Jernej Ule

Summary

Affiliation: University of Cambridge
Country: UK

Publications

  1. doi request reprint High-throughput sequencing methods to study neuronal RNA-protein interactions
    Jernej Ule
    MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
    Biochem Soc Trans 37:1278-80. 2009
  2. pmc Widespread binding of FUS along nascent RNA regulates alternative splicing in the brain
    Boris Rogelj
    Centre for Neurodegeneration Research, King s College London, Institute of Psychiatry, De Crespigny Park, London, UK
    Sci Rep 2:603. 2012
  3. pmc Analysis of CLIP and iCLIP methods for nucleotide-resolution studies of protein-RNA interactions
    Yoichiro Sugimoto
    MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
    Genome Biol 13:R67. 2012
  4. pmc The RNA-binding landscapes of two SR proteins reveal unique functions and binding to diverse RNA classes
    Minna Liisa Ankö
    Max Planck Institute of Cell Biology and Genetics, Dresden, Germany
    Genome Biol 13:R17. 2012
  5. pmc Direct competition between hnRNP C and U2AF65 protects the transcriptome from the exonization of Alu elements
    Kathi Zarnack
    European Molecular Biology Laboratory EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Cell 152:453-66. 2013
  6. doi request reprint Ribonucleoprotein complexes in neurologic diseases
    Jernej Ule
    MRC Laboratory of Molecular Biology, Cambridge, UK
    Curr Opin Neurobiol 18:516-23. 2008
  7. pmc Analysis of alternative splicing associated with aging and neurodegeneration in the human brain
    James R Tollervey
    MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
    Genome Res 21:1572-82. 2011
  8. pmc iCLIP predicts the dual splicing effects of TIA-RNA interactions
    Zhen Wang
    Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge, United Kingdom
    PLoS Biol 8:e1000530. 2010
  9. pmc CLIPing the brain: studies of protein-RNA interactions important for neurodegenerative disorders
    Miha Modic
    MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 0QH, UK Gene Center and Department of Biochemistry, Ludwig Maximilians Universitat Munchen, Feodor Lynen Strasse 25, 81377 Munich, Germany
    Mol Cell Neurosci 56:429-35. 2013
  10. pmc Characterizing the RNA targets and position-dependent splicing regulation by TDP-43
    James R Tollervey
    Medical Research Council MRC Laboratory of Molecular Biology, Cambridge, UK
    Nat Neurosci 14:452-8. 2011

Collaborators

  • Siddharthan Chandran
  • Nicholas M Luscombe
  • Gregor Rot
  • Michaela Frye
  • Christopher E Shaw
  • Zhen Wang
  • Tibor Hortobagyi
  • Boris Rogelj
  • Mark Helm
  • John Hardy
  • Blaz Zupan
  • Vincent Plagnol
  • Eduardo Eyras
  • Elizabeth S Maywood
  • Nicholas J McGlincy
  • Tyson A Clark
  • Duncan T Odom
  • Julian König
  • Yoichiro Sugimoto
  • Tomaz Curk
  • Kathi Zarnack
  • Christopher R Sibley
  • Shobbir Hussain
  • Melis Kayikci
  • James R Tollervey
  • Sandra Blanco
  • Miha Modic
  • Rickie Patani
  • Joshua T Witten
  • Miguel B Coelho
  • Manuel D Díaz-Muñoz
  • Andrea D'Ambrogio
  • Jan Attig
  • Ina Huppertz
  • Sabine Dietmann
  • Patrick Lombard
  • Mojca Tajnik
  • Joseph G Gleeson
  • Michael Briese
  • Minna Liisa Ankö
  • Nicolas Bellora
  • Martina Hallegger
  • Dimitris L Kontoyiannis
  • Martin Turner
  • Elodie Darbo
  • Adam F Cunningham
  • Simon R Andrews
  • Stephen W Wilson
  • Victoria I Bunik
  • Sarah E Bell
  • Christopher W J Smith
  • Mar Gonzàlez-Porta
  • Gary E Gibson
  • Ana Faro
  • Michael E Weale
  • Elisa Monzon-Casanova
  • Warren Emmett
  • Ward A Heggermont
  • Kirsten Fairfax
  • Lorea Blázquez
  • Mina Ryten
  • Alessandra Vigilante
  • Daniah Trabzuni
  • Alexandra Zirra
  • Nejc Haberman
  • Stephane Heymans
  • Cristina Militti
  • Thomas Klopstock
  • Martyna Popis
  • Wolfgang Wurst
  • Helmut Fuchs
  • Lillian Garrett
  • Valerie Gailus-Durner
  • Martin Hrabe de Angelis
  • Peter Humphreys
  • Joana V Flores
  • Ragnhildur T Karadottir
  • Lore Becker
  • Laura E Easton
  • Claudia Kutter
  • Stefanie Kellner
  • Sabine M Holter
  • Lucas Treps
  • Margus Lukk
  • Simon Anders
  • Isabelle Stévant
  • Abdulrahim A Sajini
  • Inigo Martincorena
  • Maike Paramor
  • Sebastian Eustermann

Detail Information

Publications23

  1. doi request reprint High-throughput sequencing methods to study neuronal RNA-protein interactions
    Jernej Ule
    MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
    Biochem Soc Trans 37:1278-80. 2009
    ..It is certain, however, that applications of new biochemical techniques followed by high-throughput sequencing will continue to provide important insights into the mechanisms of neuronal post-transcriptional regulation...
  2. pmc Widespread binding of FUS along nascent RNA regulates alternative splicing in the brain
    Boris Rogelj
    Centre for Neurodegeneration Research, King s College London, Institute of Psychiatry, De Crespigny Park, London, UK
    Sci Rep 2:603. 2012
    ..We did not observe a significant overlap in the RNA binding sites or the exons regulated by FUS and TDP-43. Nevertheless, we found that both proteins regulate genes that function in neuronal development...
  3. pmc Analysis of CLIP and iCLIP methods for nucleotide-resolution studies of protein-RNA interactions
    Yoichiro Sugimoto
    MRC Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
    Genome Biol 13:R67. 2012
    ..In conclusion, we demonstrate how each method impacts the analysis of protein-RNA binding specificity...
  4. pmc The RNA-binding landscapes of two SR proteins reveal unique functions and binding to diverse RNA classes
    Minna Liisa Ankö
    Max Planck Institute of Cell Biology and Genetics, Dresden, Germany
    Genome Biol 13:R17. 2012
    ..The complexity of their RNA targets and specificity of RNA recognition in vivo is not well understood. Here we use iCLIP to globally analyze and compare the RNA binding properties of two SR proteins, SRSF3 and SRSF4, in murine cells...
  5. pmc Direct competition between hnRNP C and U2AF65 protects the transcriptome from the exonization of Alu elements
    Kathi Zarnack
    European Molecular Biology Laboratory EMBL European Bioinformatics Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SD, UK
    Cell 152:453-66. 2013
    ..Thus, by preventing U2AF65 binding to Alu elements, hnRNP C plays a critical role as a genome-wide sentinel protecting the transcriptome. The findings have important implications for human evolution and disease...
  6. doi request reprint Ribonucleoprotein complexes in neurologic diseases
    Jernej Ule
    MRC Laboratory of Molecular Biology, Cambridge, UK
    Curr Opin Neurobiol 18:516-23. 2008
    ..As we learn more about the RNA codes and maps that guide the action of the dynamic RNP world in our brain, possibilities for new treatments of neurologic diseases are bound to emerge...
  7. pmc Analysis of alternative splicing associated with aging and neurodegeneration in the human brain
    James R Tollervey
    MRC Laboratory of Molecular Biology, Cambridge CB2 0QH, United Kingdom
    Genome Res 21:1572-82. 2011
    ..In conclusion, the alternative splicing changes identified in this study provide a new link between aging and neurodegeneration...
  8. pmc iCLIP predicts the dual splicing effects of TIA-RNA interactions
    Zhen Wang
    Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge, United Kingdom
    PLoS Biol 8:e1000530. 2010
    ..Thus, our findings indicate that changes in splicing kinetics could mediate the distal regulation of alternative splicing...
  9. pmc CLIPing the brain: studies of protein-RNA interactions important for neurodegenerative disorders
    Miha Modic
    MRC Laboratory of Molecular Biology, Hills Road, Cambridge, CB2 0QH, UK Gene Center and Department of Biochemistry, Ludwig Maximilians Universitat Munchen, Feodor Lynen Strasse 25, 81377 Munich, Germany
    Mol Cell Neurosci 56:429-35. 2013
    ..This article is part of a Special Issue entitled: RNA and splicing regulation in neurodegeneration. ..
  10. pmc Characterizing the RNA targets and position-dependent splicing regulation by TDP-43
    James R Tollervey
    Medical Research Council MRC Laboratory of Molecular Biology, Cambridge, UK
    Nat Neurosci 14:452-8. 2011
    ....
  11. doi request reprint Protein-RNA interactions: new genomic technologies and perspectives
    Julian König
    Medical Research Council Laboratory of Molecular Biology, Hills Road, Cambridge CB2 0QH, UK
    Nat Rev Genet 13:77-83. 2011
    ..Finally, we highlight current challenges in data analysis and the future steps that are needed to obtain a quantitative and high-resolution picture of protein-RNA interactions on a genome-wide scale...
  12. pmc Aberrant methylation of tRNAs links cellular stress to neuro-developmental disorders
    Sandra Blanco
    Wellcome Trust Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Cambridge, UK
    EMBO J 33:2020-39. 2014
    ..In conclusion, failure in NSun2-mediated tRNA methylation contributes to human diseases via stress-induced RNA cleavage. ..
  13. pmc Regulation of alternative splicing by the circadian clock and food related cues
    Nicholas J McGlincy
    MRC Laboratory of Molecular Biology, Cambridge, UK
    Genome Biol 13:R54. 2012
    ..Such circadian phenotypes are underpinned by daily rhythms in gene expression. Little is known, however, about the contribution of post-transcriptional processes, particularly alternative splicing...
  14. pmc hiCLIP reveals the in vivo atlas of mRNA secondary structures recognized by Staufen 1
    Yoichiro Sugimoto
    MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge Biomedical Campus, Cambridge CB2 0QH, UK
    Nature 519:491-4. 2015
    ..Our study reveals the fundamental role of mRNA secondary structures in gene expression and introduces hiCLIP as a widely applicable method for discovering new, especially long-range, RNA duplexes. ..
  15. pmc Nuclear matrix protein Matrin3 regulates alternative splicing and forms overlapping regulatory networks with PTB
    Miguel B Coelho
    Department of Biochemistry, University of Cambridge, Cambridge, UK
    EMBO J 34:653-68. 2015
    ..The identification of this clear molecular function of Matrin3 should help to clarify the molecular pathology of ALS and other diseases caused by mutations of Matrin3. ..
  16. pmc NSun2-mediated cytosine-5 methylation of vault noncoding RNA determines its processing into regulatory small RNAs
    Shobbir Hussain
    Wellcome Trust Medical Research Council Cambridge Stem Cell Institute, University of Cambridge, Tennis Court Road, Cambridge, CB2 1QR, UK
    Cell Rep 4:255-61. 2013
    ..Thus, impaired processing of vault ncRNA may contribute to the etiology of NSun2-deficiency human disorders. ..
  17. pmc iCLIP: protein-RNA interactions at nucleotide resolution
    Ina Huppertz
    Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
    Methods 65:274-87. 2014
    ..Here, we describe the improved iCLIP protocol and discuss critical optimization and control experiments that are required when applying the method to new RBPs. ..
  18. pmc The RNA-binding protein HuR is essential for the B cell antibody response
    Manuel D Díaz-Muñoz
    Laboratory of Lymphocyte Signalling and Development, The Babraham Institute, Cambridge, UK
    Nat Immunol 16:415-25. 2015
    ..Our study shows how post-transcriptional processes control the balance of energy metabolism required for the proliferation and differentiation of B cells. ..
  19. pmc Recursive splicing in long vertebrate genes
    Christopher R Sibley
    1 Department of Molecular Neuroscience, UCL Institute of Neurology, Queen Square, London WC1N 3BG, UK 2 MRC Laboratory of Molecular Biology, Francis Crick Avenue, Cambridge CB2 0QH, UK
    Nature 521:371-5. 2015
    ..Thus, by establishing a binary splicing switch, RS-sites demarcate different mRNA isoforms emerging from long genes by coupling cryptic elements with inclusion of RS-exons. ..
  20. pmc iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution
    Julian König
    Medical Research Council Laboratory of Molecular Biology, Cambridge, UK
    Nat Struct Mol Biol 17:909-15. 2010
    ..The ability of high-resolution iCLIP data to provide insights into the mechanism of this regulation holds promise for studies of other higher-order ribonucleoprotein complexes...
  21. doi request reprint Using human pluripotent stem cells to study post-transcriptional mechanisms of neurodegenerative diseases
    Rickie Patani
    Anne McLaren Laboratory for Regenerative Medicine, University of Cambridge, Forvie Site, Robinson Way, Cambridge, UK
    Brain Res 1462:129-38. 2012
    ..We conclude by discussing the improvements that could further increase the promise of human pluripotent stem for cell-based disease modeling. This article is part of a Special Issue entitled "RNA-Binding Proteins"...
  22. pmc Understanding splicing regulation through RNA splicing maps
    Joshua T Witten
    MRC Laboratory of Molecular Biology, Hills Road, Cambridge, UK, CB2 0QH
    Trends Genet 27:89-97. 2011
    ..Here, we discuss how insights from RNA splicing maps of different RBPs inform the mechanistic models of splicing regulation...