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Identification of lamin B–regulated chromatin regions based on chromatin landscapes

Lamins, the major structural components of the nuclear lamina (NL) found beneath the nuclear envelope, are known to interact with most of the nuclear peripheral chromatin in metazoan cells. Although NL–chromatin associations correlate with a repressive chromatin state, the role of lamins in tetherin...

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Autores principales: Zheng, Xiaobin, Kim, Youngjo, Zheng, Yixian
Formato: Online Artículo Texto
Lenguaje:English
Publicado: The American Society for Cell Biology 2015
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4501365/
https://www.ncbi.nlm.nih.gov/pubmed/25995381
http://dx.doi.org/10.1091/mbc.E15-04-0210
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author Zheng, Xiaobin
Kim, Youngjo
Zheng, Yixian
author_facet Zheng, Xiaobin
Kim, Youngjo
Zheng, Yixian
author_sort Zheng, Xiaobin
collection PubMed
description Lamins, the major structural components of the nuclear lamina (NL) found beneath the nuclear envelope, are known to interact with most of the nuclear peripheral chromatin in metazoan cells. Although NL–chromatin associations correlate with a repressive chromatin state, the role of lamins in tethering chromatin to NL and how such tether influences gene expression have remained challenging to decipher. Studies suggest that NL proteins regulate chromatin in a context-dependent manner. Therefore understanding the context of chromatin states based on genomic features, including chromatin–NL interactions, is important to the study of lamins and other NL proteins. By modeling genome organization based on combinatorial patterns of chromatin association with lamin B1, core histone modification, and core and linker histone occupancy, we report six distinct large chromatin landscapes, referred to as histone lamin landscapes (HiLands)-red (R), -orange (O), -yellow (Y), -green (G), -blue (B), and -purple (P), in mouse embryonic stem cells (mESCs). This HiLands model demarcates the previously mapped lamin-associated chromatin domains (LADs) into two HiLands, HiLands-B and HiLands-P, which are similar to facultative and constitutive heterochromatins, respectively. Deletion of B-type lamins in mESCs caused a reduced interaction between regions of HiLands-B and NL as measured by emerin–chromatin interaction. Our findings reveal the importance of analyzing specific chromatin types when studying the function of NL proteins in chromatin tether and regulation.
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spelling pubmed-45013652015-09-30 Identification of lamin B–regulated chromatin regions based on chromatin landscapes Zheng, Xiaobin Kim, Youngjo Zheng, Yixian Mol Biol Cell Articles Lamins, the major structural components of the nuclear lamina (NL) found beneath the nuclear envelope, are known to interact with most of the nuclear peripheral chromatin in metazoan cells. Although NL–chromatin associations correlate with a repressive chromatin state, the role of lamins in tethering chromatin to NL and how such tether influences gene expression have remained challenging to decipher. Studies suggest that NL proteins regulate chromatin in a context-dependent manner. Therefore understanding the context of chromatin states based on genomic features, including chromatin–NL interactions, is important to the study of lamins and other NL proteins. By modeling genome organization based on combinatorial patterns of chromatin association with lamin B1, core histone modification, and core and linker histone occupancy, we report six distinct large chromatin landscapes, referred to as histone lamin landscapes (HiLands)-red (R), -orange (O), -yellow (Y), -green (G), -blue (B), and -purple (P), in mouse embryonic stem cells (mESCs). This HiLands model demarcates the previously mapped lamin-associated chromatin domains (LADs) into two HiLands, HiLands-B and HiLands-P, which are similar to facultative and constitutive heterochromatins, respectively. Deletion of B-type lamins in mESCs caused a reduced interaction between regions of HiLands-B and NL as measured by emerin–chromatin interaction. Our findings reveal the importance of analyzing specific chromatin types when studying the function of NL proteins in chromatin tether and regulation. The American Society for Cell Biology 2015-07-15 /pmc/articles/PMC4501365/ /pubmed/25995381 http://dx.doi.org/10.1091/mbc.E15-04-0210 Text en © 2015 Zheng, Kim, and Zheng. This article is distributed by The American Society for Cell Biology under license from the author(s). Two months after publication it is available to the public under an Attribution–Noncommercial–Share Alike 3.0 Unported Creative Commons License (http://creativecommons.org/licenses/by-nc-sa/3.0). “ASCB®,” “The American Society for Cell Biology®,” and “Molecular Biology of the Cell®” are registered trademarks of The American Society for Cell Biology.
spellingShingle Articles
Zheng, Xiaobin
Kim, Youngjo
Zheng, Yixian
Identification of lamin B–regulated chromatin regions based on chromatin landscapes
title Identification of lamin B–regulated chromatin regions based on chromatin landscapes
title_full Identification of lamin B–regulated chromatin regions based on chromatin landscapes
title_fullStr Identification of lamin B–regulated chromatin regions based on chromatin landscapes
title_full_unstemmed Identification of lamin B–regulated chromatin regions based on chromatin landscapes
title_short Identification of lamin B–regulated chromatin regions based on chromatin landscapes
title_sort identification of lamin b–regulated chromatin regions based on chromatin landscapes
topic Articles
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC4501365/
https://www.ncbi.nlm.nih.gov/pubmed/25995381
http://dx.doi.org/10.1091/mbc.E15-04-0210
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AT zhengyixian identificationoflaminbregulatedchromatinregionsbasedonchromatinlandscapes