated; 7 treated) were included in the study. This submission includes ATAC-seq samples.

鉴于该解旋酶在各类肿瘤中存在表达异质性，且其在转录表观遗传调控中的作用日益受到关注，我们探究了TOP2B对神经胶质瘤转录调控的贡献。我们绘制了TOP2B的基因组定位图谱，并在人类神经胶质瘤细胞系及人体肿瘤标本中鉴定出其天然结合与酶活性的特异性位点。TOP2B在部分启动子及内含子区域发挥活性，抑制其功能可导致这些基因的表达下调。鉴于该解旋酶在各类肿瘤中存在表达异质性，且其在转录表观遗传调控中的作用日益受到关注，我们探究了TOP2B对神经胶质瘤转录调控的贡献。我们绘制了TOP2B的基因组定位图谱，并在人类神经胶质瘤细胞系及人体肿瘤标本中鉴定出其天然结合与酶活性的特异性位点。TOP2B在部分启动子及内含子区域发挥活性，抑制其功能可导致这些基因的表达下调。整体实验设计：我们针对TOP2A与TOP2B开展染色质免疫共沉淀测序（Chromatin immunoprecipitation and sequencing，ChIP-seq），以探究其在前神经元型神经胶质瘤基因型TS543、BT142以及两株间充质型神经胶质瘤细胞系SNB19和0777A中的基因组定位情况。为分析TOP2B对基因表达的调控作用，我们用拓扑异构酶抑制剂ICRF193（10 μM）处理细胞5小时，随后进行RNA测序（RNA-seq）。本研究纳入20份TS543样本（10份未处理组、10份处理组）及12份BT142样本（5份未处理组、7份处理组）。本数据集包含转座酶可及性测序（Assay for Transposase-Accessible Chromatin using sequencing，ATAC-seq）样本。