Epigenetics and cell-fate in early mammalian development


Rodriguez-Terrones D, Gaume X, Ishiuchi T, Weiss A, Kopp A, Kruse K, Penning A, Vaquerizas JM, Brino L, Torres-Padilla ME. (2018) A molecular roadmap for the emergence of early-embryonic-like cells in culture, Nature Genetics, 50(1):106-119>


Jachowicz JW, Bing X, Pontabry J, Boskovic A, Rando OJ, Torres-Padilla ME, 2017, LINE-1 activation after fertilization regulates global chromatin accessibility in the early mouse embryo, Nature Genetics, 49, 1502-1510 doi: 10.1038/ng.3945

Izzo A, Ziegler-Birling C, Hill PWS, Brondani L, Hajkova P, Torres-Padilla ME, Schneider R (2017) Dynamic changes in H1 subtype composition during epigenetic reprogramming, Journal of Cell Biology, DOI: 10.1083/jcb.201611012.

Iturbide A and Torres-Padilla ME (2017) Starting embryonic transcription for the first time. Nature Genetics  49,820–821, doi:10.1038/ng.3880


Eid A, Rodriguez-Terrones D, Burton A, Torres-Padilla ME. 2016. SUV4-20 activity in the preimplantation mouse embryo controls timely replication. Genes and Development, doi: 10.1101/gad.288969.116

Burton A, Torres-Padilla ME. 2016. A Pluripotency Platform for Prdm14. Developmental Cell, 38(1): 3-5

Vaquerizas JM, Torres-Padilla ME. 2016. Developmental Biology: Panoramic views of the early epigenome. Nature doi:10.1038/nature19468

Eid A, Torres-Padilla ME. 2016. Characterization of non-canonical Polycomb Repressive Complex 1 subunits during early mouse embryogenesis. Epigenetics, 1-9

Borsos M, Torres-Padilla ME. 2016. Building up the nucleus: nuclear organization in the establishment of totipotency and pluripotency during mammalian development. Genes and Development 30(6): 611-621.


Ziegler-Birling C. Daujat S. Schneider R & Torres-Padilla ME. 2015. Dynamics of histone H3 acetylation in the nucleosome core during mouse pre-implantation development. Epigenetics, Oct 19:0

Ishiuchi T, Enriquez-Gasca R, Mizutani E, Bošković A, Ziegler-Birling C, RodriguezTerrones D, Wakayama T, Vaquerizas JM & Torres-Padilla ME. 2015. Early embryonic-like cells are induced by down-regulating replication-dependent chromatin assembly. Nature Structural & Molecular Biology,  9:662-71

Gaume X & Torres-Padilla ME. 2015. Regulation of reprogramming and cellular plasticity through histone exchange and histone variant incorporation. Cold Spring Harbor Symposia on Quantitative Biology, 2015 Nov 18.

Dang-Nguyen QT, & Torres-Padilla ME. 2015 How cells build totipotency and pluripotency: nuclear, chromatin and transcriptional architecture. Current Opinion in Cell Biology, Apr 30;34:9-15.

Jachowicz W, & Torres-Padilla ME. 2015. LINEs in mice: features, families and potential roles in early development.
Chromosoma, 2015 May 16


Burton A, & Torres-Padilla ME. 2014. Chromatin dynamics in the regulation of cell fate allocation during early embryogenesis.  Nature Reviews Molecular Cell Biology Nov;15(11):723-35.

Saksouk N. Barth TK. Ziegler-Birling C. Olova N. Nowak A. Rey E. Mateos-Langerak J. Urbach S. Reik W. Torres-Padilla ME. Imhof A. & Dejardin J. 2014. Redundant mechanisms to form silent chromatin at pericentromeric regions rely on BEND3 and DNA methylation. Molecular Cell, Nov 20;56(4):580-94.

Ishiuchi T. & Torres-Padilla ME. 2014. LINEing germ and embryonic stem cells' silencing of retrotransposons. Genes & Development, Jul 1;28(13):1381-3

Bošković A. Eid A. Pontabry J. Ishiuchi T. Spiegelhalter C. Ram EVSR. Meshorer E. & Torres-Padilla ME. 2014. Higher chromatin mobility supports totipotency and precedes pluripotency in vivo. Genes & Development, May 15; 28(10):1042-7.

Almouzni, Altucci, Amati, Ashley, Baulcome, Beaujean, Bock, Bongcam, Bousquet, Braun, Bressac, Bussemakers, Claerke, Conesa, Estivill, Fazeli, Grgurevic, Gut, Heijmans, Hermouet, Houwing, Iacobucci, Ilas, Kandimalla, Krauss, Lasko, Lehmann, Lindrot, Majdic, Marcotte, Martinelli, Martinet, Meyer, Miceli, Mills, Moreno, Morvan, Nickel, Niesler, Nowacki, Nowak, Ossowski, Pelizzola, Pochet, Potocnik, Radwanska, Raes, rattray, Robinson, Roelen, Sauer, Schinzer, Slagboom, Spector, Stunnenberg, Tiligada, Torres-Padilla ME, Tsonaka, Van Soom, Vidakovic, Widschwendter. 2014. Relationship between genome and epigenome— challenges and requirements for future research. BMC Genomics, 15:487.

Torres-Padilla ME & Chambers I. 2014. Transcription factor heterogeneity in pluripotent stem cells: a stochastic advantage. Development, 2014 Jun;141(11):2173-2181


Jachowicz J. Santenard A. Bender A. Muller J. & Torres-Padilla ME. 2013. Heterochromatin establishment at pericentromeres depends on nuclear position. Genes & Development, Nov 15; 27:2427-2432.

Burton A. Muller J. Tu S. Padilla-Longoria P. Guccione E. & Torres-Padilla ME. Single cell profiling of epigenetic modifiers identifies Prdm14 as an inducer of cell fate in the mammalian embryo. Cell Reports, Nov 14; 5 (3): 687–701.

Miyanari Y. Ziegler-Birling C & Torres-Padilla ME. 2013. Live visualization of chromatin dynamics using fluorescent TALEs. Nature Structural & Molecular Biology, 20(11):1321-4.

Bošković A. & Torres-Padilla ME. 2013. How mammals pack their sperm: a variant matter. Genes & Development, Aug 1; 27(15):1635-9.

Ishiuchi T. & Torres-Padilla ME. 2013. Towards an understanding of the regulatory mechanisms of totipotency. Current Opinion in Genetics & Development, Aug 10.

Lange U. Siebert S. Wossidlo M. Weiss T. Ziegler-Birling C. Walter J. Torres-Padilla ME. Daujat S. & Schneider R. 2013. Dissecting the role of H3K64me3 in mouse pericentromeric heterochromatin. Nature Communications, Aug 1;4:2233.

Fadloun A. Le Gras S. Jost B. Ziegler-Birling C. Takahashi H. Gorab E. Carninci P & TorresPadilla ME. Chromatin signatures and retrotransposon profiling in mouse embryos reveal regulation of LINE-1 by RNA. Nature Structural & Molecular Biology, 2013 Jan 27.

Torres-Padilla ME & Ciosk R. 2013. A germline-centric view of cell fate commitment, reprogramming and immortality Development, Feb;140(3):487-91

Torres-Padilla ME. 2013. Generating different epigenotypes. Reproductive BioMedicine Online, Aug 29.

Fadloun  A. Eid A. & Torres-Padilla ME. Mechanisms and dynamics of heterochromatin formation during mammalian development: closed paths and open questions. Current Topics in Developmental Biology,104:1-45.


Beck DB. Burton A. Oda H. Ziegler-Birling C. Torres-Padilla ME. Reinberg D. 2012. The role of PR-Set7 in replication licensing depends on Suv4-20h. Genes & Development, Dec 1;26(23):2580-9.

Bošković A. Bender A. Gall L. Ziegler-Birling C. Beaujean N. Torres-Padilla ME. 2012. Analysis of active chromatin modifications in early mammalian embryos reveals uncoupling of H2A.Z acetylation and H3K36 trimethylation from embryonic genome activation. Epigenetics, Jul;7(7):747-57. 

Talbert PB. Ahmad K. Almouzni G. Ausió J. Berger F. Bhalla PL. Bonner WM. Cande ZW. Chadwick BP. Chan SWL. Cross GAM. Cui L. Dimitrov SI. Doenecke D. Eirin-López JM. Gorovsky MA. Hake SB. Hamkalo BA. Holec S. Jacobsen SE. Kamieniarz K. Khochbin S. Ladurner AG. Landsman D. Latham JA. Loppin B. Malik HS. Marzluff WF. Pehrson JR. Postberg J. Singh MB. Schneider R. Smith MM. Thompson E. Torres-Padilla ME. Tremethick DJ. Turner BM. Waterborg JH. Wollmann H. Yelagandula R. Zhu B. Henikoff S.  2012. A Unified Phylogeny-based Nomenclature for Histone Variants. BMC Epigenetics and Chromatin, Jun 21;5:7.

Miyanari, Y. Torres-Padilla ME. 2012. Control of ground state pluripotency through allelic regulation of Nanog. Nature, 2012 Feb 12;483(7390):470-3.


Burton A. Torres-Padilla ME. 2010. Epigenetic Reprogramming and Development: A unique heterochromatin organisation in the preimplantation mouse embryo. Briefings in Functional Genomics, Dec;9(5-6):444-454.

Miyanari, Y. Torres-Padilla ME. 2010. Epigenetic regulation of reprogramming factors towards pluripotency in mouse preimplantation development. Current Opinion in Endocrinology, Diabetes and Obesity, Dec;17(6):500-6.

Santenard A. Ziegler-Birling C. Koch M. Tora L. Bannister AJ. Torres-Padilla ME. 2010. Heterochromatin formation in the mouse embryo requires critical residues of the histone variant H3.3. Nature Cell Biology, 12(9):853-62.


Gazdag E. Santenard A. Ziegler-Birling C. Altobelli G. Poch O. Tora L Torres-Padilla ME 2009. TBP2 is essential for germ cell development by regulating transcription and chromatin condensation in the oocyte. Genes and Development, 23(18):2210-23

Daujat S, Weiss T, Mohn F, Lange U. C, Ziegler-Birling C, Zeissler U, Lappe M, Schübeler D, Torres-Padilla ME, Schneider R. 2009. H3K64 trimethylation marks heterochromatin and is dynamically remodeled during developmental reprogramming. Nature Structural Molecular Biology 16(7):777-81.

Oda H. Okamoto I. Murphy N. Chu J. Shen M. Torres-Padilla ME. Heard E. and Reinberg D. 2009. Monomethylation of Histone H4-Lysine 20 is involved in Chromosome Structure and Stability and is essential for Mouse Development. Molecular and Cellular Biology. 29(8): 2278-2295.

Ziegler-Birling C. Helmrich Tora L. Torres-Padilla ME. 2009. Distribution of p53 binding protein 1 (53BP1) and phosphorylated H2A.X during mouse preimplantation development in the absence of DNA damage. International Journal of Developmental Biology. 53(7):1003-11.

Santenard A. Torres-Padilla ME. 2009. Epigenetic reprogramming in mammalian reproduction: contribution from histone variants. Epigenetics 4(2) :80-84


Soares ML, Torres-Padilla ME and Zernicka-Goetz M. BMP4 signaling regulates development of the anterior visceral endoderm in the mouse embryo. Development Growth and Differentiation . 50(7):615-21.

Torres-Padilla ME. 2008. Cell identity in the preimplantation mammalian embryo : an epigenetic perspective from the mouse. Human Reproduction. (6):1246-52

Eberlin A. Grauffel C. Oulad-Abdelghani M. Robert F. Torres-Padilla ME. Lambrot R. Spehner D. Ponce-Perez L. Würtz JM. Stote RH. Kimmins S. Schultz P. Dejaegere A. and Tora L. 2008. Histone H3 tails containing dimethylated lysine and adjacent phosphorylated serine modifications adopt a specific conformation during mitosis and meiosis. Molecular and Cellular Biology. 2008 (5):1739-54


Torres-Padilla ME. and Tora L. 2007. TBP homologues in embryo transcription : who does what? EMBO Reports, 8(11):1016-8.

Gazdag E. Rajkovic A. Torres-Padilla ME. and Tora L. 2007. Analysis of TBP2 (TRF3) and TBP expression suggests different roles for the two proteins in regulation of gene expression during oogenesis and early mouse development.
Reproduction, 134(1) :51-62.

Torres-Padilla ME. Richardson L. Kolasinska P. Meilhac S. Luetke-Evelsoh M. and Zernicka-Goetz M. 2007. The anterior visceral endoderm of the mouse embryo is established from both preimplantation precursors and by de novo gene expression after implantation. Developmental Biology. 309(1) : 97-112.

Torres-Padilla ME. Parfitt D.E. Kouzarides T. and Zernicka-Goetz M. 2007. Histone arginine methylation regulates pluripotency in the early mouse embryo. Nature, 445 (7124) :214-218

Na J. Lykke-Andersen K. Torres-Padilla ME. and Zernicka-Goetz M. 2007. Dishevelled proteins regulate cell adhesion in mouse blastocyst and serve to monitor changes in Wnt signaling. Developmental Biology, 302 (1) :40-49.


Torres-Padilla ME. and Zernicka-Goetz M. 2006. Role of TIF1 α as a modulator of embryonic transcription in the mouse zygote. Journal of Cell Biology, 174 (3) : 329-338.

Torres-Padilla ME. Bannister A.J. Hurd P.J. Kouzarides T. and Zernicka-Goetz M. 2006. Dynamic distribution of the replacement histone variant H3.3 in the mouse oocyte and preimplantation embryos. International Journal of Developmental Biology, 50 (5) :455-461.

Richardson L. Torres-Padilla ME and Zernicka-Goetz M. 2006. Regionalisation of the extraembryonic ectoderm at the early egg cylinder stage controls distal visceral endoderm cells distribution in the mouse. Mechanisms of Development. 123(4) : 288-296.


Soares, ML. Haraguchi S. Torres-Padilla ME. Kalmar T. Carpenter L. Bell G. Morrison A. Ring CJ. Clarke NJ. Glover DM and Zernicka-Goetz M. 2005. Functional studies of signaling pathways in peri-implantation development of the mouse embryo by RNAi. BMC Developmental Biology. 5(1) : 28.



Torres-Padilla ME. Sladek FM. and Weiss MC. 2002. Developmentally regulated N-terminal variants of the nuclear receptor HNF4 α mediate multiple interactions through coactivator and corepressor/HDAC complexes. Journal of Biological Chemistry 277 (47): 44677-44687.


Bailly A. Torres-Padilla ME. Tinel AP and Weiss MC. 2001. An enhancer element 6 kb upstream of the mouse HNF4 α1 promoter is activated by glucocorticoids and liver-enriched transcription factors. Nucleic Acids Research 29: 3495-3505.

Torres-Padilla ME. Fougère-Deschatrette C. and Weiss MC. 2001. Expression of HNF4 α isoforms in mouse liver development is regulated by sequential promoter usage and constitutive 3' end splicing. Mechanisms of Development 109 (2):183-193.


Garcia-Sainz JA. Torres-Padilla ME. 1999. Modulation of basal intracellular calcium by inverse agonists and phorbol myristate acetate in rat-1 fibroblasts stably expressing alpha1dadrenoceptors. FEBS Letters 443(3):277-81.

Medina LC. Vazquez-Prado J. Torres-Padilla ME. Mendoza-Mendoza A. Cruz Munoz ME. Garcia-Sainz JA. 1998. Crosstalk: phosphorylation of alpha1b-adrenoceptors induced through activation of bradykinin B2 receptors. FEBS Letters 422(2):141 -5.

Torres-Padilla ME. Carrero JC. Ortiz-Ortiz L. 1997. A 148-kDa secretory proteinase from Entamoeba histolytica. Archives of Medical Research 28 Spec No:186-7.