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NEURAL AS SIGNED

Functions and evolutionary impact of transcriptomic novelties in the vertebrate brain

Total Cost €

EC-Contrib. €

Partnership

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Outcomes and
results

NEURAL AS project word cloud

Explore the words cloud of the NEURAL AS project. It provides you a very rough idea of what is the project "NEURAL AS" about.

questions rewire experimental organismal brains networks neural diversification splicing evolution fundamental genomics network gap had vertebrates fill gene rewiring species groups expression regulated regulation of conserved comprehensively neurons transcriptional functions cellular phenotypic exons unanswered interaction editing morphological emergent transcriptomic vertebrate angle genomic function models novelties neurogenesis probe unparalleled nervous bioinformatics spliced alternatively combination protein functional brain contributor suggesting seq evolutionary nature levels rna genome mirroring transcripts cas metazoans molecular manipulation alternative crispr invertebrates vn complementary highest unexplored complexity underlies

Project "NEURAL AS" data sheet

The following table provides information about the project.

Coordinator	FUNDACIO CENTRE DE REGULACIO GENOMICA Organization address address: CARRER DOCTOR AIGUADER 88 city: BARCELONA postcode: 8003 website: www.crg.es contact info title: n.a. name: n.a. surname: n.a. function: n.a. email: n.a. telephone: n.a. fax: n.a.
Coordinator Country	Spain [ES]
Project website	http://vastdb.crg.eu/
Total cost	1˙498˙852 €
EC max contribution	1˙498˙852 € (100%)
Programme	1. H2020-EU.1.1. (EXCELLENT SCIENCE - European Research Council (ERC))
Code Call	ERC-2014-STG
Funding Scheme	ERC-STG
Starting year	2015
Duration (year-month-day)	from 2015-04-01 to 2020-12-31

Partnership

Take a look of project's partnership.

#	participants	country	role	EC contrib. [€]
1	FUNDACIO CENTRE DE REGULACIO GENOMICA FUNDACIO CENTRE DE REGULACIO GENOMICA Organization address address: CARRER DOCTOR AIGUADER 88 city: BARCELONA postcode: 8003 website: www.crg.es contact info title: n.a. name: n.a. surname: n.a. function: n.a. email: n.a. telephone: n.a. fax: n.a.	ES (BARCELONA)	coordinator	1˙498˙852.00

Map

Project objective

Alternative splicing (AS) is the largest contributor to transcriptomic diversification in metazoans. In particular, mirroring their unparalleled morphological and cellular complexity, vertebrate brains show the highest levels of regulated AS known in nature. However, the functions of most of these alternative transcripts, and the evolutionary impact that the increased transcriptional complexity has had on the evolution of the vertebrate brain are still widely unexplored. In this project, we will investigate the functions and evolutionary impact of neural AS in vertebrates. We will focus on neural-specific alternative exons that are highly conserved across vertebrate groups (suggesting functional importance), but that are not conserved in invertebrates, and are thus vertebrate-specific genomic novelties. We will term these exons Vertebrate- and Neural-specific Alternatively Spliced (VN-AS) exons. Through a combination of bioinformatics, experimental manipulation in models species, and systems-level network analysis, we aim to: (i) Comprehensively identify VN-AS exons, and study their regulation during vertebrate neurogenesis and nervous system development, using RNA-seq and comparative genomics; (ii) Probe the phenotypic impact of VN-AS exons on vertebrate nervous systems, using the CRISPR-Cas technology for genome editing; and (iii) Investigate how VN-AS exons rewire protein-protein interaction networks in vertebrate neurons – an emergent molecular function for AS –, and whether this rewiring underlies novel functions of VN-AS exons in the vertebrate brains. This project will thus deliver fundamental insight into two major unanswered questions: (i) what are the functions of transcriptomic diversification, and (ii) how does transcriptomic diversification impact organismal evolution. Our results will fill a large gap of knowledge in our current understanding of brain evolution and development, providing a complementary angle to traditional gene expression studies.

Publications

List of publications.
year	authors and title	journal	last update
2018	Juan Pablo Fernandez, Miguel Angel Moreno-Mateos, Andre Gohr, Liyun Miao, Shun Hang Chan, Manuel Irimia, Antonio J. Giraldez RES complex is associated with intron definition and required for zebrafish early embryogenesis published pages: e1007473, ISSN: 1553-7404, DOI: 10.1371/journal.pgen.1007473	PLOS Genetics 14/7	2020-02-26
2019	Pinar Ustaoglu, Irmgard U Haussmann, Hongzhi Liao, Antonio Torres-Mendez, Roland Arnold, Manuel Irimia, Matthias Soller Srrm234, but not canonical SR and hnRNP proteins drive inclusion of Dscam exon 9 variable exons published pages: rna.071316.119, ISSN: 1355-8382, DOI: 10.1261/rna.071316.119	RNA	2020-02-26
2019	Antonio Torres-MÃ©ndez, Sophie Bonnal, Yamile Marquez, Jonathan Roth, Marta Iglesias, Jon Permanyer, Isabel AlmudÃ, Dave Oâ€™Hanlon, Tanit Guitart, Matthias Soller, Anne-Claude Gingras, FÃ¡tima Gebauer, Fabian Rentzsch, Benjamin J. Blencowe, Juan ValcÃ¡rcel, Manuel Irimia A novel protein domain in an ancestral splicing factor drove the evolution of neural microexons published pages: 691-701, ISSN: 2397-334X, DOI: 10.1038/s41559-019-0813-6	Nature Ecology & Evolution 3/4	2020-02-26
2018	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 Exon Junction Complex Shapes the Transcriptome by Repressing Recursive Splicing published pages: 496-509.e9, ISSN: 1097-2765, DOI: 10.1016/j.molcel.2018.09.033	Molecular Cell 72/3	2020-02-26
2018	AndrÃ© Gohr, Manuel Irimia Matt : Unix tools for alternative splicing analysis published pages: 130-132, ISSN: 1367-4803, DOI: 10.1093/bioinformatics/bty606	Bioinformatics 35/1	2020-02-26
2018	Alberto Parras, HÃ©ctor Anta, MarÃa Santos-Galindo, Vivek Swarup, Ainara Elorza, JosÃ© L. Nieto-GonzÃ¡lez, Sara PicÃ³, IvÃ³ H. HernÃ¡ndez, Juan I. DÃaz-HernÃ¡ndez, EulÃ lia Belloc, Annie Rodolosse, Neelroop N. Parikshak, Olga PeÃ±agarikano, Rafael FernÃ¡ndez-ChacÃ³n, Manuel Irimia, Pilar Navarro, Daniel H. Geschwind, RaÃºl MÃ©ndez, JosÃ© J. Lucas Autism-like phenotype and risk gene mRNA deadenylation by CPEB4 mis-splicing published pages: 441-446, ISSN: 0028-0836, DOI: 10.1038/s41586-018-0423-5	Nature 560/7719	2020-02-26
2019	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 A novel L1CAM isoform with angiogenic activity generated by NOVA2-mediated alternative splicing published pages: , ISSN: 2050-084X, DOI: 10.7554/elife.44305	eLife 8	2020-02-26
2018	Ferdinand MarlÃ©taz, 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 Amphioxus functional genomics and the origins of vertebrate gene regulation published pages: 64-70, ISSN: 0028-0836, DOI: 10.1038/s41586-018-0734-6	Nature 564/7734	2020-02-26
2016	Mathieu Quesnel-ValliÃ¨res, 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 Misregulation of an Activity-Dependent Splicing Network as a Common Mechanism Underlying Autism Spectrum Disorders published pages: 1023-1034, ISSN: 1097-2765, DOI: 10.1016/j.molcel.2016.11.033	Molecular Cell 64/6	2020-02-26
2017	Beatriz Albuixech-Crespo, Laura LÃ³pez-Blanch, Demian Burguera, Ignacio Maeso, Luisa SÃ¡nchez-Arrones, Juan Antonio Moreno-Bravo, Ildiko Somorjai, Juan Pascual-Anaya, Eduardo Puelles, Paola Bovolenta, Jordi Garcia-FernÃ ndez, Luis Puelles, Manuel Irimia, JosÃ© Luis Ferran Molecular regionalization of the developing amphioxus neural tube challenges major partitions of the vertebrate brain published pages: e2001573, ISSN: 1545-7885, DOI: 10.1371/journal.pbio.2001573	PLOS Biology 15/4	2020-02-26
2017	Demian Burguera, Yamile Marquez, Claudia Racioppi, Jon Permanyer, Antonio Torres-MÃ©ndez, Rosaria Esposito, Beatriz Albuixech-Crespo, LucÃa Fanlo, Ylenia Dâ€™Agostino, Andre Gohr, Enrique Navas-Perez, Ana Riesgo, Claudia Cuomo, Giovanna Benvenuto, Lionel A. Christiaen, Elisa MartÃ, Salvatore Dâ€™Aniello, Antonietta Spagnuolo, Filomena Ristoratore, Maria Ina Arnone, Jordi Garcia-FernÃ ndez, Manuel Irimia Evolutionary recruitment of flexible Esrp-dependent splicing programs into diverse embryonic morphogenetic processes published pages: , ISSN: 2041-1723, DOI: 10.1038/s41467-017-01961-y	Nature Communications 8/1	2020-02-26
2016	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 Genome-wide changes in lncRNA, splicing, and regional gene expression patterns in autism published pages: 423-427, ISSN: 0028-0836, DOI: 10.1038/nature20612	Nature 540/7633	2020-02-26
2017	Javier Tapial, Kevin C.H. Ha, Timothy Sterne-Weiler, AndrÃ© Gohr, Ulrich Braunschweig, Antonio Hermoso-Pulido, Mathieu Quesnel-ValliÃ¨res, Jon Permanyer, Reza Sodaei, Yamile Marquez, Luca Cozzuto, Xinchen Wang, Melisa GÃ³mez-VelÃ¡zquez, Teresa Rayon, Miguel Manzanares, Julia Ponomarenko, Benjamin J. Blencowe, Manuel Irimia An atlas of alternative splicing profiles and functional associations reveals new regulatory programs and genes that simultaneously express multiple major isoforms published pages: 1759-1768, ISSN: 1088-9051, DOI: 10.1101/gr.220962.117	Genome Research 27/10	2020-02-26
2017	Yann Le Petillon, Guillaume Luxardi, Pierluigi Scerbo, Marie Cibois, Anthony Leon, Lucie Subirana, Manuel Irimia, Laurent Kodjabachian, Hector Escriva, Stephanie Bertrand Nodalâ€“Activin pathway is a conserved neural induction signal in chordates published pages: 1192-1200, ISSN: 2397-334X, DOI: 10.1038/s41559-017-0226-3	Nature Ecology & Evolution 1/8	2020-02-26

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