Are major decisions in the cell made through pairs of interacting loci (enhancers and promoters) or larger teams of cooperating regulatory elements? A new genome-wide assay and algorithm answers this question and provides a scalable technology to link new dimensions of genome structure with cellular function.
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References
Beagrie, R. A. et al. Complex multi-enhancer contacts captured by genome architecture mapping. Nature 543, 519–524 (2017). Describes GAM, an assay to derive long-range high-order spatial proximity from fixed and barcoded thin nuclear slices.
Quinodoz, S. A. et al. Higher-order inter-chromosomal hubs shape 3D genome organization in the nucleus. Cell 174, 744–757.e24 (2018). Describes SPRITE, an assay to derive high-order spatial proximity from fixed and barcoded sonicated nuclear fragments.
Nollmann, M., Bennabi, I., Götz, M. & Gregor, T. The impact of space and time on the functional output of the genome. Cold Spring Harb. Perspect. Biol. 14, a040378 (2021). Discusses open questions about the role of cooperativity in the kinetics and spatial organization of mammalian gene regulation.
Mirny, L. & Dekker, J. Mechanisms of chromosome folding and nuclear organization: their interplay and open questions. Cold Spring Harb. Perspect. Biol. https://doi.org/10.1101/cshperspect.a040147 (2021). Discusses the opposing forces of compartmentalization and loop extrusion in driving gene expression and cell identity.
Hnisz, D., Shrinivas, K., Young, R. A., Chakraborty, A. K. & Sharp, P. A. A phase separation model for transcriptional control. Cell 169, 13–23 (2017). Proposes model in which cell identity-specific gene expression proceeds through high-order interactions in phase-separated nuclear compartments, which has since been validated at select loci.
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This is a summary of: Deshpande, A. et al. Identifying synergistic high-order 3D chromatin conformations from genome-scale nanopore concatemer sequencing. Nat. Biotechnol. https://doi.org/10.1038/s41587-022-01289-z (2022).
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Team architecture in 3D genomic interactions revealed through nanopore sequencing. Nat Biotechnol 40, 1437–1438 (2022). https://doi.org/10.1038/s41587-022-01290-6
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DOI: https://doi.org/10.1038/s41587-022-01290-6
