Multiplex-GAM: genome-wide identification of chromatin contacts yields insights not captured by Hi-C

Abstract

Summary (Abstract)Technologies for measuring 3D genome topology are increasingly important for studying mechanisms of gene regulation, for genome assembly and for mapping of genome rearrangements. Hi-C and other ligation-based methods have become routine but have specific biases. Here, we develop multiplex-GAM, a faster and more affordable version of Genome Architecture Mapping (GAM), a ligation-free technique to map chromatin contacts genomewide. We perform a detailed comparison of contacts obtained by multiplex-GAM and Hi-C using mouse embryonic stem (mES) cells. We find that both methods detect similar topologically associating domains (TADs). However, when examining the strongest contacts detected by either method, we find that only one third of these are shared. The strongest contacts specifically found in GAM often involve “active” regions, including many transcribed genes and super-enhancers, whereas in Hi-C they more often contain “inactive” regions. Our work shows that active genomic regions are involved in extensive complex contacts that currently go under-estimated in genome-wide ligation-based approaches, and highlights the need for orthogonal advances in genome-wide contact mapping technologies.

Cell-type specialization in the brain is encoded by specific long-range chromatin topologies

“…GAM was previously applied to mouse embryonic stem cells (mESCs) and shown to capture TADs, A/B compartments and pair-wise contacts across long genomic distances 3 . Recently, we developed a streamlined version of GAM, multiplexGAM, which combines three nuclear slices in each GAM sample 9 . With immunoGAM, we now considerably extend the scope of GAM to directly work in intact tissue without prior dissociation, and with small cell numbers (∼1000 cells) 3, 10 .…”

“…We also selected dopaminergic neurons (DNs) from the ventral tegmental area of the midbrain (VTA), which are normally quiescent but are activated during cue-guided reward-based learning 14 . Finally, we compared GAM data from the selected brain cell types to publicly available multiplexGAM data from mESCs 9 (see Methods, Supplemental Table 1 ).…”

“…Upon transcardial perfusion with fixative, brain tissues are dissected, cryoprotected, and ultrathin cryosectioned (1). After immunodetection using cell-type specific markers (2), single nuclear profiles are laser microdissected (3), each from a single cell, and collected in groups of three, as described for multiplex-GAM 9 . After extraction of genomic DNA and sequencing (4), the frequency of co-segregation of pairs of genomic loci is used to calculate matrices of pairwise contacts, and to compare the organization of topological domains, chromatin compaction, differential contacts, and compartments (5).…”

GAMIBHEAR: whole-genome haplotype reconstruction from Genome Architecture Mapping data

“…Chromatin contacts between DNA loci can be inferred by analysing the frequency at which the loci are captured in the same NuP. In contrast to ligation-based chromatin conformation capture (3C) type approaches, such as Hi-C (Lieberman-Aiden et al 2009), GAM is able to resolve complex contacts with three or more loci with high resolution, does not suffer from nonuniformity biases (Chandradoss et al 2020) and only requires several hundreds of cells to obtain high-resolution contact maps (Kempfer and Pombo 2019;Beagrie et al 2020;Fiorillo et al 2020). This makes GAM particularly useful for the study of chromatin contacts in rare biological materials, such as human biopsies.…”

“…Chromatin contacts between DNA loci can be inferred from the frequency at which loci are captured in the same NuP. One advantage of GAM over competing methods, such as Hi-C (Lieberman-Aiden et al , 2009), is that GAM only requires several hundreds of cells to obtain high-resolution contact maps (Kempfer and Pombo, 2019; Beagrie et al , 2020; Fiorillo et al , 2020). This makes GAM particularly useful for the study of chromatin contacts in rare biological materials, such as human biopsies.…”