Epigenetic priming by Dppa2 and 4 in pluripotency facilitates multi-lineage commitment
Eckersley-Maslin, Mélanie A; Parry, Aled; Blotenburg, Marloes; Krueger, Christel; Ito, Yoko; Franklin, Valar Nila Roamio; Narita, Masashi; D'Santos, Clive S; Reik, Wolf
(2020) Nature structural & molecular biology, volume 27, issue 8, pp. 696 - 705
(Article)
Abstract
How the epigenetic landscape is established in development is still being elucidated. Here, we uncover developmental pluripotency associated 2 and 4 (DPPA2/4) as epigenetic priming factors that establish a permissive epigenetic landscape at a subset of developmentally important bivalent promoters characterized by low expression and poised RNA-polymerase. Differentiation assays reveal
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that Dppa2/4 double knockout mouse embryonic stem cells fail to exit pluripotency and differentiate efficiently. DPPA2/4 bind both H3K4me3-marked and bivalent gene promoters and associate with COMPASS- and Polycomb-bound chromatin. Comparing knockout and inducible knockdown systems, we find that acute depletion of DPPA2/4 results in rapid loss of H3K4me3 from key bivalent genes, while H3K27me3 is initially more stable but lost following extended culture. Consequently, upon DPPA2/4 depletion, these promoters gain DNA methylation and are unable to be activated upon differentiation. Our findings uncover a novel epigenetic priming mechanism at developmental promoters, poising them for future lineage-specific activation.
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Keywords: Animals, Cell Differentiation, Cell Line, Chromatin/genetics, DNA Methylation, Dipeptidyl Peptidase 4/genetics, Epigenesis, Genetic, Gene Expression Regulation, Developmental, Gene Knockout Techniques, Histones/genetics, Mice, Mouse Embryonic Stem Cells/cytology, Transcription Factors/genetics, Molecular Biology, Structural Biology, Research Support, Non-U.S. Gov't, Journal Article
ISSN: 1545-9985
Publisher: Nature Publishing Group
Note: Funding Information: We thank all members of the Reik laboratory for helpful discussions. We also thank F. di Tullio for help generating overexpression cell lines, F. Krueger for processing sequencing data and for general bioformatics support, S. Wingett for bioinformatic assistance and S. Andrews for bioinformatic advice. We thank B. Hussey and E. Easthope at Sanger Institute and K. Tabbada at Babraham Institute for assistance with high-throughput sequencing, R. Walker for assistance with flow cytometry, and J. Webster and D. Oxley for mass spectrometry. Dnmt TKO cells were a kind gift from D. Schübeler (FMI). M.A.E.-M. is supported by a BBSRC Discovery Fellowship (BB/T009713/1) and was supported by an EMBO Fellowship (ALTF938–2014) and a Marie Sklodowska-Curie Individual Fellowship. A.P. is supported by a Sir Henry Wellcome Fellowship (215912/Z/19/Z). M.B. was supported by an Erasmus Grant. M.N. and Y.I. were supported by a Cancer Research UK Cambridge Institute Core grant (no. C9545/A29580). Research in the Reik laboratory is supported by the Biotechnology and Biological Sciences Research Council (BB/K010867/1) and the Wellcome Trust (095645/Z/11/Z). Publisher Copyright: © 2020, The Author(s), under exclusive licence to Springer Nature America, Inc. Copyright: Copyright 2020 Elsevier B.V., All rights reserved.
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