Evolution of regulatory landscapes at multiple timescales

Informazioni relative al progetto

Evoland

ID dell’accordo di sovvenzione: 740041

DOI 10.3030/740041

Progetto chiuso

Data della firma CE 20 Luglio 2017

Data di avvio 1 Settembre 2017

Data di completamento 31 Agosto 2021

Finanziato da

• EXCELLENT SCIENCE - European Research Council (ERC)

Costo totale € 1 928 091,19

Contributo UE € 1 928 091,19

Coordinato da

AGENCIA ESTATAL CONSEJO SUPERIOR DE INVESTIGACIONES CIENTIFICAS
Spain

Pubblicazioni

Peer reviewed articles (14)

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

Autori: 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
Pubblicato in: Nature Communications, Numero 12/1, 2021, ISSN 2041-1723
Editore: Nature Publishing Group
DOI: 10.1038/s41467-021-23397-1

Functional Conservation of Divergent p63-Bound cis-Regulatory Elements

Autori: Lourdes Gallardo-Fuentes, José M. Santos-Pereira, Juan J. Tena
Pubblicato in: Frontiers in Genetics, Numero 11, 2020, ISSN 1664-8021
Editore: 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

Autori: 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
Pubblicato in: Molecular Biology and Evolution, Numero 37/10, 2020, Pagina/e 2857-2864, ISSN 0737-4038
Editore: Oxford University Press
DOI: 10.1093/molbev/msaa123

An evolutionary perspective of regulatory landscape dynamics in development and disease

Autori: Martin Franke, José Luis Gómez-Skarmeta
Pubblicato in: Current Opinion in Cell Biology, Numero 55, 2018, Pagina/e 24-29, ISSN 0955-0674
Editore: Elsevier BV
DOI: 10.1016/j.ceb.2018.06.009

Amphioxus functional genomics and the origins of vertebrate gene regulation

Autori: 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
Pubblicato in: Nature, Numero 564/7734, 2018, Pagina/e 64-70, ISSN 0028-0836
Editore: Nature Publishing Group
DOI: 10.1038/s41586-018-0734-6

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

Autori: Alicia Madgwick, Marta Silvia Magri, Christelle Dantec, Damien Gailly, Ulla-Maj Fiuza, Léo Guignard, Sabrina Hettinger, Jose Luis Gomez-Skarmeta, Patrick Lemaire
Pubblicato in: Developmental Biology, 2019, ISSN 0012-1606
Editore: 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

Autori: 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
Pubblicato in: Nature Genetics, Numero 50/4, 2018, Pagina/e 504-509, ISSN 1061-4036
Editore: 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

Autori: Ibai Irastorza-Azcarate, Rafael D. Acemel, Juan J. Tena, Ignacio Maeso, José Luis Gómez-Skarmeta, Damien P. Devos
Pubblicato in: PLOS Computational Biology, Numero 14/3, 2018, Pagina/e e1006030, ISSN 1553-7358
Editore: Plos
DOI: 10.1371/journal.pcbi.1006030

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

Autori: José Luis Ruiz, Juan J Tena, Cristina Bancells, Alfred Cortés, José Luis Gómez-Skarmeta, Elena Gómez-Díaz
Pubblicato in: Nucleic Acids Research, Numero 46/18, 2018, Pagina/e 9414-9431, ISSN 0305-1048
Editore: Oxford University Press
DOI: 10.1093/nar/gky643

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

Autori: Daniel Aldea, Lucie Subirana, Celine Keime, Lydvina Meister, Ignacio Maeso, Sylvain Marcellini, Jose Luis Gomez-Skarmeta, Stephanie Bertrand, Hector Escriva
Pubblicato in: Nature Ecology & Evolution, Numero 3/8, 2019, Pagina/e 1233-1240, ISSN 2397-334X
Editore: Nature
DOI: 10.1038/s41559-019-0933-z

Assaying Chromatin Accessibility Using ATAC-Seq in Invertebrate Chordate Embryos

Autori: Marta Silvia Magri, Sandra Jiménez-Gancedo, Stephanie Bertrand, Alicia Madgwick, Hector Escrivà, Patrick Lemaire, José Luis Gómez-Skarmeta
Pubblicato in: Frontiers in Cell and Developmental Biology, Numero 7, 2020, ISSN 2296-634X
Editore: Frontiers
DOI: 10.3389/fcell.2019.00372

Pioneer and repressive functions of p63 during zebrafish embryonic ectoderm specification

Autori: José M. Santos-Pereira, Lourdes Gallardo-Fuentes, Ana Neto, Rafael D. Acemel, Juan J. Tena
Pubblicato in: Nature Communications, Numero 10/1, 2019, ISSN 2041-1723
Editore: Nature Publishing Group
DOI: 10.1038/s41467-019-11121-z

Conservative route to genome compaction in a miniature annelid

Autori: 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
Pubblicato in: Nature Ecology & Evolution, Numero 5/2, 2021, Pagina/e 231-242, ISSN 2397-334X
Editore: Nature Publishing Group
DOI: 10.1038/s41559-020-01327-6

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

Autori: 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
Pubblicato in: Nature Communications, Numero 12/1, 2021, ISSN 2041-1723
Editore: 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

Autori: Alejandro Gil-Gálvez; Sandra Jiménez-Gancedo; Rafael D. Acemel; Stéphanie Bertrand; Michael Schubert; Hector Escriva; Juan J. Tena; José Luis Gómez-Skarmeta
Pubblicato in: BioRxiv, Numero April 27, 2020, 2020, ISSN 2692-8205
Editore: bioRxiv
DOI: 10.1101/2020.04.25.061077