Irimia Lab

Irimia Lab

Systems Biology

Irimia Lab
Transcriptomics of vertebrate development and evolution
Group leader

Irimia Lab

Transcriptomics of vertebrate development and evolution
Group leader
From Dec 2018: ICREA Research professor.
From June 2014: Group Leader at the Centre for Genomic Regulation (CRG), Barcelona, Spain.
2011-2014: Postdoc in the laboratory of Prof. Blencowe, University of Toronto, Toronto, Canada.
2011-2011: Postdoc in the laboratory of Prof. Fraser, Stanford University, USA.
2006-2010: PhD in Genetics in the laboratory of Prof. Garcia-Fernandez, Universitat de Barcelona, Barcelona, Spain.
2005-2006: Postgrad researcher in the laboratory of Prof. Penny, Massey University, Parlmerston North, New Zealand.
2004-2005:  Postgrad researcher in the laboratory of Prof. Arctander, University of Copenhagen, Copenhagen, Denmark.
2000-2004: Diploma studies in Genetics, Universidad Complutense de Madrid, Madrid, Spain

News

The genomic keys to the origin of the vertebrates (21/11/2018)
An international team of scientists co-led by CRG researcher Manuel Irimia reports how more complex and specialised gene regulation proved to be pivotal in the origin of the vertebrates.
 
This change, a random error in the evolutionary process that occurred over 700 million years ago, facilitated the connection of the gene networks involved in animal embryogenesis.
 
Manuel Irimia, CRG junior group leader, has been elected EMBO Young Investigator. He is one of the two researchers elected in Spain.
 
A new study revises the development and evolutionary origin of the vertebrate brain (28/04/2017)
Researchers have made the first detailed map of the regions into which the brain of one of the most closely-related organisms to the vertebrates is divided and which could give us an idea of what our ancestor was like.
 
'Yin and Yang' Switch Lies at the Heart of Animal Stem Cells (09/08/2016)
A molecular switch that flips between different versions of genes could be crucial for maintaining stem cells across all animals from simple flatworms to humans, according to a study from scientists at the Centre for Genomic Regulation (CRG) in Barcelona, published today, in the journal eLife.

Summary

During embryo development, a single genome sequence gives rise to hundreds of cell types that are exquisitely organized in complex tissue and organ structures. This is achieved by the differential regulation of a single set of genes in time and space. However, most of those genes are expressed in most cell types, where they may need to perform their functions in sometimes radically different cellular contexts. How can the function of each gene be optimized in each cell type without jeopardizing the function they play in other cells? And, in the case of proteins with cell type-specific functions: how do these new protein functions originate during evolution and how are they integrated into pre-existing functional protein networks? Our lab focuses on two complementary mechanisms to provide answers to these questions: alternative splicing and gene duplication.

By differential processing of introns and exons, alternative splicing can generate multiple protein isoforms from individual genes. In some cases, these proteins may have very different, sometimes even antagonistic, effects on cell behavior (e.g. enhancing proliferation or triggering differentiation). Similarly, gene duplication provides redundant gene copies that can freely evolve, especially after whole genome duplication events. Thus, both mechanisms are complementary, often leading to similar outcomes: they allow specialization of protein functions in specific cell types, as well as the origin of novel protein activities in evolution that may be behind organismal innovations. In our lab, we combine computational approaches (comparative bulk and single-cell transcriptomics and functional genomics) with experiments using in vitro and in vivo systems (zebrafish, mouse and fruitfly) to investigate how these mechanisms impact embryonic development and evolution.

In particular, we focus on two highly contrasting systems: (i) early mammalian embryogenesis and (ii) vertebrate central nervous system development. These two developmental contexts show radically distinct characteristics. On the one hand, early embryogenesis captures in vivo pluripotency and the first cell fate decisions, involves relatively simple morphogenetic processes, and shows particularly high evolutionary rates. On the other hand, vertebrate brains are extremely complex systems of highly differentiated cell types that develop through very specialized processes (e.g. neuritogenesis, axon guidance, migration). Furthermore, neural-specific alternative splicing events, especially microexons, are exceptionally conserved. Therefore, combining both biological systems will provide highly complementary insights into the roles of alternative splicing and gene duplication in development and evolution. Moreover, these two systems are key to understand two evolutionary transitions we are fascinated about: the origin of vertebrates and the origin of mammals.

Group News

  • Dec 2019: We have been awarded a research grant from the EFSD and Lilly European Diabetes Research Programme.
  • Dec 2019: Niccolo Arecco has been awarded an EMBO long-term post-doctoral fellowship
  • Sep 2019: The ETN ZENITH (ZEbrafish Neuroscience Interdisciplinary Training Hub) is officially started.
  • Jun 2019: Chris Wyatt defended his PhD thesis
  • Feb 2019: Mireya Plass has been awarded a Marie Skłodowska-Curie Individual Fellowship.
  • Dec 2018: Manuel Irimia joined ICREA as a Research Professor
  • Dec 2018: Javier Tapial defended his PhD thesis.
  • Oct 2018: Federica Mantica joins the lab with a FPI PhD Fellowship.
  • Mar 2018: We have been awarded our second Plan Nacional grant, including a FPI fellowship.
  • Oct 2017: Manuel Irimia has been elected EMBO Young Investigator.
  • Sep 2017: Patryk Polinski joins the lab as part of the circRTrain ETN.
  • Sep 2017: Demian Burguera defended his PhD thesis
  • Dec 2015: Yamile Márquez has been awarded an EMBO long term post-doctoral fellowship.
  • Nov 2015: Victoria Rodriguez-Vaello has been awarded a Boehringer-Ingelheim Fonds PhD fellowship.
  • Oct 2015: Laura Lopez-Blanch has been awarded a FPI PhD Fellowship.
  • Sep 2015: Elisabeth Kita has been awarded an ImPuLSe post-doctoral fellowship.
  • May 2015: Bárbara Pernaute has been awarded a Marie Skłodowska-Curie Individual Fellowship.
  • Mar 2015: Antonio Torres-Méndez has been awarded a FPI-SO PhD Fellowship.
  • Jan 2015: Thomas Spruce has been awarded an ImPuLSe post-doctoral fellowship.
  • Nov 2014: Manuel Irimia has been awarded a Starting Grant from the European Research Council.
  • Sep 2014: Javier Tapial has been awarded a FPI-SO PhD Fellowship.
  • Mar 2014: Chris Wyatt has been awarded a La Caixa PhD Fellowship.

Type:
Database, Webservice

Atlas of alternative splicing profiles across animal tissues, cell types and developmental stages.

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