The macro and micro of chromosome conformation capture

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.

Understanding 3D genome organization by multidisciplinary methods

“…This issue was first addressed concomitantly in two techniques, DNase Hi-C and Micro-C, both based on chromatin fragmentation without using restriction enzymes [88][89][90][91] . Micro-C introduced double cross-linking and replaced the restriction enzymes used in Hi-C with micrococcal nuclease digestion [91][92][93][94] (Figure 2). This produces a fairly uniform fragmentation down to the nucleosome level, which increases local resolution.…”

Single-cell Hi-C data analysis: safety in numbers

“…It was originally designed for inputs of millions of cells and had higher statistical power than microscopy [ 23 ]. An explosion of conformation-based techniques, including the high-throughput sequencing-based Hi-C [ 64 ], has paved the way for new discoveries expanding our general understanding of DNA folding in eukaryotic cells [ 34 ], bacterial cells [ 19 ] and even viruses [ 9 ]. For eukaryotes, these patterns include topologically associating domains (TADs) , promoter-enhancer and architectural loops and compartments (reviewed in-depth by [ 6 , 21 , 22 , 84 ]).…”

FISH Going Meso-Scale: A Microscopic Search for Chromatin Domains

“…3C-derivate methods (Hi-C, 5C, ChIA-PET, Micro-C, etc.) allowed to dissect three-dimensional genome organization with resolution and throughput, unattainable by other approaches based on imaging ( Fraser et al, 2015b ; Goel and Hansen, 2020 ). Moreover, they facilitated the understanding of the functional significance of identified spatial genome folding due to the alignment of Hi-C data with other genome-wide landscapes ( Sati and Cavalli, 2017 ).…”