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对小鼠基因组进行通用染色质状态注释。

Universal chromatin state annotation of the mouse genome.

机构信息

Bioinformatics Interdepartmental Program, University of California, Los Angeles, CA, 90095, USA.

Department of Biological Chemistry, University of California, Los Angeles, Los Angeles, CA, 90095, USA.

出版信息

Genome Biol. 2023 Jun 27;24(1):153. doi: 10.1186/s13059-023-02994-x.


DOI:10.1186/s13059-023-02994-x
PMID:37370147
原文链接:https://pmc.ncbi.nlm.nih.gov/articles/PMC10294404/
Abstract

A large-scale application of the "stacked modeling" approach for chromatin state discovery previously provides a single "universal" chromatin state annotation of the human genome based jointly on data from many cell and tissue types. Here, we produce an analogous chromatin state annotation for mouse based on 901 datasets assaying 14 chromatin marks in 26 cell or tissue types. To characterize each chromatin state, we relate the states to external annotations and compare them to analogously defined human states. We expect the universal chromatin state annotation for mouse to be a useful resource for studying this key model organism's genome.

摘要

“堆积建模”方法的大规模应用之前为人类基因组提供了基于多种细胞和组织类型数据的单一“通用”染色质状态注释。在这里,我们基于 901 个数据集生成了类似的基于 26 种细胞或组织类型的 14 种染色质标记的鼠标染色质状态注释。为了描述每个染色质状态,我们将状态与外部注释相关联,并将它们与类似定义的人类状态进行比较。我们期望鼠标的通用染色质状态注释将成为研究这种关键模式生物基因组的有用资源。

https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3a56/10294404/a43e2f21c6e4/13059_2023_2994_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3a56/10294404/1370ec94ca4a/13059_2023_2994_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3a56/10294404/a43e2f21c6e4/13059_2023_2994_Fig2_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3a56/10294404/1370ec94ca4a/13059_2023_2994_Fig1_HTML.jpg
https://cdn.ncbi.nlm.nih.gov/pmc/blobs/3a56/10294404/a43e2f21c6e4/13059_2023_2994_Fig2_HTML.jpg

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本文引用的文献

[1]
Universal annotation of the human genome through integration of over a thousand epigenomic datasets.

Genome Biol. 2022-1-6

[2]
Segmentation and genome annotation algorithms for identifying chromatin state and other genomic patterns.

PLoS Comput Biol. 2021-10

[3]
Learning a genome-wide score of human-mouse conservation at the functional genomics level.

Nat Commun. 2021-5-3

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Annotation of chromatin states in 66 complete mouse epigenomes during development.

Commun Biol. 2021-2-22

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Nat Methods. 2021-3

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Nature. 2020-7

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Nature. 2020-7

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The ENCODE Blacklist: Identification of Problematic Regions of the Genome.

Sci Rep. 2019-6-27

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Identification, Characterization, and Heritability of Murine Metastable Epialleles: Implications for Non-genetic Inheritance.

Cell. 2018-10-25

[10]
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Nucleic Acids Res. 2019-1-8

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