Neutralizing Gatad2a-Chd4-Mbd3/NuRD Complex Facilitates Deterministic Induction of Naive Pluripotency

Nofar Mor; Yoach Rais; Daoud Sheban; Shani Peles; Alejandro Aguilera-Castrejon; Asaf Zviran; Dalia Elinger; Sergey Viukov; Shay Geula; Vladislav Krupalnik; Mirie Zerbib; Elad Chomsky; Lior Lasman; Tom Shani; Jonathan Bayerl; Ohad Gafni; Suhair Hanna; Jason D Buenrostro; Tzachi Hagai; Hagit Masika; Gintautas Vainorius; Yehudit Bergman; William J Greenleaf; Miguel A Esteban; Ulrich Elling; Yishai Levin; Rada Massarwa; Yifat Merbl; Noa Novershtern; Jacob H Hanna

doi:10.1016/j.stem.2018.07.004

Neutralizing Gatad2a-Chd4-Mbd3/NuRD Complex Facilitates Deterministic Induction of Naive Pluripotency

Cell Stem Cell. 2018 Sep 6;23(3):412-425.e10. doi: 10.1016/j.stem.2018.07.004. Epub 2018 Aug 16.

Authors

Nofar Mor¹, Yoach Rais², Daoud Sheban³, Shani Peles¹, Alejandro Aguilera-Castrejon¹, Asaf Zviran⁴, Dalia Elinger⁵, Sergey Viukov¹, Shay Geula¹, Vladislav Krupalnik¹, Mirie Zerbib¹, Elad Chomsky⁶, Lior Lasman¹, Tom Shani¹, Jonathan Bayerl¹, Ohad Gafni¹, Suhair Hanna⁷, Jason D Buenrostro⁸, Tzachi Hagai⁹, Hagit Masika¹⁰, Gintautas Vainorius¹¹, Yehudit Bergman¹⁰, William J Greenleaf¹², Miguel A Esteban¹³, Ulrich Elling¹¹, Yishai Levin⁵, Rada Massarwa¹, Yifat Merbl¹⁴, Noa Novershtern¹⁵, Jacob H Hanna¹⁶

Affiliations

¹ Department of Molecular Genetics, Weizmann Institute of Science, 234 Herzl, Rehovot 76100, Israel.
² Department of Molecular Genetics, Weizmann Institute of Science, 234 Herzl, Rehovot 76100, Israel. Electronic address: yoach.rais@gmail.com.
³ Department of Molecular Genetics, Weizmann Institute of Science, 234 Herzl, Rehovot 76100, Israel; Department of Immunology, Weizmann Institute of Science, Rehovot, Israel.
⁴ Department of Molecular Genetics, Weizmann Institute of Science, 234 Herzl, Rehovot 76100, Israel; New York Genome Center, New York, NY, USA.
⁵ The Nancy and Stephen Grand Israel National Center for Personalized Medicine, Weizmann Institute of Science, Rehovot, Israel.
⁶ Department of Biological Regulation, Weizmann Institute of Science, Rehovot, Israel.
⁷ Department of Pediatrics, Rambam Health Care Campus, Haifa, Israel.
⁸ Broad Institute of MIT and Harvard, Cambridge, MA, USA; Harvard Society of Fellows, Harvard University, Cambridge, MA, USA.
⁹ EMBL-European Bioinformatics Institute, Wellcome Genome Campus, Cambridge, UK.
¹⁰ Department of Developmental Biology and Cancer Research, Hebrew University, Jerusalem, Israel.
¹¹ Institute of Molecular Biotechnology (IMBA), Vienna, Austria.
¹² Department of Genetics, Stanford University, Palo Alto, CA, USA; Chan Zuckerberg Biohub, San Francisco, CA, USA.
¹³ Key Laboratory of Regenerative Biology, Guangzhou Institutes of Biomedicine and Health, Chinese Academy of Sciences, Guangzhou, China.
¹⁴ Department of Immunology, Weizmann Institute of Science, Rehovot, Israel.
¹⁵ Department of Molecular Genetics, Weizmann Institute of Science, 234 Herzl, Rehovot 76100, Israel. Electronic address: noa.novershtern@weizmann.ac.il.
¹⁶ Department of Molecular Genetics, Weizmann Institute of Science, 234 Herzl, Rehovot 76100, Israel. Electronic address: jacob.hanna@weizmann.ac.il.

Abstract

Mbd3, a member of nucleosome remodeling and deacetylase (NuRD) co-repressor complex, was previously identified as an inhibitor for deterministic induced pluripotent stem cell (iPSC) reprogramming, where up to 100% of donor cells successfully complete the process. NuRD can assume multiple mutually exclusive conformations, and it remains unclear whether this deterministic phenotype can be attributed to a specific Mbd3/NuRD subcomplex. Moreover, since complete ablation of Mbd3 blocks somatic cell proliferation, we aimed to explore functionally relevant alternative ways to neutralize Mbd3-dependent NuRD activity. We identify Gatad2a, a NuRD-specific subunit, whose complete deletion specifically disrupts Mbd3/NuRD repressive activity on the pluripotency circuitry during iPSC differentiation and reprogramming without ablating somatic cell proliferation. Inhibition of Gatad2a facilitates deterministic murine iPSC reprogramming within 8 days. We validate a distinct molecular axis, Gatad2a-Chd4-Mbd3, within Mbd3/NuRD as being critical for blocking reestablishment of naive pluripotency and further highlight signaling-dependent and post-translational modifications of Mbd3/NuRD that influence its interactions and assembly.

Keywords: CHD4; Gatad2a; Mbd3; NuRD; P66α; epigenetics; iPSCs; pluripotency; reprogramming.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Animals
Cells, Cultured
DNA Helicases / metabolism*
DNA-Binding Proteins / metabolism*
Female
GATA Transcription Factors / metabolism*
Induced Pluripotent Stem Cells / cytology
Induced Pluripotent Stem Cells / metabolism*
Male
Mi-2 Nucleosome Remodeling and Deacetylase Complex / metabolism*
Mice
Mice, Inbred C57BL
Mice, Inbred CBA
Mice, Knockout
Mice, Transgenic
Transcription Factors / metabolism*

Substances

DNA-Binding Proteins
GATA Transcription Factors
Gatad2a protein, mouse
Mbd3 protein, mouse
Transcription Factors
Mi-2 Nucleosome Remodeling and Deacetylase Complex
Mi-2beta protein, mouse
DNA Helicases

Grants and funding

726497/ERC_/European Research Council/International