Genome architecture mapping (GAM) enables understanding of 3D genome structure in the nucleus. We directly compared multiplex-GAM and Hi-C data and found that local chromatin interactions were generally detected by both methods, but active genomic regions rich in enhancers that established higher-order contacts were preferentially detected by GAM.
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References
Kempfer, R. & Pombo, A. Methods for mapping 3D chromosome architecture. Nat. Rev. Genet. 21, 207–226 (2020). Overview of recent genome-wide approaches for assessing 3D genome organization.
O’Sullivan, J. M. et al. The statistical-mechanics of chromosome conformation capture. Nucleus 4, 390–398 (2013). Theoretical limitations resulting from pairwise ligation.
Beagrie, R. A. et al. Complex multi-enhancer contacts captured by genome architecture mapping. Nature 543, 519–524 (2017). First application of the GAM procedure, finding long-range interactions in mouse embryonic stem cells.
Tan, L. et al. Three-dimensional genome structures of single diploid human cells. Science 361, 924–928 (2018). Chromatin 3D models derived from single-cell Hi-C data enable extraction of multiway contacts.
Chiariello, A. M. et al. A dynamic folded hairpin conformation is associated with α-globin activation in erythroid cells. Cell Rep. 30, 2125–2135 (2020). Multiway contacts established at the α-globin locus were successfully predicted from chromatin 3D models.
Winick-Ng, W. et al. Cell-type specialization is encoded by specific chromatin topologies. Nature 599, 684–691 (2021). Advancements combining GAM with immunolabeling to study rare brain cell types.
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This is a summary of: Beagrie, R. A. et al. Multiplex-GAM: genome-wide identification of chromatin contacts yields insights overlooked by Hi-C. Nat. Methods https://doi.org/10.1038/s41592-023-01903-1 (2023).
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Genome architecture mapping detects transcriptionally active, multiway chromatin contacts. Nat Methods 20, 993–994 (2023). https://doi.org/10.1038/s41592-023-01905-z
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DOI: https://doi.org/10.1038/s41592-023-01905-z
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