Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration

Weisheng Wu, Yong Cheng, Cheryl A. Keller Capone, Jason Ernst, Swathi Ashok Kumar, Tejaswini Mishra, Christapher Morrissey, Christine M. Dorman, Kuan Bei Chen, Daniela Drautz, Belinda Giardine, Yoichiro Shibata, Lingyun Song, Max Pimkin, Gregory E. Crawford, Terrence S. Furey, Manolis Kellis, Webb Miller, James Taylor, Stephan C. Schuster & 5 others Yu Zhang, Francesca Chiaromonte, Gerd A. Blobel, Mitchell J. Weiss, Ross Cameron Hardison

Research output: Contribution to journalArticle

75 Citations (Scopus)

Abstract

Interplays among lineage-specific nuclear proteins, chromatin modifying enzymes, and the basal transcription machinery govern cellular differentiation, but their dynamics of action and coordination with transcriptional control are not fully understood. Alterations in chromatin structure appear to establish a permissive state for gene activation at some loci, but they play an integral role in activation at other loci. To determine the predominant roles of chromatin states and factor occupancy in directing gene regulation during differentiation, we mapped chromatin accessibility, histone modifications, and nuclear factor occupancy genome-wide during mouse erythroid differentiation dependent on the master regulatory transcription factor GATA1. Notably, despite extensive changes in gene expression, the chromatin state profiles (proportions of a gene in a chromatin state dominated by activating or repressive histone modifications) and accessibility remain largely unchanged during GATA1-induced erythroid differentiation. In contrast, gene induction and repression are strongly associated with changes in patterns of transcription factor occupancy. Our results indicate that during erythroid differentiation, the broad features of chromatin states are established at the stage of lineage commitment, largely independently of GATA1. These determine permissiveness for expression, with subsequent induction or repression mediated by distinctive combinations of transcription factors.

Original languageEnglish (US)
Pages (from-to)1659-1671
Number of pages13
JournalGenome research
Volume21
Issue number10
DOIs
StatePublished - Oct 1 2011

Fingerprint

Epigenomics
Chromatin
Histone Code
GATA1 Transcription Factor
Transcription Factors
Permissiveness
Genes
Nuclear Proteins
Transcriptional Activation
Genome
Gene Expression
Enzymes

All Science Journal Classification (ASJC) codes

  • Genetics
  • Genetics(clinical)

Cite this

Wu, Weisheng ; Cheng, Yong ; Keller Capone, Cheryl A. ; Ernst, Jason ; Kumar, Swathi Ashok ; Mishra, Tejaswini ; Morrissey, Christapher ; Dorman, Christine M. ; Chen, Kuan Bei ; Drautz, Daniela ; Giardine, Belinda ; Shibata, Yoichiro ; Song, Lingyun ; Pimkin, Max ; Crawford, Gregory E. ; Furey, Terrence S. ; Kellis, Manolis ; Miller, Webb ; Taylor, James ; Schuster, Stephan C. ; Zhang, Yu ; Chiaromonte, Francesca ; Blobel, Gerd A. ; Weiss, Mitchell J. ; Hardison, Ross Cameron. / Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration. In: Genome research. 2011 ; Vol. 21, No. 10. pp. 1659-1671.
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abstract = "Interplays among lineage-specific nuclear proteins, chromatin modifying enzymes, and the basal transcription machinery govern cellular differentiation, but their dynamics of action and coordination with transcriptional control are not fully understood. Alterations in chromatin structure appear to establish a permissive state for gene activation at some loci, but they play an integral role in activation at other loci. To determine the predominant roles of chromatin states and factor occupancy in directing gene regulation during differentiation, we mapped chromatin accessibility, histone modifications, and nuclear factor occupancy genome-wide during mouse erythroid differentiation dependent on the master regulatory transcription factor GATA1. Notably, despite extensive changes in gene expression, the chromatin state profiles (proportions of a gene in a chromatin state dominated by activating or repressive histone modifications) and accessibility remain largely unchanged during GATA1-induced erythroid differentiation. In contrast, gene induction and repression are strongly associated with changes in patterns of transcription factor occupancy. Our results indicate that during erythroid differentiation, the broad features of chromatin states are established at the stage of lineage commitment, largely independently of GATA1. These determine permissiveness for expression, with subsequent induction or repression mediated by distinctive combinations of transcription factors.",
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Wu, W, Cheng, Y, Keller Capone, CA, Ernst, J, Kumar, SA, Mishra, T, Morrissey, C, Dorman, CM, Chen, KB, Drautz, D, Giardine, B, Shibata, Y, Song, L, Pimkin, M, Crawford, GE, Furey, TS, Kellis, M, Miller, W, Taylor, J, Schuster, SC, Zhang, Y, Chiaromonte, F, Blobel, GA, Weiss, MJ & Hardison, RC 2011, 'Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration', Genome research, vol. 21, no. 10, pp. 1659-1671. https://doi.org/10.1101/gr.125088.111

Dynamics of the epigenetic landscape during erythroid differentiation after GATA1 restoration. / Wu, Weisheng; Cheng, Yong; Keller Capone, Cheryl A.; Ernst, Jason; Kumar, Swathi Ashok; Mishra, Tejaswini; Morrissey, Christapher; Dorman, Christine M.; Chen, Kuan Bei; Drautz, Daniela; Giardine, Belinda; Shibata, Yoichiro; Song, Lingyun; Pimkin, Max; Crawford, Gregory E.; Furey, Terrence S.; Kellis, Manolis; Miller, Webb; Taylor, James; Schuster, Stephan C.; Zhang, Yu; Chiaromonte, Francesca; Blobel, Gerd A.; Weiss, Mitchell J.; Hardison, Ross Cameron.

In: Genome research, Vol. 21, No. 10, 01.10.2011, p. 1659-1671.

Research output: Contribution to journalArticle

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AU - Wu, Weisheng

AU - Cheng, Yong

AU - Keller Capone, Cheryl A.

AU - Ernst, Jason

AU - Kumar, Swathi Ashok

AU - Mishra, Tejaswini

AU - Morrissey, Christapher

AU - Dorman, Christine M.

AU - Chen, Kuan Bei

AU - Drautz, Daniela

AU - Giardine, Belinda

AU - Shibata, Yoichiro

AU - Song, Lingyun

AU - Pimkin, Max

AU - Crawford, Gregory E.

AU - Furey, Terrence S.

AU - Kellis, Manolis

AU - Miller, Webb

AU - Taylor, James

AU - Schuster, Stephan C.

AU - Zhang, Yu

AU - Chiaromonte, Francesca

AU - Blobel, Gerd A.

AU - Weiss, Mitchell J.

AU - Hardison, Ross Cameron

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N2 - Interplays among lineage-specific nuclear proteins, chromatin modifying enzymes, and the basal transcription machinery govern cellular differentiation, but their dynamics of action and coordination with transcriptional control are not fully understood. Alterations in chromatin structure appear to establish a permissive state for gene activation at some loci, but they play an integral role in activation at other loci. To determine the predominant roles of chromatin states and factor occupancy in directing gene regulation during differentiation, we mapped chromatin accessibility, histone modifications, and nuclear factor occupancy genome-wide during mouse erythroid differentiation dependent on the master regulatory transcription factor GATA1. Notably, despite extensive changes in gene expression, the chromatin state profiles (proportions of a gene in a chromatin state dominated by activating or repressive histone modifications) and accessibility remain largely unchanged during GATA1-induced erythroid differentiation. In contrast, gene induction and repression are strongly associated with changes in patterns of transcription factor occupancy. Our results indicate that during erythroid differentiation, the broad features of chromatin states are established at the stage of lineage commitment, largely independently of GATA1. These determine permissiveness for expression, with subsequent induction or repression mediated by distinctive combinations of transcription factors.

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