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基因组结构分析的综合方法。

Integrative approaches in genome structure analysis.

机构信息

Institute for Quantitative and Computational Biosciences, University of California Los Angeles, Los Angeles, CA 90095, USA; Department of Microbiology, Immunology and Molecular Genetics, University of California Los Angeles, Los Angeles, CA 90095, USA.

Institute for Quantitative and Computational Biosciences, University of California Los Angeles, Los Angeles, CA 90095, USA; Department of Microbiology, Immunology and Molecular Genetics, University of California Los Angeles, Los Angeles, CA 90095, USA; Department of Quantitative and Computational Biology, University of Southern California, Los Angeles, CA 90089, USA.

出版信息

Structure. 2022 Jan 6;30(1):24-36. doi: 10.1016/j.str.2021.12.003. Epub 2021 Dec 27.

Abstract

New technological advances in integrated imaging, sequencing-based assays, and computational analysis have revolutionized our view of genomes in terms of their structure and dynamics in space and time. These advances promise a deeper understanding of genome functions and mechanistic insights into how the nucleus is spatially organized and functions. These wide arrays of complementary data provide an opportunity to produce quantitative integrative models of nuclear organization. In this article, we highlight recent key developments and discuss the outlook for these fields.

摘要

在集成成像、基于测序的检测和计算分析方面的新技术进步,从基因组的结构和时空动态方面彻底改变了我们对基因组的看法。这些进步有望加深我们对基因组功能的理解,并深入了解核是如何在空间上组织和发挥作用的。这些广泛的互补数据为构建核组织的定量综合模型提供了机会。在本文中,我们重点介绍了最近的关键进展,并讨论了这些领域的展望。

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本文引用的文献

1
Evaluating the role of the nuclear microenvironment in gene function by population-based modeling.
Nat Struct Mol Biol. 2023 Aug;30(8):1193-1206. doi: 10.1038/s41594-023-01036-1. Epub 2023 Aug 14.
2
Integrative genome modeling platform reveals essentiality of rare contact events in 3D genome organizations.
Nat Methods. 2022 Aug;19(8):938-949. doi: 10.1038/s41592-022-01527-x. Epub 2022 Jul 11.
3
Multiscale and integrative single-cell Hi-C analysis with Higashi.
Nat Biotechnol. 2022 Feb;40(2):254-261. doi: 10.1038/s41587-021-01034-y. Epub 2021 Oct 11.
4
Single-cell nuclear architecture across cell types in the mouse brain.
Science. 2021 Oct 29;374(6567):586-594. doi: 10.1126/science.abj1966. Epub 2021 Sep 30.
5
The 3D Genome Structure of Single Cells.
Annu Rev Biomed Data Sci. 2021 Jul 20;4:21-41. doi: 10.1146/annurev-biodatasci-020121-084709. Epub 2021 Apr 23.
6
SnapHiC: a computational pipeline to identify chromatin loops from single-cell Hi-C data.
Nat Methods. 2021 Sep;18(9):1056-1059. doi: 10.1038/s41592-021-01231-2. Epub 2021 Aug 26.
7
Uncovering the Principles of Genome Folding by 3D Chromatin Modeling.
Cold Spring Harb Perspect Biol. 2022 Jun 14;14(6):a039693. doi: 10.1101/cshperspect.a039693.
8
DeTOKI identifies and characterizes the dynamics of chromatin TAD-like domains in a single cell.
Genome Biol. 2021 Jul 27;22(1):217. doi: 10.1186/s13059-021-02435-7.
9
Multiscale modeling of genome organization with maximum entropy optimization.
J Chem Phys. 2021 Jul 7;155(1):010901. doi: 10.1063/5.0044150.
10
Integrated spatial genomics reveals global architecture of single nuclei.
Nature. 2021 Feb;590(7845):344-350. doi: 10.1038/s41586-020-03126-2. Epub 2021 Jan 27.

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