TY - JOUR
T1 - Epigenetic priming by Dppa2 and 4 in pluripotency facilitates multi-lineage commitment
AU - Eckersley-Maslin, Mélanie A
AU - Parry, Aled
AU - Blotenburg, Marloes
AU - Krueger, Christel
AU - Ito, Yoko
AU - Franklin, Valar Nila Roamio
AU - Narita, Masashi
AU - D'Santos, Clive S
AU - Reik, Wolf
N1 - 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.
PY - 2020/8
Y1 - 2020/8
N2 - 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 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.
AB - 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 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.
KW - Animals
KW - Cell Differentiation
KW - Cell Line
KW - Chromatin/genetics
KW - DNA Methylation
KW - Dipeptidyl Peptidase 4/genetics
KW - Epigenesis, Genetic
KW - Gene Expression Regulation, Developmental
KW - Gene Knockout Techniques
KW - Histones/genetics
KW - Mice
KW - Mouse Embryonic Stem Cells/cytology
KW - Transcription Factors/genetics
UR - http://www.scopus.com/inward/record.url?scp=85086787805&partnerID=8YFLogxK
U2 - 10.1038/s41594-020-0443-3
DO - 10.1038/s41594-020-0443-3
M3 - Article
C2 - 32572255
SN - 1545-9985
VL - 27
SP - 696
EP - 705
JO - Nature structural & molecular biology
JF - Nature structural & molecular biology
IS - 8
ER -