Macrohistone Variants Preserve Cell Identity by Preventing the Gain of H3K4me2 during Reprogramming to Pluripotency

María J. Barrero; Borja Sese; Bernd Kuebler; Josipa Bilic; Stephanie Boue; Mercè Martí; Juan Carlos Izpisua Belmonte

doi:10.1016/j.celrep.2013.02.029

Macrohistone Variants Preserve Cell Identity by Preventing the Gain of H3K4me2 during Reprogramming to Pluripotency

María J. Barrero, Borja Sese, Bernd Kuebler, Josipa Bilic, Stephanie Boue, Mercè Martí, Juan Carlos Izpisua Belmonte^*

^*Corresponding author for this work

Research output: Contribution to journal › Article › peer-review

66 Scopus citations

Abstract

Transcription-factor-induced reprogramming of somatic cells to pluripotency is a very inefficient process, probably due to the existence of important epigenetic barriers that are imposed during differentiation and that contribute to preserving cell identity. In an effort to decipher the molecular nature of these barriers, we followed a genome-wide approach, in which we identified macrohistone variants (macroH2A) as highly expressed in human somatic cells but downregulated after reprogramming to pluripotency, as well as strongly induced during differentiation. Knockdown of macrohistone variants in human keratinocytes increased the efficiency of reprogramming to pluripotency, whereas overexpression had opposite effects. Genome-wide occupancy profiles show that in human keratinocytes, macroH2A.1 preferentially occupies genes that are expressed at low levels and are marked with H3K27me3, including pluripotency-related genes and bivalent developmental regulators. The presence of macroH2A.1 at these genes prevents the regain of H3K4me2 during reprogramming, imposing an additional layer of repression that preserves cell identity.

Original language	English (US)
Pages (from-to)	1005-1011
Number of pages	7
Journal	Cell reports
Volume	3
Issue number	4
DOIs	https://doi.org/10.1016/j.celrep.2013.02.029
State	Published - Apr 25 2013
Externally published	Yes

Bibliographical note

Funding Information:
We would like to thank J. Castaño, M. Carrió, C. Gómez, and L. Casano and the platforms at the Center for Regenerative Medicine in Barcelona for technical assistance and members of the J.C.I.B. laboratory for feedback and discussions. We also thank S. Malik for discussion on ChIP-seq data and A. Jordan for advice on the immunoprecipitation of HA-tagged proteins. Antibodies against macroH2A.2 and short hairpin vectors were provided by M. Bushbeck. This work was supported by grants from MICINN (RYC-2007-01510 and SAF2009-08588 to M.J.B.). M.J.B. is partially supported by the Ramón y Cajal program. B.S. is a recipient of a FPU predoctoral fellowship from MICINN. J.B. is a recipient of a Juan de la Cierva fellowship from the MICINN. Work in the laboratory of J.C.I.B. was funded by the G. Harold and Leila Y. Mathers Charitable Foundation, The Leona M. and Harry B. Helmsley Charitable Trust, TERCEL-ISCIII-MINECO, CIBER-BBN, and Fundacion Cellex.

ASJC Scopus subject areas

General Biochemistry, Genetics and Molecular Biology

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10.1016/j.celrep.2013.02.029

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title = "Macrohistone Variants Preserve Cell Identity by Preventing the Gain of H3K4me2 during Reprogramming to Pluripotency",

abstract = "Transcription-factor-induced reprogramming of somatic cells to pluripotency is a very inefficient process, probably due to the existence of important epigenetic barriers that are imposed during differentiation and that contribute to preserving cell identity. In an effort to decipher the molecular nature of these barriers, we followed a genome-wide approach, in which we identified macrohistone variants (macroH2A) as highly expressed in human somatic cells but downregulated after reprogramming to pluripotency, as well as strongly induced during differentiation. Knockdown of macrohistone variants in human keratinocytes increased the efficiency of reprogramming to pluripotency, whereas overexpression had opposite effects. Genome-wide occupancy profiles show that in human keratinocytes, macroH2A.1 preferentially occupies genes that are expressed at low levels and are marked with H3K27me3, including pluripotency-related genes and bivalent developmental regulators. The presence of macroH2A.1 at these genes prevents the regain of H3K4me2 during reprogramming, imposing an additional layer of repression that preserves cell identity.",

author = "Barrero, {Mar{\'i}a J.} and Borja Sese and Bernd Kuebler and Josipa Bilic and Stephanie Boue and Merc{\`e} Mart{\'i} and {Izpisua Belmonte}, {Juan Carlos}",

note = "Funding Information: We would like to thank J. Casta{\~n}o, M. Carri{\'o}, C. G{\'o}mez, and L. Casano and the platforms at the Center for Regenerative Medicine in Barcelona for technical assistance and members of the J.C.I.B. laboratory for feedback and discussions. We also thank S. Malik for discussion on ChIP-seq data and A. Jordan for advice on the immunoprecipitation of HA-tagged proteins. Antibodies against macroH2A.2 and short hairpin vectors were provided by M. Bushbeck. This work was supported by grants from MICINN (RYC-2007-01510 and SAF2009-08588 to M.J.B.). M.J.B. is partially supported by the Ram{\'o}n y Cajal program. B.S. is a recipient of a FPU predoctoral fellowship from MICINN. J.B. is a recipient of a Juan de la Cierva fellowship from the MICINN. Work in the laboratory of J.C.I.B. was funded by the G. Harold and Leila Y. Mathers Charitable Foundation, The Leona M. and Harry B. Helmsley Charitable Trust, TERCEL-ISCIII-MINECO, CIBER-BBN, and Fundacion Cellex. ",

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AU - Sese, Borja

AU - Kuebler, Bernd

AU - Bilic, Josipa

AU - Boue, Stephanie

AU - Martí, Mercè

AU - Izpisua Belmonte, Juan Carlos

N1 - Funding Information: We would like to thank J. Castaño, M. Carrió, C. Gómez, and L. Casano and the platforms at the Center for Regenerative Medicine in Barcelona for technical assistance and members of the J.C.I.B. laboratory for feedback and discussions. We also thank S. Malik for discussion on ChIP-seq data and A. Jordan for advice on the immunoprecipitation of HA-tagged proteins. Antibodies against macroH2A.2 and short hairpin vectors were provided by M. Bushbeck. This work was supported by grants from MICINN (RYC-2007-01510 and SAF2009-08588 to M.J.B.). M.J.B. is partially supported by the Ramón y Cajal program. B.S. is a recipient of a FPU predoctoral fellowship from MICINN. J.B. is a recipient of a Juan de la Cierva fellowship from the MICINN. Work in the laboratory of J.C.I.B. was funded by the G. Harold and Leila Y. Mathers Charitable Foundation, The Leona M. and Harry B. Helmsley Charitable Trust, TERCEL-ISCIII-MINECO, CIBER-BBN, and Fundacion Cellex.

PY - 2013/4/25

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N2 - Transcription-factor-induced reprogramming of somatic cells to pluripotency is a very inefficient process, probably due to the existence of important epigenetic barriers that are imposed during differentiation and that contribute to preserving cell identity. In an effort to decipher the molecular nature of these barriers, we followed a genome-wide approach, in which we identified macrohistone variants (macroH2A) as highly expressed in human somatic cells but downregulated after reprogramming to pluripotency, as well as strongly induced during differentiation. Knockdown of macrohistone variants in human keratinocytes increased the efficiency of reprogramming to pluripotency, whereas overexpression had opposite effects. Genome-wide occupancy profiles show that in human keratinocytes, macroH2A.1 preferentially occupies genes that are expressed at low levels and are marked with H3K27me3, including pluripotency-related genes and bivalent developmental regulators. The presence of macroH2A.1 at these genes prevents the regain of H3K4me2 during reprogramming, imposing an additional layer of repression that preserves cell identity.

AB - Transcription-factor-induced reprogramming of somatic cells to pluripotency is a very inefficient process, probably due to the existence of important epigenetic barriers that are imposed during differentiation and that contribute to preserving cell identity. In an effort to decipher the molecular nature of these barriers, we followed a genome-wide approach, in which we identified macrohistone variants (macroH2A) as highly expressed in human somatic cells but downregulated after reprogramming to pluripotency, as well as strongly induced during differentiation. Knockdown of macrohistone variants in human keratinocytes increased the efficiency of reprogramming to pluripotency, whereas overexpression had opposite effects. Genome-wide occupancy profiles show that in human keratinocytes, macroH2A.1 preferentially occupies genes that are expressed at low levels and are marked with H3K27me3, including pluripotency-related genes and bivalent developmental regulators. The presence of macroH2A.1 at these genes prevents the regain of H3K4me2 during reprogramming, imposing an additional layer of repression that preserves cell identity.

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ER -

Macrohistone Variants Preserve Cell Identity by Preventing the Gain of H3K4me2 during Reprogramming to Pluripotency

Abstract

Bibliographical note

ASJC Scopus subject areas

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