The second decade of 3C technologies: detailed insights into nuclear organization

Abstract

The relevance of three-dimensional (3D) genome organization for transcriptional regulation and thereby for cellular fate at large is now widely accepted. Our understanding of the fascinating architecture underlying this function is based on microscopy studies as well as the chromosome conformation capture (3C) methods, which entered the stage at the beginning of the millennium. The first decade of 3C methods rendered unprecedented insights into genome topology. Here, we provide an update of developments and discoveries made over the more recent years. As we discuss, established and newly developed experimental and computational methods enabled identification of novel, functionally important chromosome structures. Regulatory and architectural chromatin loops throughout the genome are being cataloged and compared between cell types, revealing tissue invariant and developmentally dynamic loops. Architectural proteins shaping the genome were disclosed, and their mode of action is being uncovered. We explain how more detailed insights into the 3D genome increase our understanding of transcriptional regulation in development and misregulation in disease. Finally, to help researchers in choosing the approach best tailored for their specific research question, we explain the differences and commonalities between the various 3C-derived methods.

Thrombopoietin signaling to chromatin elicits rapid and pervasive epigenome remodeling within poised chromatin architectures

“…Chromosome conformation capture (3C) based methods, particularly high-throughput 3C (Hi-C), have enabled targeted or genome-wide mapping of chromatin architectures (Denker and De Laat 2016). These technologies provided critical insights into key structural and functional components of three-dimensional chromatin organization such as i) A/B compartments (Lieberman-aiden et al 2009), also referred to as compartment domains (Rao et al 2017), which are closely associated with open and closed chromatin domains, respectively; ii) topologically associating domains (TADs) (Dixon et al 2012;Nora et al 2012;Sexton et al 2012), also referred to as contact domains (Rao et al 2017), chromosomal units that spatially constrain cis-regulatory interactions; iii) CTCF loops, also referred to as insulated neighborhoods (Hnisz et al 2016) or loop domains (Rao et al 2017).…”

Cis-regulatory landscapes in development and evolution

“…Furthermore, these enhancer-promoter physical interactions occur in a highly regulated manner that precludes spurious activation of non-target neighboring genes. We have now a first glimpse of how animal genomes are folded thanks to the use of several chromosome conformation capture techniques that identify DNA-DNA contacts throughout the genome (reviewed in [2]). Over the last years, the analyses of all possible contacts between a single genomic region and the rest of the genome at high resolution (4C-seq), or between all chromatin regions at low resolution (Hi-C), have shown that chromatin is compartmentalized into structures known as topologically associating domains (TADs): megabase-scale genomic regions in which sequences preferentially contact one another [3][4][5][6].…”

YY1 and CTCF orchestrate a 3D chromatin looping switch during early neural lineage commitment

“…Recent advances in proximity-ligation and deep-sequencing technologies have enabled the interrogation of genome organization at a genomewide scale and nucleosome resolution (de Laat and Dekker 2012;Denker and de Laat 2016). Within individual chromosomes, open chromatin and active genes tend to spatially cluster into "A" compartments, whereas closed, inactive chromatin spatially segregates into "B" compartments (Lieberman-Aiden et al 2009;Rao et al 2014).…”