Genome-Wide Identification And Characteristics Analysis Of Enhancer Regulatory Network

Enhancers can act as cis-regulatory elements(CREs)to control development and cellular function by regulating gene expression in a tissue-specific and ubiquitous manner.Previous studies show that active enhancers can transcribe enhancer-associated RNAs(eRNA)by recruiting DNA-binding transcription factors(TFs).However,the regulatory network and characteristic of different types of enhancers(e.g.,transcribed/non-transcribed enhancers,tissue-specific/ubiquitous enhancers)across multiple tissues are still unclear.Here,we identified a total of 53,924 active enhancers and 10,307 eRNAs in adrenal,brain,breast,heart,liver,lung,ovary,placenta,skeletal muscle and kidney through the integration of histone modifications(H3K4mel,H3K27ac and H3K4me3)and DNase I hypersensitive sites(DHSs)of 10 tissues.We found enhancers showed significant tissue specificity in all tissues and most of them(83.4%)did not produce enhancer-associated transcripts.We also found enhancers preferred to express 1D-eRNA(enhancers with unidirectional transcripts)rather than 2D-eRNA(enhancers with bidirectional transcripts)and most of the eRNAs belonged to IncRNA(69.8%)and pseudogene(22.19%).Additionally,enhancers exhibited high conservation,GC content and genomic variants in all the tissues.These characteristics were significantly different between EnhTS(tissue-specific enhancers)and EnhUE(ubiquitously expressed enhancers),EnheRNA(transcribed enhancers)and Enhno-eRNA(non-transcribed enhancers),Enh2D-eRNA and Enh1D-eRNA.Furthermore,it was indicated that transcription factor binding site(TFBS)significantly enriched in ±500 bp from enhancer center and the enrichment of TFs for EnheRNA and EnhUE are dramatically higher than that for Enhno-eRNA and Enh-TS,respectively.The results showed that enhancer significantly regulated the expression of adjacent target genes which were remarkably correlated with the corresponding tissue function.To investigate the regulation characteristics of enhancers in normal and tumor tissues,we annotated the function of specific up-regulated target genes of enhancers for A549(lung carcinoma epithelial cell line).It's indicated that A549-specifc up-regulated target genes of enhancers were significantly involved in cell division,positive regulation of cell proliferation,negative regulation of apoptotic process and other biological processes,additionally,they played an important role in ubiquitin mediated proteolysis,regulation of actin cytoskeleton,cGMP-PKG signaling pathway and other pathways.Finally,a free user-friendly tissue-specific enhancer database,TiED(http://lcbb.swjtu.edu.cn/TiED)was built to store all the data of enhancers in 10 tissues.