Multiplex-GAM: genome-wide identification of chromatin contacts yields insights overlooked by Hi-C

Beagrie, R.A.; Thieme, C.J.; Annunziatella, C.; Baugher, C.; Zhang, Y.; Schueler, M.; Kukalev, A.; Kempfer, R.; Chiariello, A.M.; Bianco, S.; Li, Y.; Davis, T.; Scialdone, A.; Welch, L.R.; Nicodemi, M.; Pombo, A.

Multiplex-GAM: genome-wide identification of chromatin contacts yields insights overlooked by Hi-C

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Item Type:	Article
Title:	Multiplex-GAM: genome-wide identification of chromatin contacts yields insights overlooked by Hi-C
Creators Name:	Beagrie, R.A., Thieme, C.J., Annunziatella, C., Baugher, C., Zhang, Y., Schueler, M., Kukalev, A., Kempfer, R., Chiariello, A.M., Bianco, S., Li, Y., Davis, T., Scialdone, A., Welch, L.R., Nicodemi, M. and Pombo, A.
Abstract:	Technology for measuring 3D genome topology is increasingly important for studying 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 that maps chromatin contacts genome-wide. We perform a detailed comparison of multiplex-GAM and Hi-C using mouse embryonic stem cells. 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 are currently underestimated in ligation-based approaches, and highlights the need for orthogonal advances in genome-wide contact mapping technologies.
Keywords:	Chromatin Analysis, Chromatin Structure, DNA Sequencing, Epigenomics, Genome Informatics, Animals, Mice
Source:	Nature Methods
ISSN:	1548-7091
Publisher:	Nature Publishing Group
Volume:	20
Number:	7
Page Range:	1037-1047
Date:	July 2023
Official Publication:	https://doi.org/10.1038/s41592-023-01903-1
PubMed:	View item in PubMed

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