Forward and reverse epigenomics in embryonic stem cells

Abstract

The self-renewing and pluripotent properties of ESCs make them a precious tool for the advancement of general biological research, discerning the process of differentiation and embryonic development, disease modeling, drug discovery, drug testing, and, ultimately, cell- and tissue-based regenerative medicine. To further these goals, it is imperative that a deep and comprehensive understanding of all aspects of ESC biology are attained, particularly the transcriptional program and its regulation. Chromatin immunoprecipitation (ChIP) followed by next-generation sequencing (NGS) (ChIP-seq) pinpoints the binding locations of factors involved in epigenomic regulation of transcription such as transcription factors, modifications on histone proteins, chromatin modifiers and remodelers, and structural and insulator proteins. Each binding map by itself leads to insights into the mechanism of regulation of a specific factor and its downstream target genes upon which it exerts its regulatory effect leading to the discovery of the epigenomic "hallmarks" of ESCs which govern these cells' state and fate. On the other hand, an integration of a combination of binding maps enables researchers to gain an additional and complementary perspective on epigenomic regulation from the genomic point of view. By combining over 450 ChIP-seq datasets from large consortiums and singleton experimental efforts in our BindDB platform, we discovered a remarkably extensive epigenomic profile at active genes in ESCs. Based on this platform, we generated a robust in silico simulation of a reverse-ChIP protocol via implementation of an easy querying and analysis webtool (http://bind-db.huji.ac.il/) to enable researchers to learn about which epigenomic features bind their genes or genomic regions of interest in ESCs. By querying several gene groups as case studies, we noted the participation of histone modifications, chromatin modifiers, chromatin remodelers, transcription factors, and structural proteins in the regulation of the same pieces of DNA, indicating how crucial and precise the epigenomic mechanism must be in ESCs. This utilization of both a forward and reverse approach to epigenomic research will greatly advance the acquisition of a more complete picture of the mechanisms of transcriptional regulation in ESCs and improve the ability to harness it toward advancing the research and medical potential of these unique cells.