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染色质可及性:方法、机制与生物学见解。

Chromatin accessibility: methods, mechanisms, and biological insights.

机构信息

Laboratory of Genome Architecture and Dynamics, The Rockefeller University, New York, NY.

出版信息

Nucleus. 2022 Dec;13(1):236-276. doi: 10.1080/19491034.2022.2143106.


DOI:10.1080/19491034.2022.2143106
PMID:36404679
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC9683059/
Abstract

Access to DNA is a prerequisite to the execution of essential cellular processes that include transcription, replication, chromosomal segregation, and DNA repair. How the proteins that regulate these processes function in the context of chromatin and its dynamic architectures is an intensive field of study. Over the past decade, genome-wide assays and new imaging approaches have enabled a greater understanding of how access to the genome is regulated by nucleosomes and associated proteins. Additional mechanisms that may control DNA accessibility include chromatin compaction and phase separation - processes that are beginning to be understood. Here, we review the ongoing development of accessibility measurements, we summarize the different molecular and structural mechanisms that shape the accessibility landscape, and we detail the many important biological functions that are linked to chromatin accessibility.

摘要

DNA 的可及性是执行包括转录、复制、染色体分离和 DNA 修复在内的基本细胞过程的前提。调节这些过程的蛋白质如何在染色质及其动态结构的背景下发挥作用,是一个深入的研究领域。在过去的十年中,全基因组分析和新的成像方法使人们对核小体和相关蛋白如何调节基因组的可及性有了更深入的了解。可能控制 DNA 可及性的其他机制包括染色质紧缩和相分离——这些过程开始被理解。在这里,我们回顾了可及性测量的不断发展,总结了形成可及性景观的不同分子和结构机制,并详细介绍了与染色质可及性相关的许多重要生物学功能。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9163/9683059/8ead6ea2d3f3/KNCL_A_2143106_F0002_OC.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9163/9683059/b127b3c9787d/KNCL_A_2143106_F0001_OC.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9163/9683059/8ead6ea2d3f3/KNCL_A_2143106_F0002_OC.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9163/9683059/b127b3c9787d/KNCL_A_2143106_F0001_OC.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/9163/9683059/8ead6ea2d3f3/KNCL_A_2143106_F0002_OC.jpg

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Chromatin accessibility: methods, mechanisms, and biological insights.

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[3]
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本文引用的文献

[1]
RNA polymerase II depletion from the inactive X chromosome territory is not mediated by physical compartmentalization.

Nat Struct Mol Biol. 2023-8

[2]
In diverse conditions, intrinsic chromatin condensates have liquid-like material properties.

Proc Natl Acad Sci U S A. 2023-5-2

[3]
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Nat Struct Mol Biol. 2023-1

[4]
Oncogene expression from extrachromosomal DNA is driven by copy number amplification and does not require spatial clustering in glioblastoma stem cells.

Elife. 2022-12-7

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Changes in chromatin accessibility are not concordant with transcriptional changes for single-factor perturbations.

Mol Syst Biol. 2022-9

[6]
Nucleosome-directed replication origin licensing independent of a consensus DNA sequence.

Nat Commun. 2022-8-23

[7]
A mitotic chromatin phase transition prevents perforation by microtubules.

Nature. 2022-9

[8]
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Mol Cell. 2022-8-18

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Generating specificity in genome regulation through transcription factor sensitivity to chromatin.

Nat Rev Genet. 2022-12

[10]
Loop-extrusion and polymer phase-separation can co-exist at the single-molecule level to shape chromatin folding.

Nat Commun. 2022-7-13

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