Epigenomics and the structure of the living genome

Abstract

Eukaryotic genomes are packaged into an extensively folded state known as chromatin. Analysis of the structure of eukaryotic chromosomes has been revolutionized by development of a suite of genome-wide measurement technologies, collectively termed "epigenomics." We review major advances in epigenomic analysis of eukaryotic genomes, covering aspects of genome folding at scales ranging from whole chromosome folding down to nucleotide-resolution assays that provide structural insights into protein-DNA interactions. We then briefly outline several challenges remaining and highlight new developments such as single-cell epigenomic assays that will help provide us with a high-resolution structural understanding of eukaryotic genomes.The past two decades have seen dramatic advances in our ability to carry out genome-wide analysis of DNA and RNA populations, first spurred by microarray technology and continuing today with deep sequencing. These technical advances have revolutionized molecular biology, with early genomic studies focused on mRNA abundance, and later studies expanding genome-wide analyses into fields ranging from cancer genome sequencing to systematic dissection of protein structure and function using massively parallel mutagenesis, selection, and sequencing. One of the most productive of these areas has been the broad area of "epigenomics," which is the use of genome-wide assays to interrogate global patterns of cytosine methylation, chromatin state, and RNA abundance. Although small RNAs (such as siRNAs and piRNAs) and DNA modifications (such as cytosine and adenine methylation) are central to many well-characterized epigenetic inheritance paradigms, this review will focus on epigenomic insights into the folding of the genome and thus will not cover DNA modifications or RNAs.Below, we introduce the general methodologies for epigenomic analysis. Then, we discuss the structural organization of the eukaryotic genome, starting with 3C-based analyses of higher-order chromosome folding and domain organization, followed by nucleosome resolution chromosome organization (∼100-to 500-bp scale), and finally ending with insights afforded by nucleotide-resolution techniques.

Micro-C XL: assaying chromosome conformation at length scales from the nucleosome to the entire genome

“…The compaction and organization of the physical genome has wide-ranging consequences for genomic function [1][2][3][4] . In eukaryotes, the first level of genome compaction is organization into the characteristic "beads on a string" structure, with nucleosomes separated by relatively accessible linker DNA.…”

Inferring gene regulatory networks from single-cell data: a mechanistic approach

“…[41]. Such aspects are still far from being completely understood [42][43][44][45] and this simple network model can hopefully be used to assess biological hypotheses. In the next part, we will introduce a more sophisticated interaction form based on an underlying probabilistic model, which is both "statistics-friendly" and interpretable as a non-equilibrium steady state of chromatin environment [43].…”

Genome-wide off-rates reveal how DNA binding dynamics shape transcription factor function

“…During transcription for example, different types of transcription factors (TFs) are continuously interacting with chromatin in a variety of ways. Each brings different functions into play: opening or closing chromatin, creating loops, modifying or evicting nucleosomes, recruiting cofactors and, in the case of activation, ultimately causing formation of a pre-initiation complex that includes RNA polymerase (Hahn & Young, 2011;de Laat & Dekker, 2012;Spitz & Furlong, 2012;Struhl & Segal, 2013;Friedman & Rando, 2015;Kubik et al, 2017;Lai & Pugh, 2017;Woo et al, 2017;Cramer, 2019;Brahma & Henikoff, 2020). TFs are therefore constantly moving off and onto different loci, probing for appropriate interactions, also under conditions of steady-state transcriptional output (Hammar et al, 2014).…”