Evolution of regulatory landscapes at multiple timescales

Project Information

Evoland

Grant agreement ID: 740041

DOI 10.3030/740041

Project closed

EC signature date 20 July 2017

Start date 1 September 2017

End date 31 August 2021

Funded under

• EXCELLENT SCIENCE - European Research Council (ERC)

Total cost € 1 928 091,19

EU contribution € 1 928 091,19

Coordinated by

AGENCIA ESTATAL CONSEJO SUPERIOR DE INVESTIGACIONES CIENTIFICAS
Spain

Publications

Peer reviewed articles (14)

Epigenomic profiling of primate lymphoblastoid cell lines reveals the evolutionary patterns of epigenetic activities in gene regulatory architectures

Author(s): Raquel García-Pérez, Paula Esteller-Cucala, Glòria Mas, Irene Lobón, Valerio Di Carlo, Meritxell Riera, Martin Kuhlwilm, Arcadi Navarro, Antoine Blancher, Luciano Di Croce, José Luis Gómez-Skarmeta, David Juan, Tomàs Marquès-Bonet
Published in: Nature Communications, Issue 12/1, 2021, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-021-23397-1

Functional Conservation of Divergent p63-Bound cis-Regulatory Elements

Author(s): Lourdes Gallardo-Fuentes, José M. Santos-Pereira, Juan J. Tena
Published in: Frontiers in Genetics, Issue 11, 2020, ISSN 1664-8021
Publisher: Frontiers Media
DOI: 10.3389/fgene.2020.00339

Ancient Genomic Regulatory Blocks Are a Source for Regulatory Gene Deserts in Vertebrates after Whole-Genome Duplications

Author(s): María Touceda-Suárez, Elizabeth M Kita, Rafael D Acemel, Panos N Firbas, Marta S Magri, Silvia Naranjo, Juan J Tena, Jose Luis Gómez-Skarmeta, Ignacio Maeso, Manuel Irimia
Published in: Molecular Biology and Evolution, Issue 37/10, 2020, Page(s) 2857-2864, ISSN 0737-4038
Publisher: Oxford University Press
DOI: 10.1093/molbev/msaa123

An evolutionary perspective of regulatory landscape dynamics in development and disease

Author(s): Martin Franke, José Luis Gómez-Skarmeta
Published in: Current Opinion in Cell Biology, Issue 55, 2018, Page(s) 24-29, ISSN 0955-0674
Publisher: Elsevier BV
DOI: 10.1016/j.ceb.2018.06.009

Amphioxus functional genomics and the origins of vertebrate gene regulation

Author(s): Ferdinand Marlétaz, Panos N. Firbas, Ignacio Maeso, Juan J. Tena, Ozren Bogdanovic, Malcolm Perry, Christopher D. R. Wyatt, Elisa de la Calle-Mustienes, Stephanie Bertrand, Demian Burguera, Rafael D. Acemel, Simon J. van Heeringen, Silvia Naranjo, Carlos Herrera-Ubeda, Ksenia Skvortsova, Sandra Jimenez-Gancedo, Daniel Aldea, Yamile Marquez, Lorena Buono, Iryna Kozmikova, Jon Permanyer, Alexandra
Published in: Nature, Issue 564/7734, 2018, Page(s) 64-70, ISSN 0028-0836
Publisher: Nature Publishing Group
DOI: 10.1038/s41586-018-0734-6

Evolution of embryonic cis-regulatory landscapes between divergent Phallusia and Ciona ascidians

Author(s): Alicia Madgwick, Marta Silvia Magri, Christelle Dantec, Damien Gailly, Ulla-Maj Fiuza, Léo Guignard, Sabrina Hettinger, Jose Luis Gomez-Skarmeta, Patrick Lemaire
Published in: Developmental Biology, 2019, ISSN 0012-1606
Publisher: Academic Press
DOI: 10.1016/j.ydbio.2019.01.003

A conserved Shh cis-regulatory module highlights a common developmental origin of unpaired and paired fins

Author(s): Joaquín Letelier, Elisa de la Calle-Mustienes, Joyce Pieretti, Silvia Naranjo, Ignacio Maeso, Tetsuya Nakamura, Juan Pascual-Anaya, Neil H. Shubin, Igor Schneider, Juan Ramón Martinez-Morales, José Luis Gómez-Skarmeta
Published in: Nature Genetics, Issue 50/4, 2018, Page(s) 504-509, ISSN 1061-4036
Publisher: Nature Publishing Group
DOI: 10.1038/s41588-018-0080-5

4Cin: A computational pipeline for 3D genome modeling and virtual Hi-C analyses from 4C data

Author(s): Ibai Irastorza-Azcarate, Rafael D. Acemel, Juan J. Tena, Ignacio Maeso, José Luis Gómez-Skarmeta, Damien P. Devos
Published in: PLOS Computational Biology, Issue 14/3, 2018, Page(s) e1006030, ISSN 1553-7358
Publisher: Plos
DOI: 10.1371/journal.pcbi.1006030

Characterization of the accessible genome in the human malaria parasite Plasmodium falciparum

Author(s): José Luis Ruiz, Juan J Tena, Cristina Bancells, Alfred Cortés, José Luis Gómez-Skarmeta, Elena Gómez-Díaz
Published in: Nucleic Acids Research, Issue 46/18, 2018, Page(s) 9414-9431, ISSN 0305-1048
Publisher: Oxford University Press
DOI: 10.1093/nar/gky643

Genetic regulation of amphioxus somitogenesis informs the evolution of the vertebrate head mesoderm

Author(s): Daniel Aldea, Lucie Subirana, Celine Keime, Lydvina Meister, Ignacio Maeso, Sylvain Marcellini, Jose Luis Gomez-Skarmeta, Stephanie Bertrand, Hector Escriva
Published in: Nature Ecology & Evolution, Issue 3/8, 2019, Page(s) 1233-1240, ISSN 2397-334X
Publisher: Nature
DOI: 10.1038/s41559-019-0933-z

Assaying Chromatin Accessibility Using ATAC-Seq in Invertebrate Chordate Embryos

Author(s): Marta Silvia Magri, Sandra Jiménez-Gancedo, Stephanie Bertrand, Alicia Madgwick, Hector Escrivà, Patrick Lemaire, José Luis Gómez-Skarmeta
Published in: Frontiers in Cell and Developmental Biology, Issue 7, 2020, ISSN 2296-634X
Publisher: Frontiers
DOI: 10.3389/fcell.2019.00372

Pioneer and repressive functions of p63 during zebrafish embryonic ectoderm specification

Author(s): José M. Santos-Pereira, Lourdes Gallardo-Fuentes, Ana Neto, Rafael D. Acemel, Juan J. Tena
Published in: Nature Communications, Issue 10/1, 2019, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-019-11121-z

Conservative route to genome compaction in a miniature annelid

Author(s): José M. Martín-Durán, Bruno C. Vellutini, Ferdinand Marlétaz, Viviana Cetrangolo, Nevena Cvetesic, Daniel Thiel, Simon Henriet, Xavier Grau-Bové, Allan M. Carrillo-Baltodano, Wenjia Gu, Alexandra Kerbl, Yamile Marquez, Nicolas Bekkouche, Daniel Chourrout, Jose Luis Gómez-Skarmeta, Manuel Irimia, Boris Lenhard, Katrine Worsaae, Andreas Hejnol
Published in: Nature Ecology & Evolution, Issue 5/2, 2021, Page(s) 231-242, ISSN 2397-334X
Publisher: Nature Publishing Group
DOI: 10.1038/s41559-020-01327-6

CTCF knockout in zebrafish induces alterations in regulatory landscapes and developmental gene expression

Author(s): Martin Franke, Elisa De la Calle-Mustienes, Ana Neto, María Almuedo-Castillo, Ibai Irastorza-Azcarate, Rafael D. Acemel, Juan J. Tena, José M. Santos-Pereira, José L. Gómez-Skarmeta
Published in: Nature Communications, Issue 12/1, 2021, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-021-25604-5

Non-peer reviewed articles (1)

Gain of gene regulatory network interconnectivity at the origin of vertebrates

Author(s): Alejandro Gil-Gálvez; Sandra Jiménez-Gancedo; Rafael D. Acemel; Stéphanie Bertrand; Michael Schubert; Hector Escriva; Juan J. Tena; José Luis Gómez-Skarmeta
Published in: BioRxiv, Issue April 27, 2020, 2020, ISSN 2692-8205
Publisher: bioRxiv
DOI: 10.1101/2020.04.25.061077