Genome-Wide Epigenetics

Abstract

WhaT is epiGeneTics? The term “epigenetics” was coined by Conrad Waddington to describe “the branch of biology which studies the causal interactions between genes and their products, which bring the phenotype into being” (Goldberg et al., 2007). Very broadly, the word has come to refer to the study of the regulation of genes, their expression, and how that translates into particular phenotypes, independent of any change to the underlying DNA sequence. More simply stated, epigenetics is the study of functionally relevant changes in gene expression (with subsequent changes in cellular phenotype) that result from mechanisms other than from changes in the underlying DNA nucleotide sequence. Despite the fact that there is no change in the nucleo tide sequence, epigenetic modifications may be heritable and can be passed down to subsequent generations through cell replication and division of alternative chromatin states. This “turning on or off” of genes explains why, despite having the same underlying DNA sequence, a keratinocyte looks and behaves so differently than a hepatocyte and why the epigenetic state is carried over to maintain celland tissue-type specification. Although a given cell’s (or individual’s) genome remains relatively stable over time, the epigenome can and does vary depending on a number of factors, including environmental conditions. These processes allow for many “good” functions, including normal organism development; however, aberrant epigenetic mechanisms are implicated in different disease processes, including malignancies. This article provides a brief overview of the field of epigenetics and offers a glimpse into some of the major techniques used to study it, with a particular focus on chromatin immunoprecipitation followed by sequencing (ChIP-seq), the current standard method for studying proteins and other epigenetic factors that bind to DNA. At the heart of epigenetic control is the organization of DNA into chromatin. This begins with 147 base pairs of DNA wrapped around eight histone proteins, which include the core histones H2A, H2B, H3, and H4 (Figure 1). Each of these histone octamers is referred to as a nucleosome. The nucleosomes are packaged tightly into even more compact fibers known as chromatin. Through this complex structure, epigenetic regulation occurs primarily through four mechanisms. First, DNA can undergo direct chemical modification by cytosine methylation, which is a general marker of gene silencing. Second, posttranslational modifications of the core histones can occur, primarily through methylation, acetylation, ubiquitylation, and phosphorylation, making up the primary chromatin structure (Figure 1). Acting in concert with these two aspects of the epigenetic machinery, noncoding RNAs contribute to the regulation of these processes (Greer and Shi, 2012). Finally, the chromatin is then packaged, via long-range interactions, into a higher-order structure within the cell nucleus. All of these organizational steps serve to modulate DNA accessibility and thus control gene expression. More open regions of chromatin, or euchromatin, are poised for activation by the transcriptional machinery, whereas more ADVANTAGES OF CHIP-SEQ