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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...

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Detalles Bibliográficos
Autores principales: Tian, Rui, Feng, Jianxing, Cai, Xiaopeng, Zhang, Yong
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Landes Bioscience 2012
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.
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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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