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Decoupling chromatin hubs from gene control.

作者信息

Lupiáñez Darío G

机构信息

Centro Andaluz de Biología del Desarrollo (CABD), CSIC/UPO/JA, Seville, Spain.

出版信息

Nat Struct Mol Biol. 2025 May 13. doi: 10.1038/s41594-025-01544-2.

DOI:10.1038/s41594-025-01544-2

PMID:40360813

Abstract

摘要

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本文引用的文献

CTCF mediates dosage- and sequence-context-dependent transcriptional insulation by forming local chromatin domains.

Nat Genet. 2021 Jul;53(7):1064-1074. doi: 10.1038/s41588-021-00863-6. Epub 2021 May 17.

Transcriptional Regulation by (Super)Enhancers: From Discovery to Mechanisms.

Annu Rev Genomics Hum Genet. 2021 Aug 31;22:127-146. doi: 10.1146/annurev-genom-122220-093818. Epub 2021 May 5.

Promoter-proximal CTCF binding promotes distal enhancer-dependent gene activation.

Nat Struct Mol Biol. 2021 Feb;28(2):152-161. doi: 10.1038/s41594-020-00539-5. Epub 2021 Jan 4.

Decreased Enhancer-Promoter Proximity Accompanying Enhancer Activation.

Mol Cell. 2019 Nov 7;76(3):473-484.e7. doi: 10.1016/j.molcel.2019.07.038. Epub 2019 Sep 4.

Live-cell imaging reveals enhancer-dependent transcription in the absence of enhancer proximity.

Elife. 2019 May 24;8:e41769. doi: 10.7554/eLife.41769.

CTCF: a Swiss-army knife for genome organization and transcription regulation.

Essays Biochem. 2019 Apr 23;63(1):157-165. doi: 10.1042/EBC20180069.

Single-allele chromatin interactions identify regulatory hubs in dynamic compartmentalized domains.

Nat Genet. 2018 Dec;50(12):1744-1751. doi: 10.1038/s41588-018-0253-2. Epub 2018 Oct 29.

Targeted Degradation of CTCF Decouples Local Insulation of Chromosome Domains from Genomic Compartmentalization.

Cell. 2017 May 18;169(5):930-944.e22. doi: 10.1016/j.cell.2017.05.004.

A Phase Separation Model for Transcriptional Control.

Cell. 2017 Mar 23;169(1):13-23. doi: 10.1016/j.cell.2017.02.007.

Comprehensive mapping of long-range interactions reveals folding principles of the human genome.

Science. 2009 Oct 9;326(5950):289-93. doi: 10.1126/science.1181369.

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Chromatin Hubs: A biological and computational outlook.

Comput Struct Biotechnol J. 2022 Jul 5;20:3796-3813. doi: 10.1016/j.csbj.2022.07.002. eCollection 2022.

CTCF depletion decouples enhancer-mediated gene activation from chromatin hub formation.

Nat Struct Mol Biol. 2025 May 13. doi: 10.1038/s41594-025-01555-z.

Bromodomains regulate dynamic targeting of the PBAF chromatin-remodeling complex to chromatin hubs.

Biophys J. 2022 May 3;121(9):1738-1752. doi: 10.1016/j.bpj.2022.03.027. Epub 2022 Mar 30.

CEBPA phase separation links transcriptional activity and 3D chromatin hubs.

Cell Rep. 2023 Aug 29;42(8):112897. doi: 10.1016/j.celrep.2023.112897. Epub 2023 Jul 29.

Decoupling of Structural and Functional Connectivity in Hubs and Cognitive Impairment After Mild Traumatic Brain Injury.

Brain Connect. 2021 Nov;11(9):745-758. doi: 10.1089/brain.2020.0852. Epub 2021 Sep 23.

Spatial configuration of the chicken alpha-globin gene domain: immature and active chromatin hubs.

Nucleic Acids Res. 2008 Aug;36(14):4629-40. doi: 10.1093/nar/gkn429. Epub 2008 Jul 11.

3D chromatin hubs as regulatory units of identity and survival in human acute leukemia.

Mol Cell. 2025 Jan 2;85(1):42-60.e7. doi: 10.1016/j.molcel.2024.11.040. Epub 2024 Dec 23.

Differential impact of quiescent non-coding loci on chromatin entropy.

Nucleic Acids Res. 2024 Aug 27;52(15):8778-8799. doi: 10.1093/nar/gkae535.

Static and Dynamic DNA Loops form AP-1-Bound Activation Hubs during Macrophage Development.

Mol Cell. 2017 Sep 21;67(6):1037-1048.e6. doi: 10.1016/j.molcel.2017.08.006. Epub 2017 Sep 7.

本文引用的文献

CTCF mediates dosage- and sequence-context-dependent transcriptional insulation by forming local chromatin domains.

Nat Genet. 2021 Jul;53(7):1064-1074. doi: 10.1038/s41588-021-00863-6. Epub 2021 May 17.

Transcriptional Regulation by (Super)Enhancers: From Discovery to Mechanisms.

Annu Rev Genomics Hum Genet. 2021 Aug 31;22:127-146. doi: 10.1146/annurev-genom-122220-093818. Epub 2021 May 5.

Promoter-proximal CTCF binding promotes distal enhancer-dependent gene activation.

Nat Struct Mol Biol. 2021 Feb;28(2):152-161. doi: 10.1038/s41594-020-00539-5. Epub 2021 Jan 4.

Decreased Enhancer-Promoter Proximity Accompanying Enhancer Activation.

Mol Cell. 2019 Nov 7;76(3):473-484.e7. doi: 10.1016/j.molcel.2019.07.038. Epub 2019 Sep 4.

Live-cell imaging reveals enhancer-dependent transcription in the absence of enhancer proximity.

Elife. 2019 May 24;8:e41769. doi: 10.7554/eLife.41769.

CTCF: a Swiss-army knife for genome organization and transcription regulation.

Essays Biochem. 2019 Apr 23;63(1):157-165. doi: 10.1042/EBC20180069.

Single-allele chromatin interactions identify regulatory hubs in dynamic compartmentalized domains.

Nat Genet. 2018 Dec;50(12):1744-1751. doi: 10.1038/s41588-018-0253-2. Epub 2018 Oct 29.

Targeted Degradation of CTCF Decouples Local Insulation of Chromosome Domains from Genomic Compartmentalization.

Cell. 2017 May 18;169(5):930-944.e22. doi: 10.1016/j.cell.2017.05.004.

A Phase Separation Model for Transcriptional Control.

Cell. 2017 Mar 23;169(1):13-23. doi: 10.1016/j.cell.2017.02.007.

Comprehensive mapping of long-range interactions reveals folding principles of the human genome.

Science. 2009 Oct 9;326(5950):289-93. doi: 10.1126/science.1181369.