Functions and evolutionary impact of transcriptomic novelties in the vertebrate brain

Publications

Peer reviewed articles (18)

Genomic adaptations to aquatic and aerial life in mayflies and the origin of insect wings

Author(s): Isabel Almudi, Joel Vizueta, Christopher D. R. Wyatt, Alex de Mendoza, Ferdinand Marlétaz, Panos N. Firbas, Roberto Feuda, Giulio Masiero, Patricia Medina, Ana Alcaina-Caro, Fernando Cruz, Jessica Gómez-Garrido, Marta Gut, Tyler S. Alioto, Carlos Vargas-Chavez, Kristofer Davie, Bernhard Misof, Josefa González, Stein Aerts, Ryan Lister, Jordi Paps, Julio Rozas, Alejandro Sánchez-Gracia, Manuel
Published in: Nature Communications, 11/1, 2020, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-020-16284-8

Alternative splicing landscapes in Arabidopsis thaliana across tissues and stress conditions highlight major functional differences with animals

Author(s): Guiomar Martín, Yamile Márquez, Federica Mantica, Paula Duque, Manuel Irimia
Published in: Genome Biology, 22/1, 2021, ISSN 1474-760X
Publisher: Springer Nature
DOI: 10.1186/s13059-020-02258-y

Huntington’s disease-specific mis-splicing unveils key effector genes and altered splicing factors

Author(s): Ainara Elorza, Yamile Márquez, Jorge R Cabrera, José Luis Sánchez-Trincado, María Santos-Galindo, Ivó H Hernández, Sara Picó, Juan I Díaz-Hernández, Ramón García-Escudero, Manuel Irimia, José J Lucas
Published in: Brain, 2021, ISSN 0006-8950
Publisher: Oxford University Press
DOI: 10.1093/brain/awab087

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, 37/10, 2020, Page(s) 2857-2864, ISSN 0737-4038
Publisher: Oxford University Press
DOI: 10.1093/molbev/msaa123

Genome-wide changes in lncRNA, splicing, and regional gene expression patterns in autism

Author(s): Neelroop N. Parikshak, Vivek Swarup, T. Grant Belgard, Manuel Irimia, Gokul Ramaswami, Michael J. Gandal, Christopher Hartl, Virpi Leppa, Luis de la Torre Ubieta, Jerry Huang, Jennifer K. Lowe, Benjamin J. Blencowe, Steve Horvath, Daniel H. Geschwind
Published in: Nature, 540/7633, 2016, Page(s) 423-427, ISSN 0028-0836
Publisher: Nature Publishing Group
DOI: 10.1038/nature20612

Nodal–Activin pathway is a conserved neural induction signal in chordates

Author(s): Yann Le Petillon, Guillaume Luxardi, Pierluigi Scerbo, Marie Cibois, Anthony Leon, Lucie Subirana, Manuel Irimia, Laurent Kodjabachian, Hector Escriva, Stephanie Bertrand
Published in: Nature Ecology & Evolution, 1/8, 2017, Page(s) 1192-1200, ISSN 2397-334X
Publisher: Springer Nature
DOI: 10.1038/s41559-017-0226-3

Misregulation of an Activity-Dependent Splicing Network as a Common Mechanism Underlying Autism Spectrum Disorders

Author(s): Mathieu Quesnel-Vallières, Zahra Dargaei, Manuel Irimia, Thomas Gonatopoulos-Pournatzis, Joanna Y. Ip, Mingkun Wu, Timothy Sterne-Weiler, Shinichi Nakagawa, Melanie A. Woodin, Benjamin J. Blencowe, Sabine P. Cordes
Published in: Molecular Cell, 64/6, 2016, Page(s) 1023-1034, ISSN 1097-2765
Publisher: Cell Press
DOI: 10.1016/j.molcel.2016.11.033

Evolutionary recruitment of flexible Esrp-dependent splicing programs into diverse embryonic morphogenetic processes

Author(s): Demian Burguera, Yamile Marquez, Claudia Racioppi, Jon Permanyer, Antonio Torres-Méndez, Rosaria Esposito, Beatriz Albuixech-Crespo, Lucía Fanlo, Ylenia D’Agostino, Andre Gohr, Enrique Navas-Perez, Ana Riesgo, Claudia Cuomo, Giovanna Benvenuto, Lionel A. Christiaen, Elisa Martí, Salvatore D’Aniello, Antonietta Spagnuolo, Filomena Ristoratore, Maria Ina Arnone, Jordi Garcia-Fernàndez, Manue
Published in: Nature Communications, 8/1, 2017, ISSN 2041-1723
Publisher: Nature Publishing Group
DOI: 10.1038/s41467-017-01961-y

Molecular regionalization of the developing amphioxus neural tube challenges major partitions of the vertebrate brain

Author(s): Beatriz Albuixech-Crespo, Laura López-Blanch, Demian Burguera, Ignacio Maeso, Luisa Sánchez-Arrones, Juan Antonio Moreno-Bravo, Ildiko Somorjai, Juan Pascual-Anaya, Eduardo Puelles, Paola Bovolenta, Jordi Garcia-Fernàndez, Luis Puelles, Manuel Irimia, José Luis Ferran
Published in: PLOS Biology, 15/4, 2017, Page(s) e2001573, ISSN 1545-7885
Publisher: Public Library Of Science
DOI: 10.1371/journal.pbio.2001573

An atlas of alternative splicing profiles and functional associations reveals new regulatory programs and genes that simultaneously express multiple major isoforms

Author(s): Javier Tapial, Kevin C.H. Ha, Timothy Sterne-Weiler, André Gohr, Ulrich Braunschweig, Antonio Hermoso-Pulido, Mathieu Quesnel-Vallières, Jon Permanyer, Reza Sodaei, Yamile Marquez, Luca Cozzuto, Xinchen Wang, Melisa Gómez-Velázquez, Teresa Rayon, Miguel Manzanares, Julia Ponomarenko, Benjamin J. Blencowe, Manuel Irimia
Published in: Genome Research, 27/10, 2017, Page(s) 1759-1768, ISSN 1088-9051
Publisher: Cold Spring Harbor Laboratory Press
DOI: 10.1101/gr.220962.117

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, 564/7734, 2018, Page(s) 64-70, ISSN 0028-0836
Publisher: Nature Publishing Group
DOI: 10.1038/s41586-018-0734-6

RES complex is associated with intron definition and required for zebrafish early embryogenesis

Author(s): Juan Pablo Fernandez, Miguel Angel Moreno-Mateos, Andre Gohr, Liyun Miao, Shun Hang Chan, Manuel Irimia, Antonio J. Giraldez
Published in: PLOS Genetics, 14/7, 2018, Page(s) e1007473, ISSN 1553-7404
Publisher: Plos Genetics
DOI: 10.1371/journal.pgen.1007473

A novel L1CAM isoform with angiogenic activity generated by NOVA2-mediated alternative splicing

Author(s): Francesca Angiolini, Elisa Belloni, Marco Giordano, Matteo Campioni, Federico Forneris, Maria Paola Paronetto, Michela Lupia, Chiara Brandas, Davide Pradella, Anna Di Matteo, Costanza Giampietro, Giovanna Jodice, Chiara Luise, Giovanni Bertalot, Stefano Freddi, Matteo Malinverno, Manuel Irimia, Jon D Moulton, James Summerton, Antonella Chiapparino, Carmen Ghilardi, Raffaella Giavazzi, Daniel Nyqvi
Published in: eLife, 8, 2019, ISSN 2050-084X
Publisher: eLife Sciences Publications
DOI: 10.7554/elife.44305

A novel protein domain in an ancestral splicing factor drove the evolution of neural microexons

Author(s): Antonio Torres-Méndez, Sophie Bonnal, Yamile Marquez, Jonathan Roth, Marta Iglesias, Jon Permanyer, Isabel Almudí, Dave O’Hanlon, Tanit Guitart, Matthias Soller, Anne-Claude Gingras, Fátima Gebauer, Fabian Rentzsch, Benjamin J. Blencowe, Juan Valcárcel, Manuel Irimia
Published in: Nature Ecology & Evolution, 3/4, 2019, Page(s) 691-701, ISSN 2397-334X
Publisher: Nature Ecology and Evolution
DOI: 10.1038/s41559-019-0813-6

Autism-like phenotype and risk gene mRNA deadenylation by CPEB4 mis-splicing

Author(s): Alberto Parras, Héctor Anta, María Santos-Galindo, Vivek Swarup, Ainara Elorza, José L. Nieto-González, Sara Picó, Ivó H. Hernández, Juan I. Díaz-Hernández, Eulàlia Belloc, Annie Rodolosse, Neelroop N. Parikshak, Olga Peñagarikano, Rafael Fernández-Chacón, Manuel Irimia, Pilar Navarro, Daniel H. Geschwind, Raúl Méndez, José J. Lucas
Published in: Nature, 560/7719, 2018, Page(s) 441-446, ISSN 0028-0836
Publisher: Nature Publishing Group
DOI: 10.1038/s41586-018-0423-5

Srrm234, but not canonical SR and hnRNP proteins drive inclusion of Dscam exon 9 variable exons

Author(s): Pinar Ustaoglu, Irmgard U Haussmann, Hongzhi Liao, Antonio Torres-Mendez, Roland Arnold, Manuel Irimia, Matthias Soller
Published in: RNA, 2019, Page(s) rna.071316.119, ISSN 1355-8382
Publisher: Cold Spring Harbor Laboratory Press
DOI: 10.1261/rna.071316.119

Matt : Unix tools for alternative splicing analysis

Author(s): André Gohr, Manuel Irimia
Published in: Bioinformatics, 35/1, 2018, Page(s) 130-132, ISSN 1367-4803
Publisher: Oxford University Press
DOI: 10.1093/bioinformatics/bty606

Exon Junction Complex Shapes the Transcriptome by Repressing Recursive Splicing

Author(s): Lorea Blazquez, Warren Emmett, Rupert Faraway, Jose Mario Bello Pineda, Simon Bajew, Andre Gohr, Nejc Haberman, Christopher R. Sibley, Robert K. Bradley, Manuel Irimia, Jernej Ule
Published in: Molecular Cell, 72/3, 2018, Page(s) 496-509.e9, ISSN 1097-2765
Publisher: Cell Press
DOI: 10.1016/j.molcel.2018.09.033

Other (2)

ExOrthist: a tool to infer exon orthologies at any evolutionary distance

Author(s): Yamile Márquez, Federica Mantica, Luca Cozzuto, Demian Burguera, Antonio Hermoso-Pulido, Julia Ponomarenko, Scott W. Roy, Manuel Irimia
Published in: bioRxiv, 2021
Publisher: Cold Spring Harbor Laboratory
DOI: 10.1101/2021.02.22.432358

Parallel evolution of a splicing program controlling neuronal excitability in flies and mammals

Author(s): Antonio Torres-Méndez, Sinziana Pop, Sophie Bonnal, Isabel Almudi, Alida Avola, Ruairí J V Roberts, Chiara Paolantoni, Ana Alcaina, Ane Martín-Anduaga, Irmgard U Haussmann, Violeta Morin, Fernando Casares, Matthias Soller, Sebastian Kadener, Jean-Yves Roignant, Lucia Prieto-Godino, Manuel Irimia
Published in: bioRxiv, 2021
Publisher: Cold Spring Harbor Laboratory
DOI: 10.1101/2021.02.24.432780