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Items: 1 to 50 of 104

1.

Cross-Regulation between TDP-43 and Paraspeckles Promotes Pluripotency-Differentiation Transition.

Modic M, Grosch M, Rot G, Schirge S, Lepko T, Yamazaki T, Lee FCY, Rusha E, Shaposhnikov D, Palo M, Merl-Pham J, Cacchiarelli D, Rogelj B, Hauck SM, von Mering C, Meissner A, Lickert H, Hirose T, Ule J, Drukker M.

Mol Cell. 2019 Jun 6;74(5):951-965.e13. doi: 10.1016/j.molcel.2019.03.041. Epub 2019 Apr 29.

2.

Charting DENR-dependent translation reinitiation uncovers predictive uORF features and links to circadian timekeeping via Clock.

Castelo-Szekely V, De Matos M, Tusup M, Pascolo S, Ule J, Gatfield D.

Nucleic Acids Res. 2019 Jun 4;47(10):5193-5209. doi: 10.1093/nar/gkz261.

3.

The origin of neural microexons.

Faraway R, Ule J.

Nat Ecol Evol. 2019 Apr;3(4):526-527. doi: 10.1038/s41559-019-0818-1. No abstract available.

PMID:
30833756
4.

P-TEFb Activation by RBM7 Shapes a Pro-survival Transcriptional Response to Genotoxic Stress.

Bugai A, Quaresma AJC, Friedel CC, Lenasi T, Düster R, Sibley CR, Fujinaga K, Kukanja P, Hennig T, Blasius M, Geyer M, Ule J, Dölken L, Barborič M.

Mol Cell. 2019 Apr 18;74(2):254-267.e10. doi: 10.1016/j.molcel.2019.01.033. Epub 2019 Feb 26.

5.

Genomic Accumulation of Retrotransposons Was Facilitated by Repressive RNA-Binding Proteins: A Hypothesis.

Attig J, Ule J.

Bioessays. 2019 Feb;41(2):e1800132. doi: 10.1002/bies.201800132. Epub 2019 Feb 1.

PMID:
30706962
6.

The key protein of endosomal mRNP transport Rrm4 binds translational landmark sites of cargo mRNAs.

Olgeiser L, Haag C, Boerner S, Ule J, Busch A, Koepke J, König J, Feldbrügge M, Zarnack K.

EMBO Rep. 2019 Jan;20(1). pii: e46588. doi: 10.15252/embr.201846588. Epub 2018 Dec 14.

PMID:
30552148
7.

Exon Junction Complex Shapes the Transcriptome by Repressing Recursive Splicing.

Blazquez L, Emmett W, Faraway R, Pineda JMB, Bajew S, Gohr A, Haberman N, Sibley CR, Bradley RK, Irimia M, Ule J.

Mol Cell. 2018 Nov 1;72(3):496-509.e9. doi: 10.1016/j.molcel.2018.09.033.

8.

Heteromeric RNP Assembly at LINEs Controls Lineage-Specific RNA Processing.

Attig J, Agostini F, Gooding C, Chakrabarti AM, Singh A, Haberman N, Zagalak JA, Emmett W, Smith CWJ, Luscombe NM, Ule J.

Cell. 2018 Aug 23;174(5):1067-1081.e17. doi: 10.1016/j.cell.2018.07.001. Epub 2018 Aug 2.

9.

The Future of Cross-Linking and Immunoprecipitation (CLIP).

Ule J, Hwang HW, Darnell RB.

Cold Spring Harb Perspect Biol. 2018 Aug 1;10(8). pii: a032243. doi: 10.1101/cshperspect.a032243. Review.

10.

'Read-through marking' reveals differential nucleotide composition of read-through and truncated cDNAs in iCLIP.

Huppertz I, Haberman N, Ule J.

Wellcome Open Res. 2018 Jun 22;3:77. doi: 10.12688/wellcomeopenres.14663.1. eCollection 2018.

11.

Intron retention and nuclear loss of SFPQ are molecular hallmarks of ALS.

Luisier R, Tyzack GE, Hall CE, Mitchell JS, Devine H, Taha DM, Malik B, Meyer I, Greensmith L, Newcombe J, Ule J, Luscombe NM, Patani R.

Nat Commun. 2018 May 22;9(1):2010. doi: 10.1038/s41467-018-04373-8.

12.

Positioning Europe for the EPITRANSCRIPTOMICS challenge.

Jantsch MF, Quattrone A, O'Connell M, Helm M, Frye M, Macias-Gonzales M, Ohman M, Ameres S, Willems L, Fuks F, Oulas A, Vanacova S, Nielsen H, Bousquet-Antonelli C, Motorin Y, Roignant JY, Balatsos N, Dinnyes A, Baranov P, Kelly V, Lamm A, Rechavi G, Pelizzola M, Liepins J, Holodnuka Kholodnyuk I, Zammit V, Ayers D, Drablos F, Dahl JA, Bujnicki J, Jeronimo C, Almeida R, Neagu M, Costache M, Bankovic J, Banovic B, Kyselovic J, Valor LM, Selbert S, Pir P, Demircan T, Cowling V, Schäfer M, Rossmanith W, Lafontaine D, David A, Carre C, Lyko F, Schaffrath R, Schwartz S, Verdel A, Klungland A, Purta E, Timotijevic G, Cardona F, Davalos A, Ballana E, O Carroll D, Ule J, Fray R.

RNA Biol. 2018;15(6):829-831. doi: 10.1080/15476286.2018.1460996. Epub 2018 May 9.

13.

The SMAD2/3 interactome reveals that TGFβ controls m6A mRNA methylation in pluripotency.

Bertero A, Brown S, Madrigal P, Osnato A, Ortmann D, Yiangou L, Kadiwala J, Hubner NC, de Los Mozos IR, Sadée C, Lenaerts AS, Nakanoh S, Grandy R, Farnell E, Ule J, Stunnenberg HG, Mendjan S, Vallier L.

Nature. 2018 Mar 8;555(7695):256-259. doi: 10.1038/nature25784. Epub 2018 Feb 28.

14.

No way out: when RNA elements promote nuclear retention.

Agostini F, Ule J, Zagalak JA.

EMBO J. 2018 Mar 15;37(6). pii: e99123. doi: 10.15252/embj.201899123. Epub 2018 Feb 27. No abstract available.

15.

Advances in CLIP Technologies for Studies of Protein-RNA Interactions.

Lee FCY, Ule J.

Mol Cell. 2018 Feb 1;69(3):354-369. doi: 10.1016/j.molcel.2018.01.005. Review.

16.

Tia1 dependent regulation of mRNA subcellular location and translation controls p53 expression in B cells.

Díaz-Muñoz MD, Kiselev VY, Le Novère N, Curk T, Ule J, Turner M.

Nat Commun. 2017 Sep 13;8(1):530. doi: 10.1038/s41467-017-00454-2.

17.

Erratum to: Insights into the design and interpretation of iCLIP experiments.

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, Ule J.

Genome Biol. 2017 Aug 15;18(1):154. doi: 10.1186/s13059-017-1294-z. No abstract available.

18.

A retained intron in the 3'-UTR of Calm3 mRNA mediates its Staufen2- and activity-dependent localization to neuronal dendrites.

Sharangdhar T, Sugimoto Y, Heraud-Farlow J, Fernández-Moya SM, Ehses J, Ruiz de Los Mozos I, Ule J, Kiebler MA.

EMBO Rep. 2017 Oct;18(10):1762-1774. doi: 10.15252/embr.201744334. Epub 2017 Aug 1.

19.

Progressive Motor Neuron Pathology and the Role of Astrocytes in a Human Stem Cell Model of VCP-Related ALS.

Hall CE, Yao Z, Choi M, Tyzack GE, Serio A, Luisier R, Harley J, Preza E, Arber C, Crisp SJ, Watson PMD, Kullmann DM, Abramov AY, Wray S, Burley R, Loh SHY, Martins LM, Stevens MM, Luscombe NM, Sibley CR, Lakatos A, Ule J, Gandhi S, Patani R.

Cell Rep. 2017 May 30;19(9):1739-1749. doi: 10.1016/j.celrep.2017.05.024.

20.

High-Resolution RNA Maps Suggest Common Principles of Splicing and Polyadenylation Regulation by TDP-43.

Rot G, Wang Z, Huppertz I, Modic M, Lenče T, Hallegger M, Haberman N, Curk T, von Mering C, Ule J.

Cell Rep. 2017 May 2;19(5):1056-1067. doi: 10.1016/j.celrep.2017.04.028.

21.

Transcript-specific characteristics determine the contribution of endo- and exonucleolytic decay pathways during the degradation of nonsense-mediated decay substrates.

Ottens F, Boehm V, Sibley CR, Ule J, Gehring NH.

RNA. 2017 Aug;23(8):1224-1236. doi: 10.1261/rna.059659.116. Epub 2017 May 1.

22.

Illustrating the Epitranscriptome at Nucleotide Resolution Using Methylation-iCLIP (miCLIP).

George H, Ule J, Hussain S.

Methods Mol Biol. 2017;1562:91-106. doi: 10.1007/978-1-4939-6807-7_7.

PMID:
28349456
23.

Regulatory feedback from nascent RNA to chromatin and transcription.

Skalska L, Beltran-Nebot M, Ule J, Jenner RG.

Nat Rev Mol Cell Biol. 2017 May;18(5):331-337. doi: 10.1038/nrm.2017.12. Epub 2017 Mar 8. Review.

PMID:
28270684
24.

Using hiCLIP to identify RNA duplexes that interact with a specific RNA-binding protein.

Sugimoto Y, Chakrabarti AM, Luscombe NM, Ule J.

Nat Protoc. 2017 Mar;12(3):611-637. doi: 10.1038/nprot.2016.188. Epub 2017 Feb 23.

PMID:
28230851
25.

Differential Binding of Mitochondrial Transcripts by MRB8170 and MRB4160 Regulates Distinct Editing Fates of Mitochondrial mRNA in Trypanosomes.

Dixit S, Müller-McNicoll M, David V, Zarnack K, Ule J, Hashimi H, Lukeš J.

MBio. 2017 Jan 31;8(1). pii: e02288-16. doi: 10.1128/mBio.02288-16.

26.

Insights into the design and interpretation of iCLIP experiments.

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, Ule J.

Genome Biol. 2017 Jan 16;18(1):7. doi: 10.1186/s13059-016-1130-x. Erratum in: Genome Biol. 2017 Aug 15;18(1):154.

27.

Major Shifts in Glial Regional Identity Are a Transcriptional Hallmark of Human Brain Aging.

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, Ule J.

Cell Rep. 2017 Jan 10;18(2):557-570. doi: 10.1016/j.celrep.2016.12.011.

28.

Splicing repression allows the gradual emergence of new Alu-exons in primate evolution.

Attig J, Ruiz de Los Mozos I, Haberman N, Wang Z, Emmett W, Zarnack K, König J, Ule J.

Elife. 2016 Nov 18;5. pii: e19545. doi: 10.7554/eLife.19545.

29.

The alternative splicing program of differentiated smooth muscle cells involves concerted non-productive splicing of post-transcriptional regulators.

Llorian M, Gooding C, Bellora N, Hallegger M, Buckroyd A, Wang X, Rajgor D, Kayikci M, Feltham J, Ule J, Eyras E, Smith CW.

Nucleic Acids Res. 2016 Oct 14;44(18):8933-8950. Epub 2016 Jun 17.

30.

Cholinergic Surveillance over Hippocampal RNA Metabolism and Alzheimer's-Like Pathology.

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, Prado MAM.

Cereb Cortex. 2017 Jul 1;27(7):3553-3567. doi: 10.1093/cercor/bhw177.

PMID:
27312991
31.

Lessons from non-canonical splicing.

Sibley CR, Blazquez L, Ule J.

Nat Rev Genet. 2016 Jul;17(7):407-421. doi: 10.1038/nrg.2016.46. Epub 2016 May 31. Review.

32.

The interaction of PRC2 with RNA or chromatin is mutually antagonistic.

Beltran M, Yates CM, Skalska L, Dawson M, Reis FP, Viiri K, Fisher CL, Sibley CR, Foster BM, Bartke T, Ule J, Jenner RG.

Genome Res. 2016 Jul;26(7):896-907. doi: 10.1101/gr.197632.115. Epub 2016 May 9.

33.

Matrin3: connecting gene expression with the nuclear matrix.

Coelho MB, Attig J, Ule J, Smith CW.

Wiley Interdiscip Rev RNA. 2016 May;7(3):303-15. doi: 10.1002/wrna.1336. Epub 2016 Jan 26. Review.

PMID:
26813864
34.

Orthogonal matrix factorization enables integrative analysis of multiple RNA binding proteins.

Stražar M, Žitnik M, Zupan B, Ule J, Curk T.

Bioinformatics. 2016 May 15;32(10):1527-35. doi: 10.1093/bioinformatics/btw003. Epub 2016 Jan 18.

35.

iCLIP identifies novel roles for SAFB1 in regulating RNA processing and neuronal function.

Rivers C, Idris J, Scott H, Rogers M, Lee YB, Gaunt J, Phylactou L, Curk T, Campbell C, Ule J, Norman M, Uney JB.

BMC Biol. 2015 Dec 22;13:111. doi: 10.1186/s12915-015-0220-7.

36.

Intergenic Alu exonisation facilitates the evolution of tissue-specific transcript ends.

Tajnik M, Vigilante A, Braun S, Hänel H, Luscombe NM, Ule J, Zarnack K, König J.

Nucleic Acids Res. 2015 Dec 2;43(21):10492-505. doi: 10.1093/nar/gkv956. Epub 2015 Sep 22.

37.

Regulation of constitutive and alternative mRNA splicing across the human transcriptome by PRPF8 is determined by 5' splice site strength.

Wickramasinghe VO, Gonzàlez-Porta M, Perera D, Bartolozzi AR, Sibley CR, Hallegger M, Ule J, Marioni JC, Venkitaraman AR.

Genome Biol. 2015 Sep 21;16:201. doi: 10.1186/s13059-015-0749-3.

38.

RNA-Binding Protein Musashi1 Is a Central Regulator of Adhesion Pathways in Glioblastoma.

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, Penalva LO.

Mol Cell Biol. 2015 Sep 1;35(17):2965-78. doi: 10.1128/MCB.00410-15. Epub 2015 Jun 22.

39.

HIF-driven SF3B1 induces KHK-C to enforce fructolysis and heart disease.

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, Krek W.

Nature. 2015 Jun 25;522(7557):444-449. doi: 10.1038/nature14508. Epub 2015 Jun 17.

40.

Recursive splicing in long vertebrate genes.

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, Ule J.

Nature. 2015 May 21;521(7552):371-375. doi: 10.1038/nature14466. Epub 2015 May 13.

41.

hiCLIP reveals the in vivo atlas of mRNA secondary structures recognized by Staufen 1.

Sugimoto Y, Vigilante A, Darbo E, Zirra A, Militti C, D'Ambrogio A, Luscombe NM, Ule J.

Nature. 2015 Mar 26;519(7544):491-4. doi: 10.1038/nature14280. Epub 2015 Mar 18.

42.

Control of a neuronal morphology program by an RNA-binding zinc finger protein, Unkempt.

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 LH, Walsh CA, Shi Y.

Genes Dev. 2015 Mar 1;29(5):501-12. doi: 10.1101/gad.258483.115.

43.

The RNA-binding protein HuR is essential for the B cell antibody response.

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, Turner M.

Nat Immunol. 2015 Apr;16(4):415-25. doi: 10.1038/ni.3115. Epub 2015 Feb 23.

44.

Splicing changes in SMA mouse motoneurons and SMN-depleted neuroblastoma cells: evidence for involvement of splicing regulatory proteins.

Huo Q, Kayikci M, Odermatt P, Meyer K, Michels O, Saxena S, Ule J, Schümperli D.

RNA Biol. 2014;11(11):1430-46. doi: 10.1080/15476286.2014.996494.

45.

Nuclear matrix protein Matrin3 regulates alternative splicing and forms overlapping regulatory networks with PTB.

Coelho MB, Attig J, Bellora N, König J, Hallegger M, Kayikci M, Eyras E, Ule J, Smith CW.

EMBO J. 2015 Mar 4;34(5):653-68. doi: 10.15252/embj.201489852. Epub 2015 Jan 19.

46.

Promiscuous RNA binding ensures effective encapsidation of APOBEC3 proteins by HIV-1.

Apolonia L, Schulz R, Curk T, Rocha P, Swanson CM, Schaller T, Ule J, Malim MH.

PLoS Pathog. 2015 Jan 15;11(1):e1004609. doi: 10.1371/journal.ppat.1004609. eCollection 2015 Jan.

47.

The coilin interactome identifies hundreds of small noncoding RNAs that traffic through Cajal bodies.

Machyna M, Kehr S, Straube K, Kappei D, Buchholz F, Butter F, Ule J, Hertel J, Stadler PF, Neugebauer KM.

Mol Cell. 2014 Nov 6;56(3):389-99. doi: 10.1016/j.molcel.2014.10.004. Epub 2014 Nov 6.

48.

3' UTR length and messenger ribonucleoprotein composition determine endocleavage efficiencies at termination codons.

Boehm V, Haberman N, Ottens F, Ule J, Gehring NH.

Cell Rep. 2014 Oct 23;9(2):555-68. doi: 10.1016/j.celrep.2014.09.012. Epub 2014 Oct 9.

49.

CPSF30 and Wdr33 directly bind to AAUAAA in mammalian mRNA 3' processing.

Chan SL, Huppertz I, Yao C, Weng L, Moresco JJ, Yates JR 3rd, Ule J, Manley JL, Shi Y.

Genes Dev. 2014 Nov 1;28(21):2370-80. doi: 10.1101/gad.250993.114. Epub 2014 Oct 9.

50.

A global regulatory mechanism for activating an exon network required for neurogenesis.

Raj B, Irimia M, Braunschweig U, Sterne-Weiler T, O'Hanlon D, Lin ZY, Chen GI, Easton LE, Ule J, Gingras AC, Eyras E, Blencowe BJ.

Mol Cell. 2014 Oct 2;56(1):90-103. doi: 10.1016/j.molcel.2014.08.011. Epub 2014 Sep 11.

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