肝癌HepG2细胞中TEAD1-增强子调控微RNA的识别与分析

Identification and Characteristic Analysis of TEAD1-Enhancers Regulating MicroRNAs in Hepatocellular Carcinoma HepG2 Cells

摘要

转录因子、增强子和微RNA (microRNA, miRNA)组成的调控网络对癌症的转录调控和进展至关重要。TEA结构域转录因子1 (TEA domain transcription factor 1, TEAD1)是TEA/ATTS结构域家族的成员, 目前尚不清楚TEAD1作为一种癌症相关转录因子, 是否参与了增强子-miRNA网络与肝细胞癌的发生发展。本研究首先通过整合肝细胞癌HepG2细胞系的CAGE-seq和GRO-seq数据, 鉴定出14 286个转录稳定与不稳定增强子RNA (enhancer RNA, eRNA)的活性增强子, 并证实这些活性增强子具有先前报道的组蛋白修饰特征(高的H3K27ac信号与H3K4me1/ H3K4me3信号比)。随后, 通过整合从ChIP-seq数据获得的35 883个TEAD1-DNA结合位点, 鉴定出2 550个与TEAD1结合的增强子(EnhTEAD1)。进一步分析显示, 与未结合TEAD1 的增强子(EnhnoTEAD1)相比, EnhTEAD1上活性增强子标记(H3K27ac、H3K4me1和H3K4me3)和eRNA的表达显著升高; TEAD1与4种转录因子(GATA4、HNF4A、YY1和CTCF)协同作用, 促进EnhTEAD1区域介导的染色质可及性和空间环化。最后, 为了研究EnhTEAD1与miRNA之间的调控网络, 在采用干扰小RNA (small interfering RNA, siRNA)干扰TEAD1后, 对HepG2肝癌细胞进行了小RNA (small RNA)测序, 并通过RNA-seq和Hi-C共获得68个由EnhTEAD1调控的差异表达miRNA (EnhTEAD1-miRNA), 这些EnhTEAD1-miRNA显著参与多种癌症相关的生物进程与通路。综上所述, 本研究阐明了EnhTEAD1-miRNA网络在肝细胞癌中的调控机制, 为肝细胞癌治疗提供了新的潜在靶点。

Abstract

The regulatory network constituted by transcription factors, enhancers, and microRNAs (miRNAs) is critical to the transcriptional regulation and progression of cancer. TEA domain transcription factor 1 (TEAD1) is a member of the TEA/ATTS domain family. However, it is unclear whether TEAD1, as a cancer-related transcription factor, is involved in the enhancer-miRNA network and the occurrence and develop-ment of hepatocellular carcinoma. Herein, 14 286 active enhancers that transcribe stable and unstable enhan-cer RNAs (eRNAs) were firstly identified by integrating CAGE-seq and GRO-seq data of HepG2 cell line, and confirmed to have previously reported histone modification characteristics (high H3K27ac signal and H3K4me1/H3K4me3 signal ratio). Subsequently, 2 550 TEAD1-binding enhancers (EnhTEAD1) were identified by in-tegrating 35 883 TEAD1-DNA binding sites obtained from ChIP-seq data. Compared with no TEAD1-binding enhancers (EnhnoTEAD1), the expression of active enhancer markers (H3K27ac, H3K4me1 and H3K4me3) and eRNAs on EnhTEAD1 was significantly increased. Furthermore, TEAD1 may act synergistically with four transcription factors (GATA4, HNF4A, YY1, and CTCF) to promote chromatin accessibility and spatial cyclization mediated by the EnhTEAD1 region. To study the regulatory network between EnhTEAD1 and miRNAs, small RNA sequencing was performed in HepG2 cells after TEAD1 was interfered using small in-terfering RNAs (siRNAs). A total of 68 differentially expressed miRNAs (EnhTEAD1-miRNAs) regulated by EnhTEAD1 were obtained by RNA-seq and Hi-C, and were found to be significantly involved in a variety of cancer-related biological processes and pathways. In summary, the study elucidates the regulatory mecha-nism of EnhTEAD1-miRNA network in hepatocellular carcinoma, and also provides a new potential target for treatment of hepatocellular carcinoma.

关键词

TEA结构域转录因子1 (TEAD1) / 肝细胞癌 / 增强子 / 微RNA (miRNA)

Key words

TEA domain transcription factor 1 (TEAD1) / hepatocellular carcinoma / enhancer / microRNA (miRNA)