Chromatin-modifying enzymes as modulators of reprogramming

Tamer T. Onder, Nergis Kara, Anne Cherry, Amit U. Sinha, Nan Zhu, Kathrin M. Bernt, Patrick Cahan, B. Ogan Marcarci, Juli Unternaehrer, Piyush B. Gupta, Eric S. Lander, Scott A. Armstrong, George Q. Daley

Research output: Contribution to journalArticle

Abstract

Generation of induced pluripotent stem cells (iPSCs) by somatic cell reprogramming involves global epigenetic remodelling. Whereas several proteins are known to regulate chromatin marks associated with the distinct epigenetic states of cells before and after reprogramming, the role of specific chromatin-modifying enzymes in reprogramming remains to be determined. To address how chromatin-modifying proteins influence reprogramming, we used short hairpin RNAs (shRNAs) to target genes in DNA and histone methylation pathways, and identified positive and negative modulators of iPSC generation. Whereas inhibition of the core components of the polycomb repressive complex 1 and 2, including the histone 3 lysine 27 methyltransferase EZH2, reduced reprogramming efficiency, suppression of SUV39H1, YY1 and DOT1L enhanced reprogramming. Specifically, inhibition of the H3K79 histone methyltransferase DOT1L by shRNA or a small molecule accelerated reprogramming, significantly increased the yield of iPSC colonies, and substituted for KLF4 and c-Myc (also known as MYC). Inhibition of DOT1L early in the reprogramming process is associated with a marked increase in two alternative factors, NANOG and LIN28, which play essential functional roles in the enhancement of reprogramming. Genome-wide analysis of H3K79me2 distribution revealed that fibroblast-specific genes associated with the epithelial to mesenchymal transition lose H3K79me2 in the initial phases of reprogramming. DOT1L inhibition facilitates the loss of this mark from genes that are fated to be repressed in the pluripotent state. These findings implicate specific chromatin-modifying enzymes as barriers to or facilitators of reprogramming, and demonstrate how modulation of chromatin-modifying enzymes can be exploited to more efficiently generate iPSCs with fewer exogenous transcription factors.

Original languageEnglish (US)
Pages (from-to)598-602
Number of pages5
JournalNature
Volume483
Issue number7391
DOIs
StatePublished - Mar 29 2012
Externally publishedYes

Fingerprint

Induced Pluripotent Stem Cells
Chromatin
Enzymes
Epigenomics
Histones
Small Interfering RNA
Polycomb Repressive Complex 1
Polycomb Repressive Complex 2
Genes
Epithelial-Mesenchymal Transition
Methyltransferases
DNA Methylation
Lysine
Proteins
Transcription Factors
Fibroblasts
Genome

ASJC Scopus subject areas

  • General

Cite this

Onder, T. T., Kara, N., Cherry, A., Sinha, A. U., Zhu, N., Bernt, K. M., ... Daley, G. Q. (2012). Chromatin-modifying enzymes as modulators of reprogramming. Nature, 483(7391), 598-602. https://doi.org/10.1038/nature10953

Chromatin-modifying enzymes as modulators of reprogramming. / Onder, Tamer T.; Kara, Nergis; Cherry, Anne; Sinha, Amit U.; Zhu, Nan; Bernt, Kathrin M.; Cahan, Patrick; Marcarci, B. Ogan; Unternaehrer, Juli; Gupta, Piyush B.; Lander, Eric S.; Armstrong, Scott A.; Daley, George Q.

In: Nature, Vol. 483, No. 7391, 29.03.2012, p. 598-602.

Research output: Contribution to journalArticle

Onder, TT, Kara, N, Cherry, A, Sinha, AU, Zhu, N, Bernt, KM, Cahan, P, Marcarci, BO, Unternaehrer, J, Gupta, PB, Lander, ES, Armstrong, SA & Daley, GQ 2012, 'Chromatin-modifying enzymes as modulators of reprogramming', Nature, vol. 483, no. 7391, pp. 598-602. https://doi.org/10.1038/nature10953
Onder TT, Kara N, Cherry A, Sinha AU, Zhu N, Bernt KM et al. Chromatin-modifying enzymes as modulators of reprogramming. Nature. 2012 Mar 29;483(7391):598-602. https://doi.org/10.1038/nature10953
Onder, Tamer T. ; Kara, Nergis ; Cherry, Anne ; Sinha, Amit U. ; Zhu, Nan ; Bernt, Kathrin M. ; Cahan, Patrick ; Marcarci, B. Ogan ; Unternaehrer, Juli ; Gupta, Piyush B. ; Lander, Eric S. ; Armstrong, Scott A. ; Daley, George Q. / Chromatin-modifying enzymes as modulators of reprogramming. In: Nature. 2012 ; Vol. 483, No. 7391. pp. 598-602.
@article{da6e1209d33443d59f0af8914c2309f1,
title = "Chromatin-modifying enzymes as modulators of reprogramming",
abstract = "Generation of induced pluripotent stem cells (iPSCs) by somatic cell reprogramming involves global epigenetic remodelling. Whereas several proteins are known to regulate chromatin marks associated with the distinct epigenetic states of cells before and after reprogramming, the role of specific chromatin-modifying enzymes in reprogramming remains to be determined. To address how chromatin-modifying proteins influence reprogramming, we used short hairpin RNAs (shRNAs) to target genes in DNA and histone methylation pathways, and identified positive and negative modulators of iPSC generation. Whereas inhibition of the core components of the polycomb repressive complex 1 and 2, including the histone 3 lysine 27 methyltransferase EZH2, reduced reprogramming efficiency, suppression of SUV39H1, YY1 and DOT1L enhanced reprogramming. Specifically, inhibition of the H3K79 histone methyltransferase DOT1L by shRNA or a small molecule accelerated reprogramming, significantly increased the yield of iPSC colonies, and substituted for KLF4 and c-Myc (also known as MYC). Inhibition of DOT1L early in the reprogramming process is associated with a marked increase in two alternative factors, NANOG and LIN28, which play essential functional roles in the enhancement of reprogramming. Genome-wide analysis of H3K79me2 distribution revealed that fibroblast-specific genes associated with the epithelial to mesenchymal transition lose H3K79me2 in the initial phases of reprogramming. DOT1L inhibition facilitates the loss of this mark from genes that are fated to be repressed in the pluripotent state. These findings implicate specific chromatin-modifying enzymes as barriers to or facilitators of reprogramming, and demonstrate how modulation of chromatin-modifying enzymes can be exploited to more efficiently generate iPSCs with fewer exogenous transcription factors.",
author = "Onder, {Tamer T.} and Nergis Kara and Anne Cherry and Sinha, {Amit U.} and Nan Zhu and Bernt, {Kathrin M.} and Patrick Cahan and Marcarci, {B. Ogan} and Juli Unternaehrer and Gupta, {Piyush B.} and Lander, {Eric S.} and Armstrong, {Scott A.} and Daley, {George Q.}",
year = "2012",
month = "3",
day = "29",
doi = "10.1038/nature10953",
language = "English (US)",
volume = "483",
pages = "598--602",
journal = "Nature",
issn = "0028-0836",
publisher = "Nature Publishing Group",
number = "7391",

}

TY - JOUR

T1 - Chromatin-modifying enzymes as modulators of reprogramming

AU - Onder, Tamer T.

AU - Kara, Nergis

AU - Cherry, Anne

AU - Sinha, Amit U.

AU - Zhu, Nan

AU - Bernt, Kathrin M.

AU - Cahan, Patrick

AU - Marcarci, B. Ogan

AU - Unternaehrer, Juli

AU - Gupta, Piyush B.

AU - Lander, Eric S.

AU - Armstrong, Scott A.

AU - Daley, George Q.

PY - 2012/3/29

Y1 - 2012/3/29

N2 - Generation of induced pluripotent stem cells (iPSCs) by somatic cell reprogramming involves global epigenetic remodelling. Whereas several proteins are known to regulate chromatin marks associated with the distinct epigenetic states of cells before and after reprogramming, the role of specific chromatin-modifying enzymes in reprogramming remains to be determined. To address how chromatin-modifying proteins influence reprogramming, we used short hairpin RNAs (shRNAs) to target genes in DNA and histone methylation pathways, and identified positive and negative modulators of iPSC generation. Whereas inhibition of the core components of the polycomb repressive complex 1 and 2, including the histone 3 lysine 27 methyltransferase EZH2, reduced reprogramming efficiency, suppression of SUV39H1, YY1 and DOT1L enhanced reprogramming. Specifically, inhibition of the H3K79 histone methyltransferase DOT1L by shRNA or a small molecule accelerated reprogramming, significantly increased the yield of iPSC colonies, and substituted for KLF4 and c-Myc (also known as MYC). Inhibition of DOT1L early in the reprogramming process is associated with a marked increase in two alternative factors, NANOG and LIN28, which play essential functional roles in the enhancement of reprogramming. Genome-wide analysis of H3K79me2 distribution revealed that fibroblast-specific genes associated with the epithelial to mesenchymal transition lose H3K79me2 in the initial phases of reprogramming. DOT1L inhibition facilitates the loss of this mark from genes that are fated to be repressed in the pluripotent state. These findings implicate specific chromatin-modifying enzymes as barriers to or facilitators of reprogramming, and demonstrate how modulation of chromatin-modifying enzymes can be exploited to more efficiently generate iPSCs with fewer exogenous transcription factors.

AB - Generation of induced pluripotent stem cells (iPSCs) by somatic cell reprogramming involves global epigenetic remodelling. Whereas several proteins are known to regulate chromatin marks associated with the distinct epigenetic states of cells before and after reprogramming, the role of specific chromatin-modifying enzymes in reprogramming remains to be determined. To address how chromatin-modifying proteins influence reprogramming, we used short hairpin RNAs (shRNAs) to target genes in DNA and histone methylation pathways, and identified positive and negative modulators of iPSC generation. Whereas inhibition of the core components of the polycomb repressive complex 1 and 2, including the histone 3 lysine 27 methyltransferase EZH2, reduced reprogramming efficiency, suppression of SUV39H1, YY1 and DOT1L enhanced reprogramming. Specifically, inhibition of the H3K79 histone methyltransferase DOT1L by shRNA or a small molecule accelerated reprogramming, significantly increased the yield of iPSC colonies, and substituted for KLF4 and c-Myc (also known as MYC). Inhibition of DOT1L early in the reprogramming process is associated with a marked increase in two alternative factors, NANOG and LIN28, which play essential functional roles in the enhancement of reprogramming. Genome-wide analysis of H3K79me2 distribution revealed that fibroblast-specific genes associated with the epithelial to mesenchymal transition lose H3K79me2 in the initial phases of reprogramming. DOT1L inhibition facilitates the loss of this mark from genes that are fated to be repressed in the pluripotent state. These findings implicate specific chromatin-modifying enzymes as barriers to or facilitators of reprogramming, and demonstrate how modulation of chromatin-modifying enzymes can be exploited to more efficiently generate iPSCs with fewer exogenous transcription factors.

UR - http://www.scopus.com/inward/record.url?scp=84859218238&partnerID=8YFLogxK

UR - http://www.scopus.com/inward/citedby.url?scp=84859218238&partnerID=8YFLogxK

U2 - 10.1038/nature10953

DO - 10.1038/nature10953

M3 - Article

VL - 483

SP - 598

EP - 602

JO - Nature

JF - Nature

SN - 0028-0836

IS - 7391

ER -