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