肝癌细胞HepG2中增强子的识别及生物信息学分析  

Identification and Bioinformatics Analysis of Enhancers in Hepatocellular Carcinoma HepG2

作　　者：丁若凡[1] 李宇鹏[1] 张一鸣[1] 朱小冬 胡海碧 刘文荣[1] 李玲[2] 郭志云 

机构地区：[1]西南交通大学生命科学与工程学院,四川成都610031 [2]成都市第三人民医院病理科,四川成都610031

出　　处：《生物技术通讯》2017年第4期455-459,523,共6页Letters in Biotechnology

基　　金：中央高校基本科研业务费专项(2682016YXZT04);国家大学生创新性实验计划(201610613066);四川省大学生创新创业训练计划(2016095)

摘　　要：目的:整合增强子特征识别肝癌细胞HepG2增强子,并对其保守性、GC含量、转录因子调控、靶基因功能等进行分析,以期解析肝癌细胞增强子参与的调控网络。方法:通过整合H3K27ac、H3K4me1和H3K4me3组蛋白修饰及DNaseⅠ高敏位点的Chip-seq数据预测HepG2中的增强子,计算每个增强子的平均Phast Cons分数和GC含量,评估整体增强子的保守性与GC含量,整合ENCODE转录因子结合位点数据寻找转录因子-增强子调控,使用GREAT和DAVID分别对增强子和增强子的靶基因进行GO与KEGG通路功能富集分析。结果:共识别2254个肝细胞癌增强子,1432个增强子靶基因,135个转录因子的9983个增强子结合位点;比较随机位点靶基因,发现增强子显著正调控靶基因的表达;保守性与GC含量分析表明增强子具有显著高的保守性与GC含量,并存在C-T/C-T/C-T-G模式的motif;增强子功能分析显示增强子显著富集于蛋白结合、酶结合、转录因子结合、RNA聚合酶Ⅱ结合等已知增强子功能,增强子GO与KEGG通路功能富集分析表明增强子靶基因显著参与细胞增殖、细胞凋亡、细胞周期调控和细胞迁移等肿瘤相关的生物进程与信号通路。结论:识别的肝细胞癌增强子具有显著高的保守性与GC含量,受多种转录因子调控,对其靶基因起正调控作用并且显著富集于肿瘤相关生物学进程与信号通路中。Objective： To resolve the enhancer regulation network of hepatoma cell, the enhancers were identified by integrating the features of the enhancers in the hepatoma cell HepG2, and GC content, regulation of transcription factors, identification of target genes and functional enrichment were analyzed. Methods： Enhancers in HepG2 were predicted by integrating Chip-seq data of histone modifications H3K27ac, H3K4mel and H3K4me3 and of DNase I hyper-sensitivity sites. The average PhastCons score and GC content of each enhancer were calculated to assess the conservation and GC content of the overall enhancers. ENCODE transcription factor binding sites data were integrated to search for transcription factor-enhancer regulation. The enrichment analysis of GO and KEGG pathway was performed by using GREAT and DAVID on enhancers and the target genes of enhancers respectively. Results： A total of 2254 enhancers in HepG2 were predicted, and 1432 target genes of enhancers, 135 transcription factors and 9983 transcription factor binding sites of enhancers were obtained. The enhancers in HepG2 significantly promoted the expression of target genes by comparing with random regions. The analysis of conservation and GC content showed that the enhancers were significantly conserved and had a remarkably high GC content, and the motif of enhancer was C-T/C-T/C-T-G. The analysis of the function enrichment of GO and KEGG pathway of enhancers showed that the target genes of enhancers were involved in cell proliferation, cell apoptosis, regulation of cell cycle and cell migration and other tumor related biological processes and signaling pathways. Conclusion： Enhancers in HepG2 were significantly conserved and had a remarkable high GC content enrichment, and they were regulated by a variety of transcription factors and played a positive role in regulation on their target genes,and were significantly enriched in tumor-related biological processes and signaling pathways.

关 键 词：增强子 肝细胞癌 CHIP-SEQ 组蛋白修饰 

分 类 号：Q751[生物学—分子生物学] Q811.4