Jernej Ule: Publications

  • Dixit, S; Müller-McNicoll, M; David, V; Zarnack, K; Ule, J; Hashimi, H and Lukeš, J (2017)
    Differential binding of mitochondrial transcripts by MRB8170 and MRB4160 regulates distinct editing fates of mitochondrial mRNA in Trypanosomes.
    mBio 8, e02288-02216 PubMed abstract
  • George, H; Ule, J and Hussain, S (2017)
    Illustrating the epitranscriptome at nucleotide resolution using methylation-iCLIP (miCLIP).
    Methods in Molecular Biology 1562, 91-106 PubMed abstract
  • Haberman, N; Huppertz, I; Attig, J; König, J; Wang, Z; Hauer, C; Hentze, MW; Kulozik, AE; Le Hir, H; Curk, T; Sibley, CR; Zarnack, K and Ule, J (2017)
    Insights into the design and interpretation of iCLIP experiments.
    Genome Biology 18, 7 PubMed abstract
  • Simone, R; Javad, F; Emmett, W; Ehteramyan, M; Zuccotti, P; Modelska, A; Siva, K; Hondhamuni, G; Trabzuni, D; Ryten, M; Wray, S; Preza, E; Kia, D; Pittman, A; Lees, A; Hardy, J; Denti, MA; Quattrone, A; Warner, TT; Plagnol, V; Ule, J and de Silva, R (2017)
    Antisense long non-coding RNA represses MAPT translation through an embedded MIR repeat.
    Neuropathology and Applied Neurobiology 43, 24-25, Abstract O24
  • Skalska, L; Beltran-Nebot, M; Ule, J and Jenner, RG (2017)
    Regulatory feedback from nascent RNA to chromatin and transcription.
    Nature Reviews Molecular Cell Biology [Epub ahead of print] PubMed abstract
  • Soreq, L; UK Brain Expression Consortium; North American Brain Expression Consortium; Rose, J; Soreq, E; Hardy, J; Trabzuni, D; Cookson, MR; Smith, C; Ryten, M; Patani, R and Ule, J (2017)
    Major shifts in glial regional identity are a transcriptional hallmark of human brain aging.
    Cell Reports 18, 557-570 PubMed abstract
  • Sugimoto, Y; Chakrabarti, AM; Luscombe, NM and Ule, J (2017)
    Using hiCLIP to identify RNA duplexes that interact with a specific RNA-binding protein.
    Nature Protocols 12, 611-637 PubMed abstract
  • Attig, J; Ruiz de Los Mozos, I; Haberman, N; Wang, Z; Emmett, W; Zarnack, K; König, J and Ule, J (2016)
    Splicing repression allows the gradual emergence of new Alu-exons in primate evolution.
    eLife 5, e19545 PubMed abstract
  • Beltran, M; Yates, CM; Skalska, L; Dawson, M; Reis, FP; Viiri, K; Fisher, CL; Sibley, CR; Foster, BM; Bartke, T; Ule, J and Jenner, RG (2016)
    The interaction of PRC2 with RNA or chromatin is mutually antagonistic.
    Genome Research 26, 896-907 PubMed abstract
  • Coelho, MB; Attig, J; Ule, J and Smith, CWJ (2016)
    Matrin3: connecting gene expression with the nuclear matrix.
    Wiley Interdisciplinary Reviews. RNA 7, 303-315 PubMed abstract
  • Kolisnyk, B; Al-Onaizi, M; Soreq, L; Barbash, S; Bekenstein, U; Haberman, N; Hanin, G; Kish, MT; Souza da Silva, J; Fahnestock, M; Ule, J; Soreq, H; Prado, VF and Prado, MAM (2016)
    Cholinergic surveillance over hippocampal RNA metabolism and Alzheimer's-like pathology.
    Cerebral Cortex [Epub ahead of print] PubMed abstract
  • Llorian, M; Gooding, C; Bellora, N; Hallegger, M; Buckroyd, A; Wang, X; Rajgor, D; Kayikci, M; Feltham, J; Ule, J; Eyras, E and Smith, CWJ (2016)
    The alternative splicing program of differentiated smooth muscle cells involves concerted non-productive splicing of post-transcriptional regulators.
    Nucleic Acids Research 44, 8933-8950 PubMed abstract
  • Sibley, CR; Blazquez, L and Ule, J (2016)
    Lessons from non-canonical splicing.
    Nature Reviews Genetics 17, 407-421 PubMed abstract
  • Stražar, M; Žitnik, M; Zupan, B; Ule, J and Curk, T (2016)
    Orthogonal matrix factorization enables integrative analysis of multiple RNA binding proteins.
    Bioinformatics 32, 1527-1535 PubMed abstract
  • Apolonia, L; Schulz, R; Curk, T; Rocha, P; Swanson, CM; Schaller, T; Ule, J and Malim, MH (2015)
    Promiscuous RNA binding ensures effective encapsidation of APOBEC3 proteins by HIV-1.
    PLOS Pathogens 11, e1004609 PubMed abstract
  • Coelho, MB; Attig, J; Bellora, N; König, J; Hallegger, M; Kayikci, M; Eyras, E; Ule, J and Smith, CWJ (2015)
    Nuclear matrix protein Matrin3 regulates alternative splicing and forms overlapping regulatory networks with PTB.
    EMBO Journal 34, 653-668 PubMed abstract
  • Diaz-Muñoz, MD; Bell, SE; Fairfax, K; Monzon-Casanova, E; Cunningham, AF; Gonzalez-Porta, M; Andrews, SR; Bunik, VI; Zarnack, K; Curk, T; Heggermont, WA; Heymans, S; Gibson, GE; Kontoyiannis, DL; Ule, J and Turner, M (2015)
    The RNA-binding protein HuR is essential for the B cell antibody response.
    Nature Immunology 16, 415-425 PubMed abstract
  • Mirtschink, P; Krishnan, J; Grimm, F; Sarre, A; Hörl, M; Kayikci, M; Fankhauser, N; Christinat, Y; Cortijo, C; Feehan, O; Vukolic, A; Sossalla, S; Stehr, SN; Ule, J; Zamboni, N; Pedrazzini, T and Krek, W (2015)
    HIF-driven SF3B1 induces KHK-C to enforce fructolysis and heart disease.
    Nature 522, 444-449 PubMed abstract
  • Murn, J; Zarnack, K; Yang, YJ; Durak, O; Murphy, EA; Cheloufi, S; Gonzalez, DM; Teplova, M; Curk, T; Zuber, J; Patel, DJ; Ule, J; Luscombe, NM; Tsai, L-H; Walsh, CA and Shi, Y (2015)
    Control of a neuronal morphology program by an RNA-binding zinc finger protein, Unkempt.
    Genes & Development 29, 501-512 PubMed abstract
  • Rivers, C; Idris, J; Scott, H; Rogers, M; Lee, Y-B; Gaunt, J; Phylactou, L; Curk, T; Campbell, C; Ule, J; Norman, M and Uney, JB (2015)
    iCLIP identifies novel roles for SAFB1 in regulating RNA processing and neuronal function.
    BMC Biology 13, 111 PubMed abstract
  • Sibley, CR; Emmett, W; Blazquez, L; Faro, A; Haberman, N; Briese, M; Trabzuni, D; Ryten, M; Weale, ME; Hardy, J; Modic, M; Curk, T; Wilson, SW; Plagnol, V and Ule, J (2015)
    Recursive splicing in long vertebrate genes.
    Nature 521, 371-375 PubMed abstract
  • Sugimoto, Y; Vigilante, A; Darbo, E; Zirra, A; Militti, C; D'Ambrogio, A; Luscombe, NM and Ule, J (2015)
    hiCLIP reveals the in vivo atlas of mRNA secondary structures recognized by Staufen 1.
    Nature 519, 491-494 PubMed abstract
  • Tajnik, M; Vigilante, A; Braun, S; Hänel, H; Luscombe, NM; Ule, J; Zarnack, K and König, J (2015)
    Intergenic Alu exonisation facilitates the evolution of tissue-specific transcript ends.
    Nucleic Acids Research 43, 10492-10505 PubMed abstract
  • Uren, PJ; Vo, DT; de Araujo, PR; Pötschke, R; Burns, SC; Bahrami-Samani, E; Qiao, M; de Sousa Abreu, R; Nakaya, HI; Correa, BR; Kühnöl, C; Ule, J; Martindale, JL; Abdelmohsen, K; Gorospe, M; Smith, AD and Penalva, LOF (2015)
    RNA-binding protein Musashi1 is a central regulator of adhesion pathways in glioblastoma.
    Molecular and Cellular Biology 35, 2965-2978 PubMed abstract
  • Wickramasinghe, VO; Gonzàlez-Porta, M; Perera, D; Bartolozzi, AR; Sibley, CR; Hallegger, M; Ule, J; Marioni, JC and Venkitaraman, AR (2015)
    Regulation of constitutive and alternative mRNA splicing across the human transcriptome by PRPF8 is determined by 5ʹ splice site strength.
    Genome Biology 16, 201 PubMed abstract
  • Blanco, S; Dietmann, S; Flores, JV; Hussain, S; Kutter, C; Humphreys, P; Lukk, M; Lombard, P; Treps, L; Popis, M; Kellner, S; Hölter, SM; Garrett, L; Wurst, W; Becker, L; Klopstock, T; Fuchs, H; Gailus-Durner, V; Hrabĕ de Angelis, M; Káradóttir, RT; Helm, M; Ule, J; Gleeson, JG; Odom, DT and Frye, M (2014)
    Aberrant methylation of tRNAs links cellular stress to neuro-developmental disorders.
    EMBO Journal 33, 2020-2039 PubMed abstract
  • Boehm, V; Haberman, N; Ottens, F; Ule, J and Gehring, NH (2014)
    3ʹ UTR length and messenger ribonucleoprotein composition determine endocleavage efficiencies at termination codons.
    Cell Reports 9, 555-568 PubMed abstract
  • Cereda, M; Pozzoli, U; Rot, G; Juvan, P; Schweitzer, A; Clark, T and Ule, J (2014)
    RNAmotifs: prediction of multivalent RNA motifs that control alternative splicing.
    Genome Biology 15, R20 PubMed abstract
  • Chan, SL; Huppertz, I; Yao, C; Weng, L; Moresco, JJ; Yates, JR, 3rd; Ule, J; Manley, JL and Shi, Y (2014)
    CPSF30 and Wdr33 directly bind to AAUAAA in mammalian mRNA 3ʹ processing.
    Genes & Development 28, 2370-2380 PubMed abstract
  • Huo, Q; Kayikci, M; Odermatt, P; Meyer, K; Michels, O; Saxena, S; Ule, J and Schümperli, D (2014)
    Splicing changes in SMA mouse motoneurons and SMN-depleted neuroblastoma cells: evidence for involvement of splicing regulatory proteins.
    RNA Biology 11, 1430-1446 PubMed abstract
  • Huppertz, I; Attig, J; D'Ambrogio, A; Easton, LE; Sibley, CR; Sugimoto, Y; Tajnik, M; König, J and Ule, J (2014)
    iCLIP: protein-RNA interactions at nucleotide resolution.
    Methods 65, 274-287 PubMed abstract
  • Machyna, M; Kehr, S; Straube, K; Kappei, D; Buchholz, F; Butter, F; Ule, J; Hertel, J; Stadler, PF and Neugebauer, KM (2014)
    The coilin interactome identifies hundreds of small noncoding RNAs that traffic through Cajal bodies.
    Molecular Cell 56, 389-399 PubMed abstract
  • Raj, B; Irimia, M; Braunschweig, U; Sterne-Weiler, T; O'Hanlon, D; Lin, Z-Y; Chen, GI; Easton, LE; Ule, J; Gingras, A-C; Eyras, E and Blencowe, BJ (2014)
    A global regulatory mechanism for activating an exon network required for neurogenesis.
    Molecular Cell 56, 90-103 PubMed abstract
  • Rinn, JL and Ule, J (2014)
    'Oming in on RNA-protein interactions.
    Genome Biology 15, 401 PubMed abstract
  • Rossbach, O; Hung, L-H; Khrameeva, E; Schreiner, S; König, J; Curk, T; Zupan, B; Ule, J; Gelfand, MS and Bindereif, A (2014)
    Crosslinking-immunoprecipitation (iCLIP) analysis reveals global regulatory roles of hnRNP L.
    RNA Biology 11, 146-155 PubMed abstract
  • Singh, RK; Xia, Z; Bland, CS; Kalsotra, A; Scavuzzo, MA; Curk, T; Ule, J; Li, W and Cooper, TA (2014)
    Rbfox2-coordinated alternative splicing of Mef2d and Rock2 controls myoblast fusion during myogenesis.
    Molecular Cell 55, 592-603 PubMed abstract
  • Anantha, RW; Alcivar, AL; Ma, J; Cai, H; Simhadri, S; Ule, J; König, J and Xia, B (2013)
    Requirement of heterogeneous nuclear ribonucleoprotein C for BRCA gene expression and homologous recombination.
    PLOS ONE 8, e61368 PubMed abstract
  • Doolittle, WF; Fraser, P; Gerstein, MB; Graveley, BR; Henikoff, S; Huttenhower, C; Oshlack, A; Ponting, CP; Rinn, JL; Schatz, MC; Ule, J; Weigel, D and Weinstock, GM (2013)
    Sixty years of genome biology.
    Genome Biology 14, 113 PubMed abstract
  • Hussain, S; Sajini, AA; Blanco, S; Dietmann, S; Lombard, P; Sugimoto, Y; Paramor, M; Gleeson, JG; Odom, DT; Ule, J and Frye, M (2013)
    NSun2-mediated cytosine-5 methylation of vault noncoding RNA determines its processing into regulatory small RNAs.
    Cell Reports 4, 255-261 PubMed abstract
  • Kiebler, MA; Scheiffele, P and Ule, J (2013)
    What, where, and when: the importance of post-transcriptional regulation in the brain.
    Frontiers in Neuroscience 7, 192 PubMed abstract
  • Lee, Y-B; Chen, H-J; Peres, JN; Gomez-Deza, J; Attig, J; Štalekar, M; Troakes, C; Nishimura, AL; Scotter, EL; Vance, C; Adachi, Y; Sardone, V; Miller, JW; Smith, BN; Gallo, J-M; Ule, J; Hirth, F; Rogelj, B; Houart, C and Shaw, CE (2013)
    Hexanucleotide repeats in ALS/FTD form length-dependent RNA foci, sequester RNA binding proteins, and are neurotoxic.
    Cell Reports 5, 1178-1186 PubMed abstract
  • Lukavsky, PJ; Daujotyte, D; Tollervey, JR; Ule, J; Stuani, C; Buratti, E; Baralle, FE; Damberger, FF and Allain, FHT (2013)
    Molecular basis of UG-rich RNA recognition by the human splicing factor TDP-43.
    Nature Structural & Molecular Biology 20, 1443-1449 PubMed abstract
  • Modic, M; Ule, J and Sibley, CR (2013)
    CLIPing the brain: studies of protein-RNA interactions important for neurodegenerative disorders.
    Molecular and Cellular Neurosciences 56, 429-435 PubMed abstract
  • Sun, W; Wagnon, JL; Mahaffey, CL; Briese, M; Ule, J and Frankel, WN (2013)
    Aberrant sodium channel activity in the complex seizure disorder of Celf4 mutant mice.
    Journal of Physiology 591, 241-255 PubMed abstract
  • Ule, J (2013)
    Alu elements: at the crossroads between disease and evolution.
    Biochemical Society Transactions 41, 1532-1535 PubMed abstract
  • Zarnack, K; König, J; Tajnik, M; Martincorena, I; Eustermann, S; Stévant, I; Reyes, A; Anders, S; Luscombe, NM and Ule, J (2013)
    Direct competition between hnRNP C and U2AF65 protects the transcriptome from the exonization of Alu elements.
    Cell 152, 453-466 PubMed abstract
  • Änkó, M-L; Müller-McNicoll, M; Brandl, H; Curk, T; Gorup, C; Henry, I; Ule, J and Neugebauer, KM (2012)
    The RNA-binding landscapes of two SR proteins reveal unique functions and binding to diverse RNA classes.
    Genome Biology 13, R17 PubMed abstract
  • Ince-Dunn, G; Okano, HJ; Jensen, KB; Park, W-Y; Zhong, R; Ule, J; Mele, A; Fak, JJ; Yang, C; Zhang, C; Yoo, J; Herre, M; Okano, H; Noebels, JL and Darnell, RB (2012)
    Neuronal Elav-like (Hu) proteins regulate RNA splicing and abundance to control glutamate levels and neuronal excitability.
    Neuron 75, 1067-1080 PubMed abstract
  • König, J; Zarnack, K; Luscombe, NM and Ule, J (2012)
    Protein-RNA interactions: new genomic technologies and perspectives.
    Nature Reviews Genetics 13, 77-83 PubMed abstract
  • McGlincy, NJ; Valomon, A; Chesham, JE; Maywood, ES; Hastings, MH and Ule, J (2012)
    Regulation of alternative splicing by the circadian clock and food related cues.
    Genome Biology 13, R54 PubMed abstract
  • Patani, R; Sibley, CR; Chandran, S and Ule, J (2012)
    Using human pluripotent stem cells to study post-transcriptional mechanisms of neurodegenerative diseases.
    Brain Research 1462, 129-138 PubMed abstract
  • Pradeepa, MM; Sutherland, HG; Ule, J; Grimes, GR and Bickmore, WA (2012)
    Psip1/Ledgf p52 binds methylated histone H3K36 and splicing factors and contributes to the regulation of alternative splicing.
    PLOS Genetics 8, e1002717 PubMed abstract
  • Rogelj, B; Easton, LE; Bogu, GK; Stanton, LW; Rot, G; Curk, T; Zupan, B; Sugimoto, Y; Modic, M; Haberman, N; Tollervey, J; Fujii, R; Takumi, T; Shaw, CE and Ule, J (2012)
    Widespread binding of FUS along nascent RNA regulates alternative splicing in the brain.
    Scientific Reports 2, 603 PubMed abstract
  • Schor, IE; Llères, D; Risso, GJ; Pawellek, A; Ule, J; Lamond, AI and Kornblihtt, AR (2012)
    Perturbation of chromatin structure globally affects localization and recruitment of splicing factors.
    PLOS ONE 7, e48084 PubMed abstract
  • Sibley, CR; Attig, J and Ule, J (2012)
    The greatest catch: big game fishing for mRNA-bound proteins.
    Genome Biology 13, 163 PubMed abstract
  • Sugimoto, Y; König, J; Hussain, S; Zupan, B; Curk, T; Frye, M and Ule, J (2012)
    Analysis of CLIP and iCLIP methods for nucleotide-resolution studies of protein-RNA interactions.
    Genome Biology 13, R67 PubMed abstract
  • Wagnon, JL; Briese, M; Sun, W; Mahaffey, CL; Curk, T; Rot, G; Ule, J and Frankel, WN (2012)
    CELF4 regulates translation and local abundance of a vast set of mRNAs, including genes associated with regulation of synaptic function.
    PLOS Genetics 8, e1003067 PubMed abstract
  • Ayala, YM; De Conti, L; Avendaño-Vázquez, SE; Dhir, A; Romano, M; D'Ambrogio, A; Tollervey, J; Ule, J; Baralle, M; Buratti, E and Baralle, FE (2011)
    TDP-43 regulates its mRNA levels through a negative feedback loop.
    EMBO Journal 30, 277-288 PubMed abstract
  • Blazek, D; Kohoutek, J; Bartholomeeusen, K; Johansen, E; Hulinkova, P; Luo, Z; Cimermancic, P; Ule, J and Peterlin, BM (2011)
    The Cyclin K/Cdk12 complex maintains genomic stability via regulation of expression of DNA damage response genes.
    Genes & Development 25, 2158-2172 PubMed abstract
  • Koepke, J; Kaffarnik, F; Haag, C; Zarnack, K; Luscombe, NM; König, J; Ule, J; Kellner, R; Begerow, D and Feldbrügge, M (2011)
    The RNA-binding protein Rrm4 is essential for efficient secretion of endochitinase Cts1.
    Molecular & Cellular Proteomics 10, M111.011213 PubMed abstract
  • König, J; Zarnack, K; Rot, G; Curk, T; Kayikci, M; Zupan, B; Turner, DJ; Luscombe, NM and Ule, J (2011)
    iCLIP--transcriptome-wide mapping of protein-RNA interactions with individual nucleotide resolution.
    Journal of Visualized Experiments 50, e2638 PubMed abstract
  • Léveillé, N; Elkon, R; Davalos, V; Manoharan, V; Hollingworth, D; Oude Vrielink, J; le Sage, C; Melo, CA; Horlings, HM; Wesseling, J; Ule, J; Esteller, M; Ramos, A and Agami, R (2011)
    Selective inhibition of microRNA accessibility by RBM38 is required for p53 activity.
    Nature Communications 2, 513 PubMed abstract
  • Tollervey, JR; Curk, T; Rogelj, B; Briese, M; Cereda, M; Kayikci, M; König, J; Hortobágyi, T; Nishimura, AL; Župunski, V; Patani, R; Chandran, S; Rot, G; Zupan, B; Shaw, CE and Ule, J (2011)
    Characterizing the RNA targets and position-dependent splicing regulation by TDP-43.
    Nature Neuroscience 14, 452-458 PubMed abstract
  • Tollervey, JR; Wang, Z; Hortobágyi, T; Witten, JT; Zarnack, K; Kayikci, M; Clark, TA; Schweitzer, AC; Rot, G; Curk, T; Zupan, B; Rogelj, B; Shaw, CE and Ule, J (2011)
    Analysis of alternative splicing associated with aging and neurodegeneration in the human brain.
    Genome Research 21, 1572-1582 PubMed abstract
  • Witten, JT and Ule, J (2011)
    Understanding splicing regulation through RNA splicing maps.
    Trends in Genetics 27, 89-97 PubMed abstract
  • Jelen, N; Ule, J and Živin, M (2010)
    Cholinergic regulation of striatal Nova mRNAs.
    Neuroscience 169, 619-627 PubMed abstract
  • König, J; Zarnack, K; Rot, G; Curk, T; Kayikci, M; Zupan, B; Turner, DJ; Luscombe, NM and Ule, J (2010)
    iCLIP reveals the function of hnRNP particles in splicing at individual nucleotide resolution.
    Nature Structural & Molecular Biology 17, 909-915 PubMed abstract
  • Racca, C; Gardiol, A; Eom, T; Ule, J; Triller, A and Darnell, RB (2010)
    The neuronal splicing factor Nova co-localizes with target RNAs in the dendrite.
    Frontiers in Neural Circuits 4, 5 PubMed abstract
  • Wang, Z; Kayikci, M; Briese, M; Zarnack, K; Luscombe, NM; Rot, G; Zupan, B; Curk, T and Ule, J (2010)
    iCLIP predicts the dual splicing effects of TIA-RNA interactions.
    PLOS Biology 8, e1000530 PubMed abstract

[Page last updated 1 May 2017]

JernejĀ Ule

jernej.ule@crick.ac.uk
+44 (0)20 379 63137

  • Qualifications and History

  • 2004 PhD, Rockefeller University, New York
  • 2004 Post Doctoral Fellow, Rockefeller University, New York
  • 2006 Group Leader, Medical Research Council, Laboratory of Molecular Biology, UK
  • 2013 Group Leader, Department of Molecular Neuroscience, UCL Institute of Neurology
  • 2016 Group Leader, the Francis Crick Institute, London, UK