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Local chromatin dynamics of transcription factors imply cell-lineage specific functions during cellular differentiation
Chromatin dynamics across cellular differentiation states is an emerging perspective from which the mechanism of global gene expression regulation may be better understood. While the roles of some histone marks have been partially interpreted in terms of their association with gene transcription, th...
Autores principales: | , , , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
Landes Bioscience
2012
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3329503/ https://www.ncbi.nlm.nih.gov/pubmed/22207356 http://dx.doi.org/10.4161/epi.7.1.18683 |
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author | Tian, Rui Feng, Jianxing Cai, Xiaopeng Zhang, Yong |
author_facet | Tian, Rui Feng, Jianxing Cai, Xiaopeng Zhang, Yong |
author_sort | Tian, Rui |
collection | PubMed |
description | Chromatin dynamics across cellular differentiation states is an emerging perspective from which the mechanism of global gene expression regulation may be better understood. While the roles of some histone marks have been partially interpreted in terms of their association with gene transcription, the dynamics of histone marks from a loci-specific perspective during cellular differentiation is not well studied. We established a method to systematically assess the histone modification variations of genes across various cellular differentiation states. We calculated the histone modification variation scores of H3K4me3, H3K27me3 and H3K36me3 for over 1300 curated transcription factors (TFs) during human blood cell differentiation. Hematopoietic-specific TFs (identified by literature mining) were significantly overrepresented by TFs with higher histone modification variation scores. Hierarchical clustering of all TFs based on the histone modification variation scores defined a group of TFs where known or potential hematopoietic-specific TFs were remarkably enriched. Our results suggest that local chromatin state dynamics of transcription factors across cellular differentiation states could imply cell lineage-specific functions. More importantly, our method can be applied to broader systems, holding the promise to discover de novo, lineage-specific TFs by interrogating their histone modification dynamics across cell lineages. |
format | Online Article Text |
id | pubmed-3329503 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2012 |
publisher | Landes Bioscience |
record_format | MEDLINE/PubMed |
spelling | pubmed-33295032012-05-07 Local chromatin dynamics of transcription factors imply cell-lineage specific functions during cellular differentiation Tian, Rui Feng, Jianxing Cai, Xiaopeng Zhang, Yong Epigenetics Research Paper Chromatin dynamics across cellular differentiation states is an emerging perspective from which the mechanism of global gene expression regulation may be better understood. While the roles of some histone marks have been partially interpreted in terms of their association with gene transcription, the dynamics of histone marks from a loci-specific perspective during cellular differentiation is not well studied. We established a method to systematically assess the histone modification variations of genes across various cellular differentiation states. We calculated the histone modification variation scores of H3K4me3, H3K27me3 and H3K36me3 for over 1300 curated transcription factors (TFs) during human blood cell differentiation. Hematopoietic-specific TFs (identified by literature mining) were significantly overrepresented by TFs with higher histone modification variation scores. Hierarchical clustering of all TFs based on the histone modification variation scores defined a group of TFs where known or potential hematopoietic-specific TFs were remarkably enriched. Our results suggest that local chromatin state dynamics of transcription factors across cellular differentiation states could imply cell lineage-specific functions. More importantly, our method can be applied to broader systems, holding the promise to discover de novo, lineage-specific TFs by interrogating their histone modification dynamics across cell lineages. Landes Bioscience 2012-01-01 /pmc/articles/PMC3329503/ /pubmed/22207356 http://dx.doi.org/10.4161/epi.7.1.18683 Text en Copyright © 2012 Landes Bioscience http://creativecommons.org/licenses/by-nc/3.0/ This is an open-access article licensed under a Creative Commons Attribution-NonCommercial 3.0 Unported License. The article may be redistributed, reproduced, and reused for non-commercial purposes, provided the original source is properly cited. |
spellingShingle | Research Paper Tian, Rui Feng, Jianxing Cai, Xiaopeng Zhang, Yong Local chromatin dynamics of transcription factors imply cell-lineage specific functions during cellular differentiation |
title | Local chromatin dynamics of transcription factors imply cell-lineage specific functions during cellular differentiation |
title_full | Local chromatin dynamics of transcription factors imply cell-lineage specific functions during cellular differentiation |
title_fullStr | Local chromatin dynamics of transcription factors imply cell-lineage specific functions during cellular differentiation |
title_full_unstemmed | Local chromatin dynamics of transcription factors imply cell-lineage specific functions during cellular differentiation |
title_short | Local chromatin dynamics of transcription factors imply cell-lineage specific functions during cellular differentiation |
title_sort | local chromatin dynamics of transcription factors imply cell-lineage specific functions during cellular differentiation |
topic | Research Paper |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3329503/ https://www.ncbi.nlm.nih.gov/pubmed/22207356 http://dx.doi.org/10.4161/epi.7.1.18683 |
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