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Research
General Information
ZIRC
ZFIN ID: ZDB-LAB-110304-2
Skarmeta Lab
PI/Director: Gómez-Skarmeta, José Luis
Contact Person: Gómez-Skarmeta, José Luis
Email: jlgomska@upo.es
URL: http://www.cabd.es/
Address: Centro Andaluz de Biología del Desarrollo CSIC/ Universidad Pablo de Olavide Carretera de Utrera Km1 41013 Sevilla Spain
Country: Spain
Phone: 34-954348948
Fax: 4-954349376
Line Designation: upo


GENOMIC FEATURES ORIGINATING FROM THIS LAB
Show first 50 of 333 genomic features


STATEMENT OF RESEARCH INTERESTS


LAB MEMBERS
Bessa, Jose Post-Doc Freitas, Renata Post-Doc Miñan, Ana Fernández Post-Doc
Naranjo, Silvia Post-Doc Royo, Jose Luis Post-Doc Tena, Juan Post-Doc
de la Calle-Mustienes, Elisa Technical Staff Ariza, Ana Gómez, Carlos
Luengo, Mario Neto, Ana


ZEBRAFISH PUBLICATIONS OF LAB MEMBERS x
Santos-Pereira, J.M., Gallardo-Fuentes, L., Neto, A., Acemel, R.D., Tena, J.J. (2019) Pioneer and repressive functions of p63 during zebrafish embryonic ectoderm specification. Nature communications. 10:3049
Vázquez-Marín, J., Gutiérrez-Triana, J.A., Almuedo-Castillo, M., Buono, L., Gómez-Skarmeta, J.L., Mateo, J.L., Wittbrodt, J., Martínez-Morales, J.R. (2019) Yap1b, a divergent Yap/Taz family member, cooperates with yap1 in survival and morphogenesis via common transcriptional targets. Development (Cambridge, England). 146(13):
Caro, C., Egea-Benavente, D., Polvillo, R., Royo, J.L., Pernia Leal, M., García-Martín, M.L. (2019) Comprehensive Toxicity Assessment of PEGylated Magnetic Nanoparticles for in vivo applications. Colloids and surfaces. B, Biointerfaces. 177:253-259
Marlétaz, F., Firbas, P.N., Maeso, I., Tena, J.J., Bogdanovic, O., Perry, M., Wyatt, C.D.R., de la Calle-Mustienes, E., Bertrand, S., Burguera, D., Acemel, R.D., van Heeringen, S.J., Naranjo, S., Herrera-Ubeda, C., Skvortsova, K., Jimenez-Gancedo, S., Aldea, D., Marquez, Y., Buono, L., Kozmikova, I., Permanyer, J., Louis, A., Albuixech-Crespo, B., Le Petillon, Y., Leon, A., Subirana, L., Balwierz, P.J., Duckett, P.E., Farahani, E., Aury, J.M., Mangenot, S., Wincker, P., Albalat, R., Benito-Gutiérrez, È., Cañestro, C., Castro, F., D'Aniello, S., Ferrier, D.E.K., Huang, S., Laudet, V., Marais, G.A.B., Pontarotti, P., Schubert, M., Seitz, H., Somorjai, I., Takahashi, T., Mirabeau, O., Xu, A., Yu, J.K., Carninci, P., Martinez-Morales, J.R., Crollius, H.R., Kozmik, Z., Weirauch, M.T., Garcia-Fernàndez, J., Lister, R., Lenhard, B., Holland, P.W.H., Escriva, H., Gómez-Skarmeta, J.L., Irimia, M. (2018) Amphioxus functional genomics and the origins of vertebrate gene regulation. Nature. 564:64-70
Letelier, J., Terriente, J., Belzunce, I., Voltes, A., Undurraga, C.A., Polvillo, R., Devos, L., Tena, J.J., Maeso, I., Retaux, S., Gomez-Skarmeta, J.L., Martínez-Morales, J.R., Pujades, C. (2018) Evolutionary emergence of the rac3b/rfng/sgca regulatory cluster refined mechanisms for hindbrain boundaries formation.. Proceedings of the National Academy of Sciences of the United States of America. 115(16):E3731-E3740
Letelier, J., de la Calle-Mustienes, E., Pieretti, J., Naranjo, S., Maeso, I., Nakamura, T., Pascual-Anaya, J., Shubin, N.H., Schneider, I., Martinez-Morales, J.R., Gómez-Skarmeta, J.L. (2018) A conserved Shh cis-regulatory module highlights a common developmental origin of unpaired and paired fins. Nature Genetics. 50(4):504-509
Royo, J.L., Valls, J., Acemel, R.D., Gómez-Marin, C., Pascual-Pons, M., Lupiañez, A., Gomez-Skarmeta, J.L., Fibla, J. (2018) A common copy-number variant within SIRPB1 correlates with human Out-of-Africa migration after genetic drift correction. PLoS One. 13:e0193614
Seixas, A.I., Loureiro, J.R., Costa, C., Ordóñez-Ugalde, A., Marcelino, H., Oliveira, C.L., Loureiro, J.L., Dhingra, A., Brandão, E., Cruz, V.T., Timóteo, A., Quintáns, B., Rouleau, G.A., Rizzu, P., Carracedo, Á., Bessa, J., Heutink, P., Sequeiros, J., Sobrido, M.J., Coutinho, P., Silveira, I. (2017) A Pentanucleotide ATTTC Repeat Insertion in the Non-coding Region of DAB1, Mapping to SCA37, Causes Spinocerebellar Ataxia. American journal of human genetics. 101:87-103
Bogdanović, O., Smits, A.H., de la Calle Mustienes, E., Tena, J.J., Ford, E., Williams, R., Senanayake, U., Schultz, M.D., Hontelez, S., van Kruijsbergen, I., Rayon, T., Gnerlich, F., Carell, T., Veenstra, G.J., Manzanares, M., Sauka-Spengler, T., Ecker, J.R., Vermeulen, M., Gómez-Skarmeta, J.L., Lister, R. (2016) Active DNA demethylation at enhancers during the vertebrate phylotypic period. Nature Genetics. 48(4):417-26
Fernández-Miñán, A., Bessa, J., Tena, J.J., Gómez-Skarmeta, J.L. (2016) Assay for transposase-accessible chromatin and circularized chromosome conformation capture, two methods to explore the regulatory landscapes of genes in zebrafish. Methods in cell biology. 135:413-30
de la Calle Mustienes, E., Gómez-Skarmeta, J.L., Bogdanović, O. (2015) Genome-wide epigenetic cross-talk between DNA methylation and H3K27me3 in zebrafish embryos. Genomics Data. 6:7-9
Gómez-Marín, C., Tena, J.J., Acemel, R.D., López-Mayorga, M., Naranjo, S., de la Calle-Mustienes, E., Maeso, I., Beccari, L., Aneas, I., Vielmas, E., Bovolenta, P., Nobrega, M.A., Carvajal, J., Gómez-Skarmeta, J.L. (2015) Evolutionary comparison reveals that diverging CTCF sites are signatures of ancestral topological associating domains borders. Proceedings of the National Academy of Sciences of the United States of America. 112(24):7542-7
Gago-Rodrigues, I., Fernández-Miñán, A., Letelier, J., Naranjo, S., Tena, J.J., Gómez-Skarmeta, J.L., Martinez-Morales, J.R. (2015) Analysis of opo cis-regulatory landscape uncovers Vsx2 requirement in early eye morphogenesis. Nature communications. 6:7054
Cebola, I., Rodríguez-Seguí, S.A., Cho, C.H., Bessa, J., Rovira, M., Luengo, M., Chhatriwala, M., Berry, A., Ponsa-Cobas, J., Maestro, M.A., Jennings, R.E., Pasquali, L., Morán, I., Castro, N., Hanley, N.A., Gomez-Skarmeta, J.L., Vallier, L., Ferrer, J. (2015) TEAD and YAP regulate the enhancer network of human embryonic pancreatic progenitors. Nature cell biology. 17:615-26
Gehrke, A.R., Schneider, I., de la Calle-Mustienes, E., Tena, J.J., Gomez-Marin, C., Chandran, M., Nakamura, T., Braasch, I., Postlethwait, J.H., Gómez-Skarmeta, J.L., Shubin, N.H. (2015) Deep conservation of wrist and digit enhancers in fish. Proceedings of the National Academy of Sciences of the United States of America. 112(3):803-8
Ariza-Cosano, A., Bensimon-Brito, A., Gómez-Skarmeta, J.L., Bessa, J. (2015) sox21a directs lateral line patterning by modulating FGF signaling. Developmental Neurobiology. 75(1):80-92
Laplana, M., Royo, J.L., García, L.F., Aluja, A., Gomez-Skarmeta, J.L., Fibla, J. (2014) SIRPB1 Copy-Number Polymorphism as Candidate Quantitative Trait Locus for Impulsive-Disinhibited Personality. Genes, brain, and behavior. 13(7):653-62
Tena, J.J., González-Aguilera, C., Fernández-Miñán, A., Vázquez-Marín, J., Parra-Acero, H., Cross, J.W., Rigby, P.W., Carvajal, J.J., Wittbrodt, J., Gómez-Skarmeta, J.L., Martinez-Morales, J.R. (2014) Comparative epigenomics in distantly related teleost species identifies conserved cis-regulatory nodes active during the vertebrate phylotypic period. Genome research. 24(7):1075-85
Spieler, D., Kaffe, M., Knauf, F., Bessa, J., Tena, J.J., Giesert, F., Schormair, B., Tilch, E., Lee, H., Horsch, M., Czamara, D., Karbalai, N., von Toerne, C., Waldenberger, M., Gieger, C., Lichtner, P., Claussnitzer, M., Naumann, R., Müller-Myhsok, B., Torres, M., Garrett, L., Rozman, J., Klingenspor, M., Gailus-Durner, V., Fuchs, H., Hrabě de Angelis, M., Beckers, J., Holter, S.M., Meitinger, T., Hauck, S.M., Laumen, H., Wurst, W., Casares, F., Gómez-Skarmeta, J.L., Winkelmann, J. (2014) Restless legs syndrome-associated intronic common variant in Meis1 alters enhancer function in the developing telencephalon. Genome research. 24:592-603
Smemo, S., Tena, J.J., Kim, K.H., Gamazon, E.R., Sakabe, N.J., Gómez-Marín, C., Aneas, I., Credidio, F.L., Sobreira, D.R., Wasserman, N.F., Lee, J.H., Puviindran, V., Tam, D., Shen, M., Son, J.E., Vakili, N.A., Sung, H.K., Naranjo, S., Acemel, R.D., Manzanares, M., Nagy, A., Cox, N.J., Hui, C.C., Gómez-Skarmeta, J.L., Nóbrega, M.A. (2014) Obesity-associated variants within FTO form long-range functional connections with IRX3. Nature. 507:371-5
Bessa, J., Luengo, M., Rivero-Gil, S., Ariza-Cosano, A., Maia, A.H., Ruiz-Ruano, F.J., Caballero, P., Naranjo, S., Carvajal, J.J., and Gómez-Skarmeta, J.L. (2014) A mobile insulator system to detect and disrupt cis-regulatory landscapes in vertebrates. Genome research. 24(3):487-95
Bogdanovic, O., and Gómez-Skarmeta, J.L. (2014) Embryonic DNA methylation: insights from the genomics era. Briefings in Functional Genomics. 13(2):121-30
Regadas, I., Matos, M.R., Monteiro, F.A., Gomez-Skarmeta, J.L., Lima, D., Bessa, J., Casares, F., and Reguenga, C. (2013) Several Cis-regulatory Elements Control mRNA Stability, Translation Efficiency, and Expression Pattern of Prrxl1 (Paired Related Homeobox Protein-like 1). The Journal of biological chemistry. 288(51):36285-301
Peralta, M., Steed, E., Harlepp, S., González-Rosa, J.M., Monduc, F., Ariza-Cosano, A., Cortés, A., Rayón, T., Gómez-Skarmeta, J.L., Zapata, A., Vermot, J., and Mercader, N. (2013) Heartbeat-Driven Pericardiac Fluid Forces Contribute to Epicardium Morphogenesis. Current biology : CB. 23(18):1726-35
Bogdanovic, O., Fernández-Miñán, A., Tena, J.J., de la Calle-Mustienes, E., and Gómez-Skarmeta, J.L. (2013) The developmental epigenomics toolbox: ChIP-seq and MethylCap-seq profiling of early zebrafish embryos. Methods (San Diego, Calif.). 62(3):207-15
Medina, C., and Royo, J.L. (2013) Zebrafish as a model organism to study host-pathogen interactions. Methods (San Diego, Calif.). 62(3):241-5
Ariza-Cosano, A., Visel, A., Pennacchio, L.A., Fraser, H.B., Gómez-Skarmeta, J.L., Irimia, M., and Bessa, J. (2012) Differences in enhancer activity in mouse and zebrafish reporter assays are often associated with changes in gene expression. BMC Genomics. 13(1):713
Freitas, R., Gómez-Marín, C., Wilson, J.M., Casares, F., and Gómez-Skarmeta, J.L. (2012) Hoxd13 contribution to the evolution of vertebrate appendages. Developmental Cell. 23(6):1219-1229
Irimia, M., Tena, J.J., Alexis, M., Fernandez-Miñan, A., Maeso, I., Bogdanovic, O., de la Calle-Mustienes, E., Roy, S.W., Gómez-Skarmeta, J.L., and Fraser, H.B. (2012) Extensive conservation of ancient microsynteny across metazoans due to cis-regulatory constraints. Genome research. 22(12):2356-2367
Bogdanovic, O., Fernandez-Minan, A., Tena, J.J., de Lacalle-Mustienes, E., Hidalgo, C., van Kruysbergen, I., van Heeringen, S.J., Veenstra, G.J., and Gomez-Skarmeta, J.L. (2012) Dynamics of enhancer chromatin signatures mark the transition from pluripotency to cell specification during embryogenesis. Genome research. 22(10):2043-2053
Tiana, M., Villar, D., Pérez-Guijarro, E., Gómez-Maldonado, L., Moltó, E., Fernández-Miñán, A., Gómez-Skarmeta, J.L., Montoliu, L., and Del Peso, L. (2012) A role for insulator elements in the regulation of gene expression response to hypoxia. Nucleic acids research. 40(5):1916-1927
Medina, C., Santero, E., Gómez-Skarmeta, J.L., and Royo, J.L. (2012) Engineered Salmonella allows real-time heterologous gene expression monitoring within infected zebrafish embryos. Journal of Biotechnology. 157(3):413-416
Irimia, M., Royo, J.L., Burguera, D., Maeso, I., Gómez-Skarmeta, J.L., and Garcia-Fernandez, J. (2012) Comparative genomics of the Hedgehog loci in chordates and the origins of Shh regulatory novelties. Scientific Reports. 2:433
Neto, A., Mercader, N., and Gómez-Skarmeta, J.L. (2012) The osr1 and osr2 genes act in the pronephric anlage downstream of retinoic acid signaling and upstream of wnt2b to maintain pectoral fin development. Development (Cambridge, England). 139(2):301-11
Royo, J.L., Bessa, J., Hidalgo, C., Fernández-Miñán, A., Tena, J.J., Roncero, Y., Gómez-Skarmeta, J.L., and Casares, F. (2012) Identification and Analysis of Conserved cis-Regulatory Regions of the MEIS1 Gene. PLoS One. 7(3):e33617
Royo, J.L., Hidalgo, C., Roncero, Y., Seda, M.A., Akalin, A., Lenhard, B., Casares, F., and Gómez-Skarmeta, J.L. (2011) Dissecting the transcriptional regulatory properties of human chromosome 16 highly conserved non-coding regions. PLoS One. 6(9):e24824
Tena, J.J., Alonso, M.E., de la Calle-Mustienes, E., Splinter, E., de Laat, W., Manzanares, M., and Gómez-Skarmeta, J.L. (2011) An evolutionarily conserved three-dimensional structure in the vertebrate Irx clusters facilitates enhancer sharing and coregulation. Nature communications. 2:310
Robert-Moreno, A., Naranjo, S., de la Calle-Mustienes, E., Gomez-Skarmeta, J.L., and Alsina, B. (2010) Characterization of new otic enhancers of the pou3f4 gene reveal distinct signaling pathway regulation and spatio-temporal patterns. PLoS One. 5(12):e15907
Naranjo, S., Voesenek, K., de la Calle-Mustienes, E., Robert-Moreno, A., Kokotas, H., Grigoriadou, M., Economides, J., Van Camp, G., Hilgert, N., Moreno, F., Alsina, B., Petersen, M.B., Kremer, H., and Gómez-Skarmeta, J.L. (2010) Multiple enhancers located in a 1-Mb region upstream of POU3F4 promote expression during inner ear development and may be required for hearing. Human genetics. 128(4):411-419
Bessa, J., Tena, J.J., de la Calle-Mustienes, E., Fernández-Miñán, A., Naranjo, S., Fernández, A., Montoliu, L., Akalin, A., Lenhard, B., Casares, F., and Gómez-Skarmeta, J.L. (2009) Zebrafish enhancer detection (ZED) vector: A new tool to facilitate transgenesis and the functional analysis of cis-regulatory regions in zebrafish. Developmental dynamics : an official publication of the American Association of Anatomists. 238(9):2409-2417
Feijoo, C.G., Saldias, M.P., De la Paz, J.F., Gómez-Skarmeta, J.L., and Allende, M.L. (2009) Formation of posterior cranial placode derivatives requires the Iroquois transcription factor irx4a. Molecular and cellular neurosciences. 40(3):328-337
Freitas, R., Zhang, G., and Cohn, M.J. (2007) Biphasic Hoxd gene expression in shark paired fins reveals an ancient origin of the distal limb domain. PLoS One. 2(1):e754
Tena, J.J., Neto, A., de la Calle-Mustienes, E., Bras-Pereira, C., Casares, F., and Gomez-Skarmeta, J.L. (2007) Odd-skipped genes encode repressors that control kidney development. Developmental Biology. 301(2):518-531
de la Calle-Mustienes, E., Feijoo, C.G., Manzanares, M., Tena, J.J., Rodriguez-Seguel, E., Leticia, A., Allende, M.L., and Gomez-Skarmeta, J.L. (2005) A functional survey of the enhancer activity of conserved non-coding sequences from vertebrate Iroquois cluster gene deserts. Genome research. 15(8):1061-1072
Feijoo, C.G., Manzanares, M., De La Calle-Mustienes, E., Gómez-Skarmeta, J.L., and Allende, M.L. (2004) The Irx gene family in zebrafish: genomic structure, evolution and initial characterization of irx5b. Development genes and evolution. 214(6):277-284