Jernej Ule

Summary

Affiliation: University of Cambridge
Country: UK

Publications

  1. ncbi 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

Detail Information

Publications18

  1. ncbi 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. ncbi 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 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...
  13. 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. ..
  14. 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. ..
  15. 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...
  16. ncbi 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"...
  17. 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...