Abstract
The 3D organization of the genome facilitates gene regulation, replication, and repair, making it a key feature of genomic function and one that remains to be properly understood. Over the past two decades, a variety of chromosome conformation capture (3C) methods have delineated genome folding from megabase‐scale compartments and topologically associating domains (TADs) down to kilobase‐scale enhancer‐promoter interactions. Understanding the functional role of each layer of genome organization is a gateway to understanding cell state, development, and disease. Here, we discuss the evolution of 3C‐based technologies for mapping 3D genome organization. We focus on genomics methods and provide a historical account of the development from 3C to Hi‐C. We also discuss ChIP‐based techniques that focus on 3D genome organization mediated by specific proteins, capture‐based methods that focus on particular regions or regulatory elements, 3C‐orthogonal methods that do not rely on restriction digestion and proximity ligation, and methods for mapping the DNA–RNA and RNA–RNA interactomes. We consider the biological discoveries that have come from these methods, examine the mechanistic contributions of CTCF, cohesin, and loop extrusion to genomic folding, and detail the 3D genome field's current understanding of nuclear architecture. Finally, we give special consideration to Micro‐C as an emerging frontier in chromosome conformation capture and discuss recent Micro‐C findings uncovering fine‐scale chromatin organization in unprecedented detail.This article is categorized under:Gene Expression and Transcriptional Hierarchies > Regulatory MechanismsGene Expression and Transcriptional Hierarchies > Gene Networks and Genomics
Highlights
For all of their complexity and rich diversity of constituent cellular phenotypes, multicellular organisms can be characterized by a common foundation—their genome
Examples of early applications of ChIA-PET include investigations of the chromatin interactomes of ERα (Fullwood et al, 2009) and CCCTC-binding factor (CTCF) (Handoko et al, 2011). By virtue of their enrichment of protein-centered chromatin interactions, genome-wide chromatin immunoprecipitation (ChIP)-based conformation capture methods are capable of recapitulating key features of the 3D genome (e.g., topologically associating domains (TADs) and loops) and achieving finer resolution than high-throughput chromosome conformation capture (Hi-C)
We review the development of chromosome conformation capture technologies, the biological mechanisms underpinning observed organizational features, and Micro-C's contributions at the frontier of our understanding of nuclear architecture
Summary
For all of their complexity and rich diversity of constituent cellular phenotypes, multicellular organisms can be characterized by a common foundation—their genome. The first high-resolution contact maps generated by the application of in situ Hi-C in human and mouse cell lines revealed levels of genome organization as fine as the 1-kb scale from ~5 billion sequencing reads (Rao et al, 2014).
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