Retinoic acid signaling is critical during the totipotency window in early mammalian development.


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:
06 2021
Historique:
received: 05 06 2020
accepted: 07 04 2021
pubmed: 29 5 2021
medline: 25 8 2021
entrez: 28 5 2021
Statut: ppublish

Résumé

Totipotent cells hold enormous potential for regenerative medicine. Thus, the development of cellular models recapitulating totipotent-like features is of paramount importance. Cells resembling the totipotent cells of early embryos arise spontaneously in mouse embryonic stem (ES) cell cultures. Such '2-cell-like-cells' (2CLCs) recapitulate 2-cell-stage features and display expanded cell potential. Here, we used 2CLCs to perform a small-molecule screen to identify new pathways regulating the 2-cell-stage program. We identified retinoids as robust inducers of 2CLCs and the retinoic acid (RA)-signaling pathway as a key component of the regulatory circuitry of totipotent cells in embryos. Using single-cell RNA-seq, we reveal the transcriptional dynamics of 2CLC reprogramming and show that ES cells undergo distinct cellular trajectories in response to RA. Importantly, endogenous RA activity in early embryos is essential for zygotic genome activation and developmental progression. Overall, our data shed light on the gene regulatory networks controlling cellular plasticity and the totipotency program.

Identifiants

pubmed: 34045724
doi: 10.1038/s41594-021-00590-w
pii: 10.1038/s41594-021-00590-w
pmc: PMC8195742
doi:

Substances chimiques

LY2955303 0
Piperazines 0
Pyrazoles 0
RNA, Messenger 0
RNA, Small Interfering 0
Receptors, Retinoic Acid 0
retinoic acid binding protein I, cellular 0
Tretinoin 5688UTC01R
Isotretinoin EH28UP18IF
Acitretin LCH760E9T7

Types de publication

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

Langues

eng

Sous-ensembles de citation

IM

Pagination

521-532

Commentaires et corrections

Type : ErratumIn

Références

Ishiuchi, T. & Torres-Padilla, M.-E. Towards an understanding of the regulatory mechanisms of totipotency. Curr. Opin. Genet. Dev. 23, 512–518 (2013).
pubmed: 23942314 doi: 10.1016/j.gde.2013.06.006
Wu, G. & Schöler, H. R. Lineage segregation in the totipotent embryo. Curr. Top. Dev. Biol. 117, 301–317 (2016).
pubmed: 26969985 doi: 10.1016/bs.ctdb.2015.10.014
Tarkowski, A. K. Experiments on the development of isolated blastomeres of mouse eggs. Nature 184, 1286–1287 (1959).
pubmed: 13836947 doi: 10.1038/1841286a0
Togashi, M. Production of monozygotic twins by splitting of 2-cell stage embryos in mice. Jpn J. Anim. Reprod. 33, 51–57 (1987).
doi: 10.1262/jrd1977.33.51
Sotomaru, Y., Kato, Y. & Tsunoda, Y. Production of monozygotic twins after freezing and thawing of bisected mouse embryos. Cryobiology 37, 139–145 (1998).
pubmed: 9769164 doi: 10.1006/cryo.1998.2111
Rossant, J. & Tam, P. P. L. Blastocyst lineage formation, early embryonic asymmetries and axis patterning in the mouse. Development 136, 701–713 (2009).
pubmed: 19201946 doi: 10.1242/dev.017178
Shahbazi, M. N. & Zernicka-Goetz, M. Deconstructing and reconstructing the mouse and human early embryo. Nat. Cell Biol. 20, 878–887 (2018).
pubmed: 30038253 doi: 10.1038/s41556-018-0144-x
Macfarlan, T. S. et al. Embryonic stem cell potency fluctuates with endogenous retrovirus activity. Nature 487, 57–63 (2012).
pubmed: 22722858 pmcid: 3395470 doi: 10.1038/nature11244
Hendrickson, P. G. et al. Conserved roles of mouse DUX and human DUX4 in activating cleavage-stage genes and MERVL/HERVL retrotransposons. Nat. Genet. 49, 925–934 (2017).
pubmed: 28459457 pmcid: 5703070 doi: 10.1038/ng.3844
Rodriguez-Terrones, D. et al. A molecular roadmap for the emergence of early-embryonic-like cells in culture. Nat. Genet. 50, 106–119 (2018).
pubmed: 29255263 doi: 10.1038/s41588-017-0016-5
Cerulo, L. et al. Identification of a novel gene signature of ES cells self-renewal fluctuation through system-wide analysis. PloS ONE 9, e83235 (2014).
pubmed: 24392082 pmcid: 3879232 doi: 10.1371/journal.pone.0083235
Peaston, A. E. et al. Retrotransposons regulate host genes in mouse oocytes and preimplantation embryos. Dev. Cell 7, 597–606 (2004).
pubmed: 15469847 doi: 10.1016/j.devcel.2004.09.004
Bošković, A. et al. Higher chromatin mobility supports totipotency and precedes pluripotency in vivo. Genes Dev. 28, 1042–1047 (2014).
pubmed: 24831699 pmcid: 4035533 doi: 10.1101/gad.238881.114
Rodriguez-Terrones, D. et al. A distinct metabolic state arises during the emergence of 2-cell-like cells. EMBO Rep. 21, e48354 (2020).
pubmed: 31849178 doi: 10.15252/embr.201948354
Tagliaferri, D. et al. Retinoic acid induces embryonic stem cells (ESCs) transition to 2 cell-like state through a coordinated expression of Dux and Duxbl1. Front. Cell Dev. Biol. 7, 385 (2019).
pubmed: 32010697 doi: 10.3389/fcell.2019.00385
Ishiuchi, T. et al. Early embryonic-like cells are induced by downregulating replication-dependent chromatin assembly. Nat. Struct. Mol. Biol. 22, 662–671 (2015).
pubmed: 26237512 doi: 10.1038/nsmb.3066
De Iaco, A. et al. DUX-family transcription factors regulate zygotic genome activation in placental mammals. Nat. Genet. 49, 941–945 (2017).
pubmed: 28459456 pmcid: 5446900 doi: 10.1038/ng.3858
De Iaco, A., Coudray, A., Duc, J. & Trono, D. DPPA2 and DPPA4 are necessary to establish a 2C-like state in mouse embryonic stem cells. EMBO Rep. 20, e47382 (2019).
pubmed: 30948459 pmcid: 6500978
Eckersley-Maslin, M. et al. Dppa2 and Dppa4 directly regulate the Dux-driven zygotic transcriptional program. Genes Dev. 33, 194–208 (2019).
pubmed: 30692203 pmcid: 6362816 doi: 10.1101/gad.321174.118
Choi, Y. J. et al. Deficiency of microRNA miR-34a expands cell fate potential in pluripotent stem cells. Science 355, eaag1927 (2017).
pubmed: 28082412 pmcid: 6138252 doi: 10.1126/science.aag1927
Yang, F. et al. DUX-miR-344-ZMYM2-mediated activation of MERVL LTRs induces a totipotent 2C-like state. Cell Stem Cell 26, 234–250 (2020).
pubmed: 32032525 pmcid: 8074926 doi: 10.1016/j.stem.2020.01.004
Rhinn, M. & Dollé, P. Retinoic acid signalling during development. Development 139, 843–858 (2012).
pubmed: 22318625 doi: 10.1242/dev.065938
Cunningham, T. J. & Duester, G. Mechanisms of retinoic acid signalling and its roles in organ and limb development. Nat. Rev. Mol. Cell Biol. 16, 110–123 (2015).
pubmed: 25560970 pmcid: 4636111 doi: 10.1038/nrm3932
Napoli, J. L. in The Biochemistry of Retinoid Signaling II: The Physiology of Vitamin A—Uptake, Transport, Metabolism and Signaling (eds Asson-Batres, M. A. & Rochette-Egly, C.) 21–76 (Springer, 2016).
Benbrook, D. M., Chambon, P., Rochette-Egly, C. & Asson-Batres, M. A. in The Biochemistry of Retinoic Acid Receptors I: Structure, Activation and Function at the Molecular Level (eds Asson-Batres, M. A. & Rochette-Egly, C.) 1–20 (Springer, 2014).
Lee, S. & Privalsky, M. L. Heterodimers of retinoic acid receptors and thyroid hormone receptors display unique combinatorial regulatory properties. Mol. Endocrinol. 19, 863–878 (2005).
pubmed: 15650024 doi: 10.1210/me.2004-0210
Agarwal, C., Chandraratna, R. A., Johnson, A. T., Rorke, E. A. & Eckert, R. L. AGN193109 is a highly effective antagonist of retinoid action in human ectocervical epithelial cells. J. Biol. Chem. 271, 12209–12212 (1996).
pubmed: 8647816 doi: 10.1074/jbc.271.21.12209
Germain, P. et al. Differential action on coregulator interaction defines inverse retinoid agonists and neutral antagonists. Chem. Biol. 16, 479–489 (2009).
pubmed: 19477412 doi: 10.1016/j.chembiol.2009.03.008
Monaghan, J. R. & Maden, M. Visualization of retinoic acid signaling in transgenic axolotls during limb development and regeneration. Dev. Biol. 368, 63–75 (2012).
pubmed: 22627291 pmcid: 3383931 doi: 10.1016/j.ydbio.2012.05.015
Eckersley-Maslin, M. A. et al. MERVL/Zscan4 network activation results in transient genome-wide DNA demethylation of mESCs. Cell Rep. 17, 179–192 (2016).
pubmed: 27681430 pmcid: 5055476 doi: 10.1016/j.celrep.2016.08.087
Fraichard, A. et al. In vitro differentiation of embryonic stem cells into glial cells and functional neurons. J. Cell Sci. 108, 3181–3188 (1995).
pubmed: 7593279 doi: 10.1242/jcs.108.10.3181
La Manno, G. et al. RNA velocity of single cells. Nature 560, 494–498 (2018).
pubmed: 30089906 pmcid: 6130801 doi: 10.1038/s41586-018-0414-6
Kalmar, T. et al. Regulated fluctuations in Nanog expression mediate cell fate decisions in embryonic stem cells. PLoS Biol. 7, e1000149 (2009).
pubmed: 19582141 pmcid: 2700273 doi: 10.1371/journal.pbio.1000149
Osorno, R. & Chambers, I. Transcription factor heterogeneity and epiblast pluripotency. Philos. Trans. R. Soc. Lond. B Biol. Sci. 366, 2230–2237 (2011).
pubmed: 21727128 pmcid: 3130424 doi: 10.1098/rstb.2011.0043
Mark, M., Ghyselinck, N. B. & Chambon, P. Function of retinoic acid receptors during embryonic development. Nucl. Recept. Signal. 7, e002 (2009).
pubmed: 19381305 pmcid: 2670431 doi: 10.1621/nrs.07002
Ulven, S. M. et al. Identification of endogenous retinoids, enzymes, binding proteins and receptors during early postimplantation development in mouse: important role of retinal dehydrogenase type 2 in synthesis of all-trans-retinoic acid. Dev. Biol. 220, 379–391 (2000).
pubmed: 10753524 doi: 10.1006/dbio.2000.9634
Wu, J. et al. The landscape of accessible chromatin in mammalian preimplantation embryos. Nature 534, 652–657 (2016).
pubmed: 27309802 doi: 10.1038/nature18606
Iqbal, K. et al. Cytoplasmic injection of circular plasmids allows targeted expression in mammalian embryos. BioTechniques 47, 959–968 (2009).
pubmed: 20041849 doi: 10.2144/000113270
Warner, C. M. & Versteegh, L. R. In vivo and in vitro effect of α-amanitin on preimplantation mouse embryo RNA polymerase. Nature 248, 678–680 (1974).
pubmed: 4833268 doi: 10.1038/248678a0
Picelli, S. et al. Smart-Seq2 for sensitive full-length transcriptome profiling in single cells. Nat. Methods 10, 1096–1098 (2013).
pubmed: 24056875 doi: 10.1038/nmeth.2639
Whiddon, J. L., Langford, A. T., Wong, C.-J., Zhong, J. W. & Tapscott, S. J. Conservation and innovation in the DUX4-family gene network. Nat. Genet. 49, 935–940 (2017).
pubmed: 28459454 pmcid: 5446306 doi: 10.1038/ng.3846
Yan, Y.-L. et al. DPPA2/4 and SUMO E3 ligase PIAS4 opposingly regulate zygotic transcriptional program. PLoS Biol. 17, e3000324 (2019).
pubmed: 31226106 pmcid: 6608977 doi: 10.1371/journal.pbio.3000324
Tagliaferri, D. et al. Retinoic acid specifically enhances embryonic stem cell metastate marked by Zscan4. PloS ONE 11, e0147683 (2016).
pubmed: 26840068 pmcid: 4740454 doi: 10.1371/journal.pone.0147683
Penvose, A., Keenan, J. L., Bray, D., Ramlall, V. & Siggers, T. Comprehensive study of nuclear receptor DNA binding provides a revised framework for understanding receptor specificity. Nat. Commun. 10, 2514 (2019).
pubmed: 31175293 pmcid: 6555819 doi: 10.1038/s41467-019-10264-3
Watson, L. C. et al. The glucocorticoid receptor dimer interface allosterically transmits sequence-specific DNA signals. Nat. Struct. Mol. Biol. 20, 876–883 (2013).
pubmed: 23728292 pmcid: 3702670 doi: 10.1038/nsmb.2595
Giguère, V. Orphan nuclear receptors: from gene to function. Endocr. Rev. 20, 689–725 (1999).
pubmed: 10529899
Chatagnon, A. et al. RAR/RXR binding dynamics distinguish pluripotency from differentiation associated cis-regulatory elements. Nucleic Acids Res. 43, 4833–4854 (2015).
pubmed: 25897113 pmcid: 4446430 doi: 10.1093/nar/gkv370
Wu, J. et al. Chromatin analysis in human early development reveals epigenetic transition during ZGA. Nature 557, 256–260 (2018).
pubmed: 29720659 doi: 10.1038/s41586-018-0080-8
Lohnes, D. et al. Function of the retinoic acid receptors (RARs) during development (I). Craniofacial and skeletal abnormalities in RAR double mutants. Development 120, 2723–2748 (1994).
pubmed: 7607067 doi: 10.1242/dev.120.10.2723
Mendelsohn, C. et al. Function of the retinoic acid receptors (RARs) during development (II). Multiple abnormalities at various stages of organogenesis in RAR double mutants. Development 120, 2749–2771 (1994).
pubmed: 7607068 doi: 10.1242/dev.120.10.2749
Lohnes, D. et al. Function of retinoic acid receptor γ in the mouse. Cell 73, 643–658 (1993).
pubmed: 8388780 doi: 10.1016/0092-8674(93)90246-M
Deng, Q., Ramsköld, D., Reinius, B. & Sandberg, R. Single-cell RNA-seq reveals dynamic, random monoallelic gene expression in mammalian cells. Science 343, 193–196 (2014).
pubmed: 24408435 doi: 10.1126/science.1245316
Hogan, B., Beddington, R. & Costantini, F. (eds) Manipulating the Mouse Embryo: A Laboratory Manual (Cold Spring Harbor Laboratory Press, 1994).
Torres-Padilla, M. E. & Zernicka-Goetz, M. Role of TIF1α as a modulator of embryonic transcription in the mouse zygote. J. Cell Biol. 174, 329–338 (2006).
pubmed: 16880268 pmcid: 2064229 doi: 10.1083/jcb.200603146
Melsted, P. et al. Modular, efficient and constant-memory single-cell RNA-seq preprocessing. Nat. Biotechnol. https://doi.org/10.1038/s41587-021-00870-2 (2021).
Lun, A. T. L. et al. EmptyDrops: distinguishing cells from empty droplets in droplet-based single-cell RNA sequencing data. Genome Biol. 20, 63 (2019).
pubmed: 30902100 pmcid: 6431044 doi: 10.1186/s13059-019-1662-y
Wolf, F. A., Angerer, P. & Theis, F. J. SCANPY: large-scale single-cell gene expression data analysis. Genome Biol. 19, 15 (2018).
pubmed: 29409532 pmcid: 5802054 doi: 10.1186/s13059-017-1382-0
Lun, A. T. L., McCarthy, D. J. & Marioni, J. C. A step-by-step workflow for low-level analysis of single-cell RNA-seq data with Bioconductor. F1000Res. 5, 2122 (2016).
pubmed: 27909575 pmcid: 5112579
Haghverdi, L., Lun, A. T. L., Morgan, M. D. & Marioni, J. C. Batch effects in single-cell RNA-sequencing data are corrected by matching mutual nearest neighbors. Nat. Biotechnol. 36, 421–427 (2018).
pubmed: 29608177 pmcid: 6152897 doi: 10.1038/nbt.4091
McInnes, L., Healy, J. & Melville, J. UMAP: Uniform Manifold Approximation and Projection for dimension reduction. Preprint at https://arxiv.org/pdf/1802.03426.pdf (2018).
Haghverdi, L., Buettner, F. & Theis, F. J. Diffusion maps for high-dimensional single-cell analysis of differentiation data. Bioinformatics 31, 2989–2998 (2015).
pubmed: 26002886 doi: 10.1093/bioinformatics/btv325
La Manno, G. et al. RNA velocity of single cells. Nature 560, 494–498 (2018).
pubmed: 30089906 pmcid: 6130801 doi: 10.1038/s41586-018-0414-6
Dobin, A. et al. STAR: ultrafast universal RNA-seq aligner. Bioinformatics 29, 15–21 (2013).
pubmed: 23104886 doi: 10.1093/bioinformatics/bts635
Li, H. et al. The Sequence Alignment/Map format and SAMtools. Bioinformatics 25, 2078–2079 (2009).
pubmed: 19505943 pmcid: 2723002 doi: 10.1093/bioinformatics/btp352
Bergen, V., Lange, M., Peidli, S., Wolf, F. A. & Theis, F. J. Generalizing RNA velocity to transient cell states through dynamical modeling. Nat. Biotechnol. 38, 1408–1414 (2020).
pubmed: 32747759 doi: 10.1038/s41587-020-0591-3
Street, K. et al. Slingshot: cell lineage and pseudotime inference for single-cell transcriptomics. BMC Genomics 19, 477 (2018).
pubmed: 29914354 pmcid: 6007078 doi: 10.1186/s12864-018-4772-0
Angerer, P. et al. destiny: diffusion maps for large-scale single-cell data in R. Bioinformatics 32, 1241–1243 (2016).
pubmed: 26668002 doi: 10.1093/bioinformatics/btv715
Stuart, T. et al. Comprehensive integration of single-cell data. Cell 177, 1888–1902 (2019).
pubmed: 31178118 pmcid: 6687398 doi: 10.1016/j.cell.2019.05.031
Van den Berge, K. et al. Trajectory-based differential expression analysis for single-cell sequencing data. Nat. Commun. 11, 1201 (2020).
pubmed: 32139671 pmcid: 7058077 doi: 10.1038/s41467-020-14766-3
Park, S.-J. et al. Inferring the choreography of parental genomes during fertilization from ultralarge-scale whole-transcriptome analysis. Genes Dev. 27, 2736–2748 (2013).
pubmed: 24352427 pmcid: 3877761 doi: 10.1101/gad.227926.113

Auteurs

Ane Iturbide (A)

Institute of Epigenetics and Stem Cells (IES), Helmholtz Zentrum München, Munich, Germany.

Mayra L Ruiz Tejada Segura (ML)

Institute of Epigenetics and Stem Cells (IES), Helmholtz Zentrum München, Munich, Germany.
Institute of Functional Epigenetics (IFE), Helmholtz Zentrum München, Neuherberg, Germany.
Institute of Computational Biology (ICB), Helmholtz Zentrum München, Neuherberg, Germany.

Camille Noll (C)

Institute of Epigenetics and Stem Cells (IES), Helmholtz Zentrum München, Munich, Germany.

Kenji Schorpp (K)

Assay Development & Screening Platform, Institute of Molecular Toxicology & Pharmacology (TOXI), Helmholtz Zentrum München, Neuherberg, Germany.

Ina Rothenaigner (I)

Assay Development & Screening Platform, Institute of Molecular Toxicology & Pharmacology (TOXI), Helmholtz Zentrum München, Neuherberg, Germany.

Elias R Ruiz-Morales (ER)

Institute of Epigenetics and Stem Cells (IES), Helmholtz Zentrum München, Munich, Germany.
Wellcome Sanger Institute, Wellcome Genome Campus, Hinxton, Cambridge, UK.

Gabriele Lubatti (G)

Institute of Epigenetics and Stem Cells (IES), Helmholtz Zentrum München, Munich, Germany.
Institute of Functional Epigenetics (IFE), Helmholtz Zentrum München, Neuherberg, Germany.
Institute of Computational Biology (ICB), Helmholtz Zentrum München, Neuherberg, Germany.

Ahmed Agami (A)

Institute of Epigenetics and Stem Cells (IES), Helmholtz Zentrum München, Munich, Germany.

Kamyar Hadian (K)

Assay Development & Screening Platform, Institute of Molecular Toxicology & Pharmacology (TOXI), Helmholtz Zentrum München, Neuherberg, Germany.

Antonio Scialdone (A)

Institute of Epigenetics and Stem Cells (IES), Helmholtz Zentrum München, Munich, Germany.
Institute of Functional Epigenetics (IFE), Helmholtz Zentrum München, Neuherberg, Germany.
Institute of Computational Biology (ICB), Helmholtz Zentrum München, Neuherberg, Germany.

Maria-Elena Torres-Padilla (ME)

Institute of Epigenetics and Stem Cells (IES), Helmholtz Zentrum München, Munich, Germany. torres-padilla@helmholtz-muenchen.de.
Faculty of Biology, Ludwig-Maximilians Universität, Munich, Germany. torres-padilla@helmholtz-muenchen.de.

Articles similaires

Smoking Cessation and Incident Cardiovascular Disease.

Jun Hwan Cho, Seung Yong Shin, Hoseob Kim et al.
1.00
Humans Male Smoking Cessation Cardiovascular Diseases Female
Humans United States Aged Cross-Sectional Studies Medicare Part C
1.00
Humans Yoga Low Back Pain Female Male
Humans Meals Time Factors Female Adult

Classifications MeSH