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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...
Autores principales: | , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
The American Society for Cell Biology
2015
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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. |
format | Online Article Text |
id | pubmed-4501365 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2015 |
publisher | The American Society for Cell Biology |
record_format | MEDLINE/PubMed |
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 |
work_keys_str_mv | AT zhengxiaobin identificationoflaminbregulatedchromatinregionsbasedonchromatinlandscapes AT kimyoungjo identificationoflaminbregulatedchromatinregionsbasedonchromatinlandscapes AT zhengyixian identificationoflaminbregulatedchromatinregionsbasedonchromatinlandscapes |