Gómez-Skarmeta Laboratory

Publications

Selected papers from the last 5 years

1. Active DNA demethylation during the vertebrate phylotypic period.

Bogdanovic´ O, Smits AH, de la Calle Mustienes E, Tena JJ, Ford E, Williams R, Senanayake U, Schultz MD, Hontelez S, van  Kruijsbergen I, Rayon T, Gnerlich F, Carell T, Veenstra JGC, Manzanares M, Sauka-Spengler T, Ecker JR, Vermeulen, Gómez-Skarmeta JL, Lister R.

Nature Genetics. 2016

doi: 10.1038/ng.3522

http://www.nature.com/ng/journal/vaop/ncurrent/full/ng.3522.html

2. A single 3D chromatin compartment in amphioxus reveals stepwise evolution of vertebrate Hox bimodal regulation.

Acemel RD, Tena JJ, Irastorza I, Marlétaz F, Gómez-Marín C, de la Calle-Mustienes E, Bertrand S, Diaz S, Aldea D, Aury J-M, Mangenot S, Holland PWH, Devos DP, Maeso I, Escrivá H, Gómez-Skarmeta JL.

Nature Genetics, 48,336-341 (2016).

http://www.nature.com/ng/journal/v48/n3/full/ng.3497.html

3. Evolutionary comparison reveals that diverging CTCF sites are signatures of ancestral topological associating domains borders.

Gómez-Marín C, Tena JJ, Acemel RD, López-Mayorga M, Naranjo S, de la Calle-Mustienes E, Maeso I, Beccari L, Aneas I, Vielmas E, Bovolenta P, Nobrega MA, Carvajal J, Gómez-Skarmeta JL.

PNAS, 112, 7542-7548 (2015).

http://www.pnas.org/content/112/24/7542.long

4. TEAD and YAP regulate the enhancer network of human embryonic pancreatic progenitors.

Cebola I, Rodríguez-Seguí SA, Cho CH, Bessa J, Rovira M, Luengo M, Chhatriwala M, Berry A, Ponsa-Cobas J, Maestro MA, Jennings RE, Pasquali L, Morán I, Castro N, Hanley NA, Gómez-Skarmeta JL, Vallier L, Ferrer J.

Nat Cell Biol. 7, 615-626 (2015).

http://www.nature.com/ncb/journal/v17/n5/full/ncb3160.html

5. Comparative epigenomics in distantly related teleost species identifies conserved cis-regulatory nodes active during the vertebrate phylotypic period.

Tena JJ, González-Aguilera C, Fernández-Miñán A, Vázquez-Marín J, Parra-Acero H, Cross JW, Rigby PW, Carvajal JJ, Wittbrodt J , Gómez-Skarmeta JL, Martínez-Morales JR.

Genome Res. 2014 Jul;24(7):1075-85.

http://genome.cshlp.org/content/24/7/1075.long

6. Obesity-associated variants within FTO form long-range functional connections with IRX3.

S. Smemo, J. J. Tena, K-H. Kim, E. R. Gamazon, N. J. Sakabe, C. Gómez-Marín, I. Aneas, F. L. Credidio, D. R. Sobreira, N. F. Wasserman, J. H. Lee, V. Puviindran, D. Tam, M. Shen, J. E. Son, N. A. Vakili, H-K. Sung, S. Naranjo, R.D. Acemel, M. Manzanares, A. Nagy, N. J. Cox, C-C. Hui, J. L. Gomez-Skarmeta and M. A. Nóbrega.

Nature 507, 371-5 (2014).

http://www.nature.com/nature/journal/v507/n7492/full/nature13138.html

7. Early evolution of the T-box transcription factor family.

A. Sebé-Pedrós, A. Ariza-Cosano, M.T. Weirauch, S. Leininger, A. Yang, G. Torruella, M. Adamski, M. Adamska, T. R. Hughes, J. L. Gómez-Skarmeta and I. Ruiz-Trillo.

PNAS 110, 16050-16055 (2013).

http://www.pnas.org/content/110/40/16050.long

8. A mobile insulator system to detect and disrupt cis-regulatory landscapes in vertebrates.

J. Bessa, M. Luengo, S. Rivero-Gil, A. Ariza-Cosano, A. H. F. Maia, F. J. Ruiz-Ruano, P. Caballero, S. Naranjo, J. J. Carvajal and J. L. Gómez-Skarmeta.

Genome Research 24, 487-95 (2014).

http://genome.cshlp.org/content/24/3/487.long

9. Hoxd13 contribution to the evolution of vertebrate appendages.

R. Freitas, C. Gómez-Marin., J. Mark Wilson, F. Casares and J. L. Gómez-Skarmeta.

Dev. Cell 23, 1219-1229 (2012).

http://www.sciencedirect.com/science/article/pii/S1534580712004789

10. An ancient genomic regulatory block conserved across bilaterians and its dismantling in tetrapods by retrogene replacement.

S. I. Maeso, M. Irimia, J. Tena, E. González-Pérez, D. Tran, V. Ravi, B. Venkatesh, S. Campuzano, J. L. Gómez-Skarmeta and J.Garcia-Fernàndez.

Genome Res. 22, 642-655 (2012).

http://genome.cshlp.org/content/22/4/642.long

11. Dynamics of enhancer chromatin signatures mark the transition from pluripotency to cell specification during embryogenesis.

O. Bogdanovic, A. Fernández Miñán, J. J. Tena, E. de la Calle-Mustienes , C. Hidalgo, I. van Kruysbergen, S. J. van Heeringen, G. J. Veenstra and J. L. Gómez-Skarmeta.

Genome Res. 22, 2043-2053 (2012).

http://genome.cshlp.org/content/22/10/2043.long

12. The osr1 and osr2 genes act in the pronephric anlage downstream of retinoic acid signaling and upstream of wnt2b to maintain pectoral fin development.

A. Neto, N. Mercader and J. L. Gómez-Skarmeta.

Development 139, 301-311 (2012).

http://dev.biologists.org/content/139/2/301.long

13. Genome-wide CTCF distribution in vertebrates defines equivalent sites that aid the identification of disease-associated genes.

D. Martin, C. Pantoja, A. Fernández Miñán, C. Valdes-Quezada, E. Moltó, F. Matesanz, O. Bogdanovic, E. de la Calle-Mustienes, O. Domínguez, L. Taher, M. Furlan-Magaril, A. Alcina, S. Cañón, M. Fedetz, M. A Blasco, P. S. Pereira, I. Ovcharenko, F. Recillas-Targa, L. Montoliu, M. Manzanares, R. Guigó, M. Serrano, F. Casares, J. L. Gómez-Skarmeta.

Nat. Struct. Mol. Biol. 6, 708-714 (2011).

http://www.nature.com/nsmb/journal/v18/n6/full/nsmb.2059.html

14. An evolutionarily conserved three-dimensional structure in the vertebrate Irx clusters facilitates enhancer sharing and co-regulation.

J. J. Tena, M. E. Alonso, E. de la Calle-Mustienes, E. Splinter, W. de Laat, M. Manzanares, J. L. Gómez-Skarmeta.

Nat. Commun. 2, 310 (2011).

http://www.nature.com/ncomms/journal/v2/n5/full/ncomms1301.html

15. Trans-phyletic conservation of developmental regulatory state in animal evolution.

J. L. Royo, I. Maeso, M. Irimia, F. Gao, I. S. Peter, C. Lopes, S. D'Aniello, F. Casares, E. H. Davidson, J.Garcia-Fernández and J. L. Gómez-Skarmeta.

PNAS 108, 14186-14191 (2011).

http://www.pnas.org/content/108/34/14186.long