DNA methylation restricts coordinated germline and neural fates in embryonic stem cell differentiation.
Journal
Nature structural & molecular biology
ISSN: 1545-9985
Titre abrégé: Nat Struct Mol Biol
Pays: United States
ID NLM: 101186374
Informations de publication
Date de publication:
04 Jan 2024
04 Jan 2024
Historique:
received:
22
11
2022
accepted:
26
10
2023
medline:
5
1
2024
pubmed:
5
1
2024
entrez:
4
1
2024
Statut:
aheadofprint
Résumé
As embryonic stem cells (ESCs) transition from naive to primed pluripotency during early mammalian development, they acquire high DNA methylation levels. During this transition, the germline is specified and undergoes genome-wide DNA demethylation, while emergence of the three somatic germ layers is preceded by acquisition of somatic DNA methylation levels in the primed epiblast. DNA methylation is essential for embryogenesis, but the point at which it becomes critical during differentiation and whether all lineages equally depend on it is unclear. Here, using culture modeling of cellular transitions, we found that DNA methylation-free mouse ESCs with triple DNA methyltransferase knockout (TKO) progressed through the continuum of pluripotency states but demonstrated skewed differentiation abilities toward neural versus other somatic lineages. More saliently, TKO ESCs were fully competent for establishing primordial germ cell-like cells, even showing temporally extended and self-sustained capacity for the germline fate. By mapping chromatin states, we found that neural and germline lineages are linked by a similar enhancer dynamic upon exit from the naive state, defined by common sets of transcription factors, including methyl-sensitive ones, that fail to be decommissioned in the absence of DNA methylation. We propose that DNA methylation controls the temporality of a coordinated neural-germline axis of the preferred differentiation route during early development.
Identifiants
pubmed: 38177678
doi: 10.1038/s41594-023-01162-w
pii: 10.1038/s41594-023-01162-w
doi:
Types de publication
Journal Article
Langues
eng
Sous-ensembles de citation
IM
Informations de copyright
© 2024. The Author(s), under exclusive licence to Springer Nature America, Inc.
Références
Li, E., Bestor, T. H. & Jaenisch, R. Targeted mutation of the DNA methyltransferase gene results in embryonic lethality. Cell 69, 915–926 (1992).
pubmed: 1606615
doi: 10.1016/0092-8674(92)90611-F
Okano, M., Bell, D. W., Haber, D. A. & Li, E. DNA methyltransferases Dnmt3a and Dnmt3b are essential for de novo methylation and mammalian development. Cell 99, 247–257 (1999).
pubmed: 10555141
doi: 10.1016/S0092-8674(00)81656-6
Zhang, Y. et al. Dynamic epigenomic landscapes during early lineage specification in mouse embryos. Nat. Genet. 50, 96–105 (2018).
pubmed: 29203909
doi: 10.1038/s41588-017-0003-x
Leitch, H. G. et al. Naive pluripotency is associated with global DNA hypomethylation. Nat. Struct. Mol. Biol. 20, 311–316 (2013).
pubmed: 23416945
doi: 10.1038/nsmb.2510
pmcid: 3591483
Nichols, J. & Smith, A. Naive and primed pluripotent states. Cell Stem Cell 4, 487–492 (2009).
Morgani, S., Nichols, J. & Hadjantonakis, A.-K. The many faces of pluripotency: in vitro adaptations of a continuum of in vivo states. BMC Dev. Biol. 17, 7 (2017).
pubmed: 28610558
doi: 10.1186/s12861-017-0150-4
pmcid: 5470286
Smith, A. Formative pluripotency: the executive phase in a developmental continuum. Development 144, 365–373 (2017).
pubmed: 28143843
doi: 10.1242/dev.142679
pmcid: 5430734
Yamaji, M. et al. Critical function of Prdm14 for the establishment of the germ cell lineage in mice. Nat. Genet. 40, 1016–1022 (2008).
pubmed: 18622394
doi: 10.1038/ng.186
Ohinata, Y. et al. Blimp1 is a critical determinant of the germ cell lineage in mice. Nature 436, 207–213 (2005).
pubmed: 15937476
doi: 10.1038/nature03813
Seisenberger, S. et al. The dynamics of genome-wide DNA methylation reprogramming in mouse primordial germ cells. Mol. Cell 48, 849–862 (2012).
pubmed: 23219530
doi: 10.1016/j.molcel.2012.11.001
pmcid: 3533687
Tsumura, A. et al. Maintenance of self-renewal ability of mouse embryonic stem cells in the absence of DNA methyltransferases Dnmt1, Dnmt3a and Dnmt3b. Genes Cells 11, 805–814 (2006).
pubmed: 16824199
doi: 10.1111/j.1365-2443.2006.00984.x
Sakaue, M. et al. DNA methylation is dispensable for the growth and survival of the extraembryonic lineages. Curr. Biol. 20, 1452–1457 (2010).
pubmed: 20637626
doi: 10.1016/j.cub.2010.06.050
Schmidt, C. S. et al. Global DNA hypomethylation prevents consolidation of differentiation programs and allows reversion to the embryonic stem cell state. PLoS ONE 7, e52629 (2012).
pubmed: 23300728
doi: 10.1371/journal.pone.0052629
pmcid: 3531338
Bell, E. et al. Dynamic CpG methylation delineates subregions within super-enhancers selectively decommissioned at the exit from naive pluripotency. Nat. Commun. 11, 1112 (2020).
pubmed: 32111830
doi: 10.1038/s41467-020-14916-7
pmcid: 7048827
Kalkan, T. et al. Tracking the embryonic stem cell transition from ground state pluripotency. Development 144, 1221–1234 (2017).
pubmed: 28174249
pmcid: 5399622
Rulands, S. et al. Genome-scale oscillations in DNA methylation during exit from pluripotency. Cell Syst. 7, 63–76 (2018).
pubmed: 30031774
doi: 10.1016/j.cels.2018.06.012
pmcid: 6066359
King, A. D. et al. Reversible regulation of promoter and enhancer histone landscape by DNA methylation in mouse embryonic stem cells. Cell Rep. 17, 289–302 (2016).
pubmed: 27681438
doi: 10.1016/j.celrep.2016.08.083
pmcid: 5507178
Zhu, H., Wang, G. & Qian, J. Transcription factors as readers and effectors of DNA methylation. Nat. Rev. Genet. 17, 551–565 (2016).
pubmed: 27479905
doi: 10.1038/nrg.2016.83
pmcid: 5559737
Kreibich, E., Kleinendorst, R., Barzaghi, G., Kaspar, S. & Krebs, A. R. Single-molecule footprinting identifies context-dependent regulation of enhancers by DNA methylation. Mol. Cell 83, 787–802 (2023).
pubmed: 36758546
doi: 10.1016/j.molcel.2023.01.017
Damelin, M. & Bestor, T. H. Biological functions of DNA methyltransferase 1 require its methyltransferase activity. Mol. Cell. Biol. 27, 3891–3899 (2007).
pubmed: 17371843
doi: 10.1128/MCB.00036-07
pmcid: 1900033
Nowialis, P. et al. Catalytically inactive Dnmt3b rescues mouse embryonic development by accessory and repressive functions. Nat. Commun. 10, 4374 (2019).
pubmed: 31558711
doi: 10.1038/s41467-019-12355-7
pmcid: 6763448
Hayashi, K., Ohta, H., Kurimoto, K., Aramaki, S. & Saitou, M. Reconstitution of the mouse germ cell specification pathway in culture by pluripotent stem cells. Cell 146, 519–532 (2011).
pubmed: 21820164
doi: 10.1016/j.cell.2011.06.052
Buecker, C. et al. Reorganization of enhancer patterns in transition from naive to primed pluripotency. Cell Stem Cell 14, 838–853 (2014).
Blaschke, K. et al. Vitamin C induces Tet-dependent DNA demethylation and a blastocyst-like state in ES cells. Nature 500, 222–226 (2013).
pubmed: 23812591
doi: 10.1038/nature12362
pmcid: 3893718
Choi, H. W. et al. Distinct enhancer activity of Oct4 in naive and primed mouse pluripotency. Stem Cell Reports 7, 911–926 (2016).
Dubois, A. et al. H3K9 tri-methylation at Nanog times differentiation commitment and enables the acquisition of primitive endoderm fate. Development 149, dev201074 (2022).
pubmed: 35976266
doi: 10.1242/dev.201074
pmcid: 9482333
Kinoshita, M. et al. Disabling de novo DNA methylation in embryonic stem cells allows an illegitimate fate trajectory. Proc. Natl Acad. Sci. USA 118, e2109475118 (2021).
pubmed: 34518230
doi: 10.1073/pnas.2109475118
pmcid: 8463881
Bao, S. et al. Derivation of hypermethylated pluripotent embryonic stem cells with high potency. Cell Res. 28, 22–34 (2018).
pubmed: 29076502
doi: 10.1038/cr.2017.134
Borgel, J. et al. Targets and dynamics of promoter DNA methylation during early mouse development. Nat. Genet. 42, 1093–1100 (2010).
pubmed: 21057502
doi: 10.1038/ng.708
Hargan-Calvopina, J. et al. Stage-specific demethylation in primordial germ cells safeguards against precocious differentiation. Dev. Cell 39, 75–86 (2016).
pubmed: 27618282
doi: 10.1016/j.devcel.2016.07.019
pmcid: 5064860
Ying, Q. L., Stavridis, M., Griffiths, D., Li, M. & Smith, A. Conversion of embryonic stem cells into neuroectodermal precursors in adherent monoculture. Nat. Biotechnol. 21, 183–186 (2003).
pubmed: 12524553
doi: 10.1038/nbt780
Argelaguet, R. et al. Multi-omics profiling of mouse gastrulation at single-cell resolution. Nature 576, 487–491 (2019).
pubmed: 31827285
doi: 10.1038/s41586-019-1825-8
pmcid: 6924995
Bleckwehl, T. & Rada-Iglesias, A. Transcriptional and epigenetic control of germline competence and specification. Curr. Opin. Cell Biol. 61, 1–8 (2019).
pubmed: 31233905
doi: 10.1016/j.ceb.2019.05.006
Gruhn, W. H. & Günesdogan, U. in Epigenetic Reprogramming During Mouse Embryogenesis (eds Ancelin, K. & Borensztein, M.) 75–89 (Springer, 2021).
Mulas, C., Kalkan, T. & Smith, A. NODAL secures pluripotency upon embryonic stem cell progression from the ground state. Stem Cell Reports 9, 77–91 (2017).
Hackett, J. A. et al. Tracing the transitions from pluripotency to germ cell fate with CRISPR screening. Nat. Commun. 9, 4292 (2018).
pubmed: 30327475
doi: 10.1038/s41467-018-06230-0
pmcid: 6191455
Kim, I. S. et al. Parallel single-cell RNA-seq and genetic recording reveals lineage decisions in developing embryoid bodies. Cell Rep. 33, 108222 (2020).
pubmed: 33027665
doi: 10.1016/j.celrep.2020.108222
pmcid: 7646252
Aramaki, S. et al. Residual pluripotency is required for inductive germ cell segregation. EMBO Rep. 22, e52553 (2021).
pubmed: 34156139
doi: 10.15252/embr.202152553
pmcid: 8344911
Shirane, K. et al. Global landscape and regulatory principles of DNA methylation reprogramming for germ cell specification by mouse pluripotent stem cells. Dev. Cell 39, 87–103 (2016).
pubmed: 27642137
doi: 10.1016/j.devcel.2016.08.008
Greenberg, M., Teissandier, A., Walter, M., Noordermeer, D. & Bourc’his, D. Dynamic enhancer partitioning instructs activation of a growth-related gene during exit from naïve pluripotency. eLife 8, e44057 (2019).
pubmed: 30990414
doi: 10.7554/eLife.44057
pmcid: 6488298
Creyghton, M. P. et al. Histone H3K27ac separates active from poised enhancers and predicts developmental state. Proc. Natl Acad. Sci. USA 107, 21931–21936 (2010).
pubmed: 21106759
doi: 10.1073/pnas.1016071107
pmcid: 3003124
Cruz-Molina, S. et al. PRC2 facilitates the regulatory topology required for poised enhancer function during pluripotent stem cell differentiation. Cell Stem Cell 20, 689–705 (2017).
Kalkan, T. et al. Complementary activity of ETV5, RBPJ, and TCF3 drives formative transition from naive pluripotency. Cell Stem Cell 24, 785–801 (2019).
Yang, S.-H. et al. ZIC3 controls the transition from naïve to primed pluripotency. Cell Rep. 27, 3215–3227 (2019).
pubmed: 31189106
doi: 10.1016/j.celrep.2019.05.026
pmcid: 6581693
Okashita, N. et al. PRDM14 drives OCT3/4 recruitment via active demethylation in the transition from primed to naive pluripotency. Stem Cell Reports 7, 1072–1086 (2016).
Eckersley-Maslin, M. A. et al. Epigenetic priming by Dppa2 and 4 in pluripotency facilitates multi-lineage commitment. Nat. Struct. Mol. Biol. 27, 696–705 (2020).
Gretarsson, K. H. & Hackett, J. A. Dppa2 and Dppa4 counteract de novo methylation to establish a permissive epigenome for development. Nat. Struct. Mol. Biol. 27, 706–716 (2020).
pubmed: 32572256
doi: 10.1038/s41594-020-0445-1
Schwarz, B. A. et al. Prospective isolation of poised iPSC intermediates reveals principles of cellular reprogramming. Cell Stem Cell 23, 289–305 (2018).
Hon, G. C. et al. Epigenetic memory at embryonic enhancers identified in DNA methylation maps from adult mouse tissues. Nat. Genet. 45, 1198–1206 (2013).
pubmed: 23995138
doi: 10.1038/ng.2746
pmcid: 4095776
Heinz, S. et al. Simple combinations of lineage-determining transcription factors prime cis-regulatory elements required for macrophage and B cell identities. Mol. Cell 38, 576–589 (2010).
pubmed: 20513432
doi: 10.1016/j.molcel.2010.05.004
pmcid: 2898526
Domcke, S. et al. Competition between DNA methylation and transcription factors determines binding of NRF1. Nature 528, 575–579 (2015).
pubmed: 26675734
doi: 10.1038/nature16462
Luo, X. et al. Coordination of germ layer lineage choice by TET1 during primed pluripotency. Genes Dev. 34, 598–618 (2020).
pubmed: 32115407
doi: 10.1101/gad.329474.119
pmcid: 7111260
Dura, M. et al. DNMT3A-dependent DNA methylation is required for spermatogonial stem cells to commit to spermatogenesis. Nat. Genet. 54, 469–480 (2022).
pubmed: 35410378
doi: 10.1038/s41588-022-01040-z
Park, J. et al. Targeted erasure of DNA methylation by TET3 drives adipogenic reprogramming and differentiation. Nat. Metab. 4, 918–931 (2022).
pubmed: 35788760
doi: 10.1038/s42255-022-00597-7
Akagi, T. et al. ETS-related transcription factors ETV4 and ETV5 are involved in proliferation and induction of differentiation-associated genes in embryonic stem (ES) cells. J. Biol. Chem. 290, 22460–22473 (2015).
pubmed: 26224636
doi: 10.1074/jbc.M115.675595
pmcid: 4566222
Mayer, D. et al. Zfp281 orchestrates interconversion of pluripotent states by engaging Ehmt1 and Zic2. EMBO J. 39, e102591 (2020).
pubmed: 31782544
doi: 10.15252/embj.2019102591
Bentsen, M. et al. ATAC-seq footprinting unravels kinetics of transcription factor binding during zygotic genome activation. Nat. Commun. 11, 4267 (2020).
pubmed: 32848148
doi: 10.1038/s41467-020-18035-1
pmcid: 7449963
Tischler, J. et al. Metabolic regulation of pluripotency and germ cell fate through α‐ketoglutarate. EMBO J. 38, e99518 (2019).
pubmed: 30257965
doi: 10.15252/embj.201899518
Betto, R. M. et al. Metabolic control of DNA methylation in naive pluripotent cells. Nat. Genet. 53, 215–229 (2021).
pubmed: 33526924
doi: 10.1038/s41588-020-00770-2
pmcid: 7116828
Kaluscha, S. et al. Evidence that direct inhibition of transcription factor binding is the prevailing mode of gene and repeat repression by DNA methylation. Nat. Genet. 54, 1895–1906 (2022).
pubmed: 36471082
doi: 10.1038/s41588-022-01241-6
pmcid: 9729108
Banerjee, K. K. et al. Enhancer, transcriptional, and cell fate plasticity precedes intestinal determination during endoderm development. Genes Dev. 32, 1430–1442 (2018).
pubmed: 30366903
doi: 10.1101/gad.318832.118
pmcid: 6217732
Rauch, A. et al. Osteogenesis depends on commissioning of a network of stem cell transcription factors that act as repressors of adipogenesis. Nat. Genet. 51, 716–727 (2019).
pubmed: 30833796
doi: 10.1038/s41588-019-0359-1
Charlton, J. et al. TETs compete with DNMT3 activity in pluripotent cells at thousands of methylated somatic enhancers. Nat. Genet. 52, 819–827 (2020).
pubmed: 32514123
doi: 10.1038/s41588-020-0639-9
pmcid: 7415576
Ginno, P. A. et al. A genome-scale map of DNA methylation turnover identifies site-specific dependencies of DNMT and TET activity. Nat. Commun. 11, 2680 (2020).
pubmed: 32471981
doi: 10.1038/s41467-020-16354-x
pmcid: 7260214
Clark, S. J. et al. Single-cell multi-omics profiling links dynamic DNA methylation to cell fate decisions during mouse early organogenesis. Genome Biol. 23, 202 (2022).
pubmed: 36163261
doi: 10.1186/s13059-022-02762-3
pmcid: 9511790
Matos, B., Publicover, S. J., Castro, L. F. C., Esteves, P. J. & Fardilha, M. Brain and testis: more alike than previously thought? Open Biol. 11, 200322 (2021).
pubmed: 34062096
doi: 10.1098/rsob.200322
pmcid: 8169208
Wilda, M. et al. Do the constraints of human speciation cause expression of the same set of genes in brain, testis, and placenta? Cytogenet. Cell Genet. 91, 300–302 (2000).
pubmed: 11173873
doi: 10.1159/000056861
Karlsson, M. et al. A single-cell type transcriptomics map of human tissues. Sci. Adv. 7, eabh2169 (2021).
pubmed: 34321199
doi: 10.1126/sciadv.abh2169
pmcid: 8318366
Gibson, D. G. et al. Enzymatic assembly of DNA molecules up to several hundred kilobases. Nat. Methods 6, 343–345 (2009).
pubmed: 19363495
doi: 10.1038/nmeth.1318
Karimi, M. et al. LUMA (luminometric methylation assay)—a high throughput method to the analysis of genomic DNA methylation. Exp. Cell. Res. 312, 1989–1995 (2006).
pubmed: 16624287
doi: 10.1016/j.yexcr.2006.03.006
Schomacher, L. et al. Neil DNA glycosylases promote substrate turnover by Tdg during DNA demethylation. Nat. Struct. Mol. Biol. 23, 116–124 (2016).
pubmed: 26751644
doi: 10.1038/nsmb.3151
pmcid: 4894546
Picelli, S. et al. Full-length RNA-seq from single cells using Smart-seq2. Nat. Protoc. 9, 171–181 (2014).
pubmed: 24385147
doi: 10.1038/nprot.2014.006
Skene, P. J. & Henikoff, S. An efficient targeted nuclease strategy for high-resolution mapping of DNA binding sites. eLife 6, e21856 (2017).
pubmed: 28079019
doi: 10.7554/eLife.21856
pmcid: 5310842
Buenrostro, J. D., Wu, B., Chang, H. Y. & Greenleaf, W. J. ATAC-seq: a method for assaying chromatin accessibility genome-wide. Curr. Protoc. Mol. Biol. 2015, 21.29.1–21.29.9 (2015).
Buenrostro, J. D., Giresi, P. G., Zaba, L. C., Chang, H. Y. & Greenleaf, W. J. Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position. Nat. Methods 10, 1213–1218 (2013).
pubmed: 24097267
doi: 10.1038/nmeth.2688
pmcid: 3959825
Walter, M., Teissandier, A., Pérez-Palacios, R. & Bourc’his, D. An epigenetic switch ensures transposon repression upon dynamic loss of DNA methylation in embryonic stem cells. eLife 5, e11418 (2016).
pubmed: 26814573
doi: 10.7554/eLife.11418
pmcid: 4769179
Krueger, F. & Andrews, S. R. Bismark: a flexible aligner and methylation caller for bisulfite-seq applications. Bioinformatics 27, 1571–1572 (2011).
pubmed: 21493656
doi: 10.1093/bioinformatics/btr167
pmcid: 3102221
Langmead, B. & Salzberg, S. L. Fast gapped-read alignment with Bowtie 2. Nat. Methods 9, 357–359 (2012).
pubmed: 22388286
doi: 10.1038/nmeth.1923
pmcid: 3322381