Manuel Irimia

Summary

Publications

  1. pmc Stepwise assembly of the Nova-regulated alternative splicing network in the vertebrate brain
    Manuel Irimia
    Departament de Genetica, Facultat de Biologia, Universitat de Barcelona, Barcelona E08028, Spain
    Proc Natl Acad Sci U S A 108:5319-24. 2011
  2. doi request reprint Origin of introns by 'intronization' of exonic sequences
    Manuel Irimia
    Departament de Genetica, Facultat de Biologia, Universitat de Barcelona, Barcelona 08028, Spain
    Trends Genet 24:378-81. 2008
  3. pmc Widespread recurrent evolution of genomic features
    Ignacio Maeso
    Department of Zoology, University of Oxford, United Kingdom
    Genome Biol Evol 4:486-500. 2012
  4. pmc Differences in enhancer activity in mouse and zebrafish reporter assays are often associated with changes in gene expression
    Ana Ariza-Cosano
    Centro Andaluz de Biologia del Desarrollo CABD, CSIC Universidad Pablo de Olavide Junta de Andalucía, Ctra Utrera km 1, Seville 41013, Spain
    BMC Genomics 13:713. 2012
  5. doi request reprint Ancient cis-regulatory constraints and the evolution of genome architecture
    Manuel Irimia
    The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
    Trends Genet 29:521-8. 2013
  6. pmc Comparative genomics of the Hedgehog loci in chordates and the origins of Shh regulatory novelties
    Manuel Irimia
    Departament de Genetica, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
    Sci Rep 2:433. 2012
  7. doi request reprint Evolutionarily conserved A-to-I editing increases protein stability of the alternative splicing factor Nova1
    Manuel Irimia
    Departament de Genetica, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
    RNA Biol 9:12-21. 2012
  8. pmc Intron mis-splicing: no alternative?
    Scott William Roy
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20814, USA
    Genome Biol 9:208. 2008
  9. doi request reprint Quantitative regulation of alternative splicing in evolution and development
    Manuel Irimia
    Departament de Genetica, and Institut de Biomedicina IBUB, Universitat de Barcelona, Barcelona, Spain
    Bioessays 31:40-50. 2009
  10. pmc Evolution of alternative splicing regulation: changes in predicted exonic splicing regulators are not associated with changes in alternative splicing levels in primates
    Manuel Irimia
    Departament de Genetica, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
    PLoS ONE 4:e5800. 2009

Detail Information

Publications40

  1. pmc Stepwise assembly of the Nova-regulated alternative splicing network in the vertebrate brain
    Manuel Irimia
    Departament de Genetica, Facultat de Biologia, Universitat de Barcelona, Barcelona E08028, Spain
    Proc Natl Acad Sci U S A 108:5319-24. 2011
    ..In addition, we find that tissue-specific Nova expression patterns emerged independently in other lineages, suggesting independent assembly of tissue-specific regulatory networks...
  2. doi request reprint Origin of introns by 'intronization' of exonic sequences
    Manuel Irimia
    Departament de Genetica, Facultat de Biologia, Universitat de Barcelona, Barcelona 08028, Spain
    Trends Genet 24:378-81. 2008
    ..Intronization is more common than the reverse process, loss of splicing of retained introns. Finally, these findings link alternative splicing with modern intron creation...
  3. pmc Widespread recurrent evolution of genomic features
    Ignacio Maeso
    Department of Zoology, University of Oxford, United Kingdom
    Genome Biol Evol 4:486-500. 2012
    ....
  4. pmc Differences in enhancer activity in mouse and zebrafish reporter assays are often associated with changes in gene expression
    Ana Ariza-Cosano
    Centro Andaluz de Biologia del Desarrollo CABD, CSIC Universidad Pablo de Olavide Junta de Andalucía, Ctra Utrera km 1, Seville 41013, Spain
    BMC Genomics 13:713. 2012
    ..While isolated examples of trans-changes have been identified, the scale of their overall contribution to regulatory and phenotypic evolution remains unclear...
  5. doi request reprint Ancient cis-regulatory constraints and the evolution of genome architecture
    Manuel Irimia
    The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
    Trends Genet 29:521-8. 2013
    ..We discuss implications, questions raised, and new research directions arising from these studies, as well as evidence for similar phenomena in other eukaryotic groups. ..
  6. pmc Comparative genomics of the Hedgehog loci in chordates and the origins of Shh regulatory novelties
    Manuel Irimia
    Departament de Genetica, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
    Sci Rep 2:433. 2012
    ..In addition, we show that the linkage of Shh to Lmbr1 and Rnf32, necessary for the unique gnatostomate-specific Shh limb expression, is a vertebrate novelty occurred between the two whole-genome duplications...
  7. doi request reprint Evolutionarily conserved A-to-I editing increases protein stability of the alternative splicing factor Nova1
    Manuel Irimia
    Departament de Genetica, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
    RNA Biol 9:12-21. 2012
    ....
  8. pmc Intron mis-splicing: no alternative?
    Scott William Roy
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20814, USA
    Genome Biol 9:208. 2008
    ..This striking inefficiency deepens the mystery of the proliferation and persistence of introns...
  9. doi request reprint Quantitative regulation of alternative splicing in evolution and development
    Manuel Irimia
    Departament de Genetica, and Institut de Biomedicina IBUB, Universitat de Barcelona, Barcelona, Spain
    Bioessays 31:40-50. 2009
    ..We discuss the potential role of changes in developmental regulation of AS as an additional layer in complex gene regulatory networks and in the emergence of genetic novelties...
  10. pmc Evolution of alternative splicing regulation: changes in predicted exonic splicing regulators are not associated with changes in alternative splicing levels in primates
    Manuel Irimia
    Departament de Genetica, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
    PLoS ONE 4:e5800. 2009
    ....
  11. pmc Contrasting 5' and 3' evolutionary histories and frequent evolutionary convergence in Meis/hth gene structures
    Manuel Irimia
    Department of Genetics, School of Biology, University of Barcelona, Barcelona, Spain
    Genome Biol Evol 3:551-64. 2011
    ..These results attest to the importance of locus-specific splicing functions in differences in structural evolution across genes, as well as to commonalities of forces shaping the evolution of individual genes along different lineages...
  12. pmc Conserved developmental expression of Fezf in chordates and Drosophila and the origin of the Zona Limitans Intrathalamica (ZLI) brain organizer
    Manuel Irimia
    Departament de Genètica and Institut de Biomedicina IBUB, Universitat de Barcelona, Barcelona, Spain
    Evodevo 1:7. 2010
    ..These organizers are located at the interface of the expression domains of key patterning genes (Fezf-Irx and Otx-Gbx, respectively). To gain insights into the evolutionary origin of the ZLI, we studied Fezf in bilaterians...
  13. pmc Evolutionary convergence on highly-conserved 3' intron structures in intron-poor eukaryotes and insights into the ancestral eukaryotic genome
    Manuel Irimia
    Departament de Genetica, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
    PLoS Genet 4:e1000148. 2008
    ....
  14. pmc Functional and evolutionary analysis of alternatively spliced genes is consistent with an early eukaryotic origin of alternative splicing
    Manuel Irimia
    Allan Wilson Centre for Molecular Evolution and Ecology, Massey University, Palmerston North, New Zealand
    BMC Evol Biol 7:188. 2007
    ....
  15. ncbi request reprint Widespread evolutionary conservation of alternatively spliced exons in Caenorhabditis
    Manuel Irimia
    Departament de Genetica, Universitat de Barcelona, Barcelona, Spain
    Mol Biol Evol 25:375-82. 2008
    ..Finally, we demonstrate an inverse relationship between AS and gene duplication, suggesting that the latter may be primarily responsible for the emergence of new functional transcripts in nematodes...
  16. doi request reprint From the American to the European amphioxus: towards experimental Evo-Devo at the origin of chordates
    Jordi Garcia-Fernandez
    Departament de Genetica, Facultat de Biologia, Universitat de Barcelona, Spain
    Int J Dev Biol 53:1359-66. 2009
    ..We summarise here our progress towards the dream of the experimental manipulation of the amphioxus embryo, to enter the era of Experimental Evo-Devo...
  17. pmc An ancient genomic regulatory block conserved across bilaterians and its dismantling in tetrapods by retrogene replacement
    Ignacio Maeso
    Departament de Genetica, Facultat de Biologia, Universitat de Barcelona 08028, Barcelona, Spain
    Genome Res 22:642-55. 2012
    ....
  18. ncbi request reprint Coevolution of genomic intron number and splice sites
    Manuel Irimia
    Allan Wilson Centre for Molecular Evolution and Ecology, Massey University, Palmerston North, New Zealand
    Trends Genet 23:321-5. 2007
    ..It seems that eukaryotic ancestors had relatively large intron numbers and 'weak' 5'ss, a pattern associated with frequent alternative splicing in modern organisms...
  19. ncbi request reprint Gene expansion and retention leads to a diverse tyrosine kinase superfamily in amphioxus
    Salvatore D'Aniello
    Departament de Genetica, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
    Mol Biol Evol 25:1841-54. 2008
    ....
  20. doi request reprint The evolutionary landscape of alternative splicing in vertebrate species
    Nuno L Barbosa-Morais
    Banting and Best Department of Medical Research, Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
    Science 338:1587-93. 2012
    ..These events likely further contributed to the diversification of splicing and other transcriptomic changes that underlie phenotypic differences among vertebrate species...
  21. pmc Complex selection on 5' splice sites in intron-rich organisms
    Manuel Irimia
    Departament de Genetica, Facultat de Biologia, Universitat de Barcelona, 08028 Barcelona, Spain
    Genome Res 19:2021-7. 2009
    ....
  22. pmc Internal and external paralogy in the evolution of tropomyosin genes in metazoans
    Manuel Irimia
    Departament de Genetica, Facultat de Biologia, Universitat de Barcelona, Barcelona, Spain
    Mol Biol Evol 27:1504-17. 2010
    ..This parallel evolution of TPM genes in diverse metazoans attests to common selective forces driving divergence of different gene transcripts and represents a striking case of emergence of evolutionary novelty by alternative splicing...
  23. pmc Distinct types of disorder in the human proteome: functional implications for alternative splicing
    Recep Colak
    The Donnelly Centre, University of Toronto, Toronto, Ontario, Canada
    PLoS Comput Biol 9:e1003030. 2013
    ....
  24. pmc Spliceosomal introns as tools for genomic and evolutionary analysis
    Manuel Irimia
    Departament de Genetica, Universitat de Barcelona, Barcelona, Spain
    Nucleic Acids Res 36:1703-12. 2008
    ..We conclude with a discussion of phylogenetic methods utilizing intron sequences and positions...
  25. pmc Deep conservation of cis-regulatory elements in metazoans
    Ignacio Maeso
    Department of Zoology, University of Oxford, Oxford, UK
    Philos Trans R Soc Lond B Biol Sci 368:20130020. 2013
    ..Here, we review recent studies that revealed such deeply conserved CREs do exist, discuss the difficulties associated with their identification and describe new approaches that will facilitate this search...
  26. ncbi request reprint Rare coding sequence changes are consistent with Ecdysozoa, not Coelomata
    Manuel Irimia
    Departament de Genetica, Universitat de Barcelona, Barcelona, Spain
    Mol Biol Evol 24:1604-7. 2007
    ..Including the additional species paints a very different picture, with 13 remaining characters consistent with Ecdysozoa versus only 1 consistent with Coelomata...
  27. pmc A compendium of RNA-binding motifs for decoding gene regulation
    Debashish Ray
    Donnelly Centre, University of Toronto, Toronto M5S 3E1, Canada
    Nature 499:172-7. 2013
    ..These data provide an unprecedented overview of RNA-binding proteins and their targets, and constitute an invaluable resource for determining post-transcriptional regulatory mechanisms in eukaryotes. ..
  28. doi request reprint When good transcripts go bad: artifactual RT-PCR 'splicing' and genome analysis
    Scott William Roy
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD 20894, USA
    Bioessays 30:601-5. 2008
    ..Supplementary material for this article can be found on the BioEssays website (http://www.interscience.wiley.com/jpages/0265-9247/suppmat/index.html)...
  29. pmc Origins of human malaria: rare genomic changes and full mitochondrial genomes confirm the relationship of Plasmodium falciparum to other mammalian parasites but complicate the origins of Plasmodium vivax
    Scott William Roy
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
    Mol Biol Evol 25:1192-8. 2008
    ..Finally, we find a lack of synapomorphic gene losses, suggesting a low rate of ancestral gene loss in Plasmodium...
  30. doi request reprint Rare genomic characters do not support Coelomata: intron loss/gain
    Scott William Roy
    National Center for Biotechnology Information, National Library of Medicine, National Institutes of Health, Bethesda, MD, USA
    Mol Biol Evol 25:620-3. 2008
    ..2005a. Resolution of a deep animal divergence by the pattern of intron conservation. Proc Natl Acad Sci USA. 102:4403-4408.). Instead, we show that our conclusions are likely to be robust to such concerns...
  31. pmc MBNL proteins repress ES-cell-specific alternative splicing and reprogramming
    Hong Han
    Banting and Best Department of Medical Research and Donnelly Centre, University of Toronto, Toronto, Ontario M5S 3E1, Canada
    Nature 498:241-5. 2013
    ....
  32. ncbi request reprint Alternative splicing: decoding an expansive regulatory layer
    Manuel Irimia
    Banting and Best Department of Medical Research, Donnelly Centre, University of Toronto, Canada
    Curr Opin Cell Biol 24:323-32. 2012
    ..Particularly intriguing is the discovery of new AS 'switches' that control transcriptional networks required for animal development and behavior...
  33. doi request reprint Impact of gene gains, losses and duplication modes on the origin and diversification of vertebrates
    Cristian Canestro
    Departament de Genetica, Facultat de Biologia, Universitat de Barcelona, Av Diagonal 645, 08028 Barcelona, Spain
    Semin Cell Dev Biol 24:83-94. 2013
    ....
  34. pmc 5-hmC in the brain is abundant in synaptic genes and shows differences at the exon-intron boundary
    Tarang Khare
    The Krembil Family Epigenetics Laboratory, The Campbell Family Mental Health Research Institute, Centre for Addiction and Mental Health, Toronto, Ontario, Canada
    Nat Struct Mol Biol 19:1037-43. 2012
    ..Moreover, in human frontal cortex, constitutive exons contained higher levels of 5-hmC relative to alternatively spliced exons. Our study suggests a new role for 5-hmC in RNA splicing and synaptic function in the brain...
  35. doi request reprint Tissue-specific alternative splicing remodels protein-protein interaction networks
    Jonathan D Ellis
    Banting and Best Department of Medical Research, Donnelly Centre, University of Toronto, Toronto, ON M5S 3E1, Canada
    Mol Cell 46:884-92. 2012
    ..Collectively, our results provide evidence that regulated alternative exons frequently remodel interactions to establish tissue-dependent PPI networks...
  36. doi request reprint A comparative transcriptomic analysis reveals conserved features of stem cell pluripotency in planarians and mammals
    Roselyne M Labbé
    The Hospital for Sick Children, Program in Developmental and Stem Cell Biology, University of Toronto, Toronto, Ontario, Canada
    Stem Cells 30:1734-45. 2012
    ..These results provide insights into which genes comprised the ancestral circuitry underlying the control of stem cell self-renewal and pluripotency...
  37. doi request reprint Convergent evolution of clustering of Iroquois homeobox genes across metazoans
    Manuel Irimia
    Mol Biol Evol 25:1521-5. 2008
    ..Finally, we discuss the possible causes and implications of the convergent evolution of this genomic and regulatory organization throughout metazoans...
  38. ncbi request reprint High qualitative and quantitative conservation of alternative splicing in Caenorhabditis elegans and Caenorhabditis briggsae
    Jakob Lewin Rukov
    Molecular Evolution Group, Department of Molecular Biology, University of Copenhagen, Ole Maaløes Vej 5, DK 2200 Copenhagen N, Denmark
    Mol Biol Evol 24:909-17. 2007
    ..Moreover, our results indicate that AS contributes little to transcript variation in Caenorhabditis genes and that gene duplication may be the major evolutionary mechanism for the origin of novel transcripts in these 2 species...
  39. doi request reprint Rare genomic characters do not support Coelomata: RGC_CAMs
    Scott William Roy
    J Mol Evol 66:308-15. 2008
    ..These results indicate that the Coelomata signal is a long-branch artifact...
  40. ncbi request reprint Very little intron gain in Entamoeba histolytica genes laterally transferred from prokaryotes
    Scott William Roy
    Mol Biol Evol 23:1824-7. 2006
    ..5 billion years. Nine other predicted introns are due to annotation errors reflecting apparent mistakes in the E. histolytica genome assembly. These results underscore the massive differences in intron gain rates through evolution...