远程染色质相互作用
Long-Range Chromatin Interactions.
作者信息
Dekker Job, Misteli Tom
机构信息
University of Massachusetts Medical School, Worcester, Massachusetts 01605.
National Cancer Institute, National Institutes of Health, Bethesda, Maryland 20892.
出版信息
Cold Spring Harb Perspect Biol. 2015 Oct 1;7(10):a019356. doi: 10.1101/cshperspect.a019356.
Abstract
To accommodate genomes in the limited space of the cell nucleus and ensure the correct execution of gene expression programs, genomes are packaged in complex fashion in the three-dimensional cell nucleus. As a consequence of the extensive higher-order organization of chromosomes, distantly located genomic regions on the same or distinct chromosomes undergo long-range interactions. This article discusses the nature of long interactions, mechanisms of their formation, and their emerging functional roles in gene regulation and genome maintenance.
摘要
为了在细胞核的有限空间内容纳基因组并确保基因表达程序的正确执行，基因组以复杂的方式包装在三维细胞核中。由于染色体广泛的高阶组织，同一或不同染色体上远距离的基因组区域会发生长程相互作用。本文讨论了长程相互作用的性质、其形成机制以及它们在基因调控和基因组维持中新兴的功能作用。
相似文献
1
Long-Range Chromatin Interactions.远程染色质相互作用
Cold Spring Harb Perspect Biol. 2015 Oct 1;7(10):a019356. doi: 10.1101/cshperspect.a019356.
2
The contribution of nuclear compartmentalization to gene regulation.核区室化对基因调控的作用。
Cell. 2002 Feb 22;108(4):513-21. doi: 10.1016/s0092-8674(02)00650-5.
3
Genomics tools for unraveling chromosome architecture.用于解析染色体结构的基因组学工具。
Nat Biotechnol. 2010 Oct;28(10):1089-95. doi: 10.1038/nbt.1680.
4
The cell nucleus taking centre stage. Workshop on the functional organization of the cell nucleus.细胞核成为焦点。细胞核功能组织研讨会。
EMBO Rep. 2006 Dec;7(12):1211-5. doi: 10.1038/sj.embor.7400840. Epub 2006 Oct 27.
5
Chromatin organization in the mammalian nucleus.哺乳动物细胞核中的染色质组织。
Int Rev Cytol. 2005;242:283-336. doi: 10.1016/S0074-7696(04)42007-5.
6
The budding yeast nucleus.芽殖酵母核。
Cold Spring Harb Perspect Biol. 2010 Aug;2(8):a000612. doi: 10.1101/cshperspect.a000612. Epub 2010 Jun 16.
7
Functional architecture in the cell nucleus.细胞核中的功能结构
Biochem J. 2001 Jun 1;356(Pt 2):297-310. doi: 10.1042/0264-6021:3560297.
8
[Nuclear and chromatin dynamics].[核与染色质动力学]
Tanpakushitsu Kakusan Koso. 2006 Apr;51(4):302-9.
9
Liquid-Liquid Phase Separation in Chromatin.染色质中的液-液相分离。
Cold Spring Harb Perspect Biol. 2022 Feb 1;14(2):a040683. doi: 10.1101/cshperspect.a040683.
10
Chromatin position in human HepG2 cells: although being non-random, significantly changed in daughter cells.人类肝癌细胞系HepG2中的染色质位置：尽管是非随机的，但在子细胞中发生了显著变化。
J Struct Biol. 2009 Feb;165(2):107-17. doi: 10.1016/j.jsb.2008.10.007. Epub 2008 Nov 12.
引用本文的文献
1
Single-cell DNA methylome and 3D genome atlas of human subcutaneous adipose tissue.人类皮下脂肪组织的单细胞DNA甲基化组和三维基因组图谱
Nat Genet. 2025 Aug 20. doi: 10.1038/s41588-025-02300-4.
2
Establishment of chromatin architecture interplays with embryo hypertranscription.染色质结构的建立与胚胎超转录相互作用。
Nature. 2025 Aug 13. doi: 10.1038/s41586-025-09400-5.
3
Single-stranded DNA-binding proteins are essential components of the architectural LDB1 protein complex.单链DNA结合蛋白是结构LDB1蛋白复合体的重要组成部分。
Mol Cell. 2025 Aug 21;85(16):3074-3089.e8. doi: 10.1016/j.molcel.2025.07.012. Epub 2025 Aug 12.
4
StripePy: fast and robust characterization of architectural stripes.StripePy：对结构条纹进行快速且稳健的特征描述。
Bioinformatics. 2025 Jun 2;41(6). doi: 10.1093/bioinformatics/btaf351.
5
Interplay and Dynamics of Chromatin Architecture and DNA Damage Response: An Overview.染色质结构与DNA损伤反应的相互作用及动力学：概述
Cancers (Basel). 2025 Mar 11;17(6):949. doi: 10.3390/cancers17060949.
6
Multi-level genomic convergence of secondary aquatic adaptation in marine mammals.海洋哺乳动物次生水生适应的多层次基因组趋同
Innovation (Camb). 2025 Jan 3;6(3):100798. doi: 10.1016/j.xinn.2025.100798. eCollection 2025 Mar 3.
7
DNALongBench: A Benchmark Suite for Long-Range DNA Prediction Tasks.DNA长序列基准测试集：用于长程DNA预测任务的基准测试套件。
bioRxiv. 2025 Jan 8:2025.01.06.631595. doi: 10.1101/2025.01.06.631595.
8
DNA damage and its links to neuronal aging and degeneration.DNA损伤及其与神经元衰老和退化的联系。
Neuron. 2025 Jan 8;113(1):7-28. doi: 10.1016/j.neuron.2024.12.001.
9
LDB1 establishes multi-enhancer networks to regulate gene expression.LDB1建立多增强子网络以调控基因表达。
Mol Cell. 2025 Jan 16;85(2):376-393.e9. doi: 10.1016/j.molcel.2024.11.037. Epub 2024 Dec 24.
10
Inter-chromosomal transcription hubs shape the 3D genome architecture of African trypanosomes.染色体间转录中心塑造了非洲锥虫的三维基因组结构。
Nat Commun. 2024 Dec 23;15(1):10716. doi: 10.1038/s41467-024-55285-9.
本文引用的文献
1
Histone and DNA Modifications as Regulators of Neuronal Development and Function.组蛋白和DNA修饰作为神经元发育和功能的调节因子
Cold Spring Harb Perspect Biol. 2016 Jul 1;8(7):a024208. doi: 10.1101/cshperspect.a024208.
2
Dosage compensation in mammals.哺乳动物中的剂量补偿。
Cold Spring Harb Perspect Biol. 2015 Mar 2;7(3):a019406. doi: 10.1101/cshperspect.a019406.
3
Transcriptional silencing by polycomb-group proteins.多梳蛋白家族介导的转录沉默
Cold Spring Harb Perspect Biol. 2014 Nov 3;6(11):a019331. doi: 10.1101/cshperspect.a019331.
4
Epigenetic control of immunity.免疫的表观遗传控制。
Cold Spring Harb Perspect Biol. 2014 Jun 2;6(6):a019307. doi: 10.1101/cshperspect.a019307.
5
Genomic imprinting in mammals.哺乳动物中的基因组印记
Cold Spring Harb Perspect Biol. 2014 Feb 1;6(2):a018382. doi: 10.1101/cshperspect.a018382.
6
The hierarchy of the 3D genome.三维基因组的层次结构。
Mol Cell. 2013 Mar 7;49(5):773-82. doi: 10.1016/j.molcel.2013.02.011.
7
Functional implications of genome topology.基因组拓扑结构的功能意义。
Nat Struct Mol Biol. 2013 Mar;20(3):290-9. doi: 10.1038/nsmb.2474.
8
Correlated alterations in genome organization, histone methylation, and DNA-lamin A/C interactions in Hutchinson-Gilford progeria syndrome.亨廷顿病样 2 型综合征中基因组组织、组蛋白甲基化和 DNA-核纤层 A/C 相互作用的关联改变。
Genome Res. 2013 Feb;23(2):260-9. doi: 10.1101/gr.138032.112. Epub 2012 Nov 14.
9
The long-range interaction landscape of gene promoters.基因启动子的远程相互作用景观。
Nature. 2012 Sep 6;489(7414):109-13. doi: 10.1038/nature11279.
10
An integrated encyclopedia of DNA elements in the human genome.人类基因组中 DNA 元件的综合百科全书。
Nature. 2012 Sep 6;489(7414):57-74. doi: 10.1038/nature11247.
Zotero 插件