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Breadcrumb Jernej Ule Ule lab RNA Networks Laboratory : Publications Lab contentLab contentIn this section Overview Areas of interest Publications Members Vacancies Genes in the brain are very long and can be transcribed into diverse RNAs. Toggle to view hero caption PublicationsYear published2023 (2)2022 (9)2021 (16)2020 (6)2019 (10)2018 (13)2017 (7)2015 (3)2013 (1) Facet Year publishedResearch topicsComputational & Systems Biology (64)Gene Expression (64)Genetics & Genomics (64)Biochemistry & Proteomics (63)Neurosciences (63)Stem Cells (63)Tumour Biology (23)Cell Biology (12)Chemical Biology & High Throughput (7)Model Organisms (5)Cell Cycle & Chromosomes (4)Metabolism (4)Signalling & Oncogenes (4)Structural Biology & Biophysics (4)Synthetic Biology (4)Developmental Biology (3)Genome Integrity & Repair (3)Human Biology & Physiology (3)Immunology (3)Infectious Disease (3)Imaging (1)Microfabrication & Bioengineering (1) Facet Research topicsPublication typeJournal article (67)Primary research (52)Review (10)Commentary (2)Method (2)Editorial (1) Facet Publication typeJournalMolecular Cell (7)Nature Communications (6)Nature (5)Nucleic Acids Research (5)Genome Biology (4)Cell (3)Cell Reports (3)eLife (3)International Journal of Molecular Sciences (3)Brain (2)EMBO Journal (2)EMBO Reports (2)Nature Reviews Methods Primers (2)Nature Structural and Molecular Biology (2)Wellcome Open Research (2)Annual Review of Biomedical Data Science (1)BioEssays (1)Cell Death & Differentiation (1)Cold Spring Harbor Perspectives in Biology (1)Developmental Cell (1)Frontiers in Genetics (1)Genes & Development (1)Genome Research (1)Journal of Biological Chemistry (1)Molecular Therapy - Nucleic Acids (1)Nature Ecology & Evolution (1)Nature Protocols (1)Nature Reviews Molecular Cell Biology (1)RNA (1)RNA Biology (1)The Lancet (1) Facet Journal Publications Displaying 1 - 20 of 67Last updated : 28 March 2023 02:35 clipplotr - a comparative visualisation and analysis tool for CLIP data Authors (4)Anob ChakrabartiCharlotte CapitanchikJernej UleNicholas Luscombe RNA Published 9 March 2023 Crick labsJernej UleNicholas LuscombeFull details RNA polymerase II-associated proteins reveal pathways affected in VCP-related amyotrophic lateral sclerosis Authors (5)Sina Rafiee Sara Rohban Karen DaveyJernej UleNicholas Luscombe Brain Published 15 February 2023 Crick labsJernej UleNicholas LuscombeFull details N6-methyladenosine (m6A) reader Pho92 is recruited co-transcriptionally and couples translation to mRNA decay to promote meiotic fitness in yeast Authors (18) Radhika A VarierTheodora SideriCharlotte CapitanchikZornitsa ManovaEnrica CalvaniAlice Rossi[...] Michiel VermeulenMarkus RalserJernej UleNicholas LuscombeFolkert Van Werven eLife Published 24 November 2022 Crick labs/ facilitiesFolkert van WervenJernej UleMarkus RalserNicholas LuscombeProteomicsMetabolomicsBioinformatics and BiostatisticsGenomics/Equipment ParkFermentationAdvanced SequencingFull details Cell-specific bioorthogonal tagging of glycoproteins Authors (31)Anna CioceBea CalleTatiana Rizou Sarah C LoweryVicky Bridgeman Keira E Mahoney[...] Stuart M Haslam Sabine L Flitsch Stacy A MalakerIlaria MalanchiBen Schumann Nature Communications Published 25 October 2022 Crick labs/ facilitiesJernej UleBen SchumannIlaria MalanchiLuiz Pedro CarvalhoStructural BiologyProteomicsBioinformatics and BiostatisticsPeptide ChemistryLight MicroscopyCell ServicesBiological Research FacilityAdvanced SequencingFull details CDK11 regulates pre-mRNA splicing by phosphorylation of SF3B1 Authors (15) Milan Hluchý Pavla GajduškováIgor Ruiz De Los Mozos Michal Rájecký Michael Kluge Benedict-Tilman Berger[...] Zbyněk Zdráhal Stefan Knapp Kamil Paruch Caroline C Friedel Dalibor Blazek Nature Published 22 September 2022 Crick labsJernej UleFull details Positional motif analysis reveals the extent of specificity of protein-RNA interactions observed by CLIP Authors (5) Klara Kuret Aram Gustav Amalietti D Marc JonesCharlotte CapitanchikJernej Ule Genome Biology Published 9 September 2022 Crick labsJernej UleFull details Identifying ribosome heterogeneity using ribosome profiling Authors (7) Ferhat AlkanOscar Wilkins Santiago Hernández-Pérez Sofia Ramalho Joana SilvaJernej Ule William J Faller Nucleic Acids Research Published 9 September 2022 Crick labsJernej UleFull details Determination of IgG1 and IgG3 SARS-CoV-2 spike protein and nucleocapsid binding-who is binding who and why? Authors (12) Jason K Iles Raminta Zmuidinaite Christoph Sadee Anna Gardiner Jonathan Lacey Stephen Harding[...] Roshani Patel Debra Roblett Jonathan Heeney Helen Baxendale Ray Kruse Iles International Journal of Molecular Sciences Published 27 May 2022 Crick labsJernej UleFull details U1A is a positive regulator of the expression of heterologous and cellular genes involved in cell proliferation and migration Authors (11) Eric Rovira Beatriz Moreno Nerea Razquin Roland Hjerpe Monika Gonzalez-Lopez Rosa Barrio Igor Ruiz De Los MozosJernej Ule Fernando Pastor Lorea Blazquez Puri Fortes Molecular Therapy - Nucleic Acids Published 14 June 2022 Crick labsJernej UleFull details SARS‐CoV‐2 spike protein binding of glycated serum albumin—its potential role in the pathogenesis of the COVID‐19 clinical syndromes and bias towards individuals with pre‐diabetes/type 2 diabetes and metabolic diseases Authors (11) Jason Iles Raminta Zmuidinaite Christoph Sadée Anna Gardiner Jonathan Lacey Stephen HardingJernej Ule Debra Roblett Jonathan Heeney Helen Baxendale Ray K Iles International Journal of Molecular Sciences Published 8 April 2022 Crick labsJernej UleFull details TDP-43 loss and ALS-risk SNPs drive mis-splicing and depletion of UNC13A Authors (32) Anna-Leigh BrownOscar Wilkins Matthew J Keuss Sarah E Hill Matteo Zanovello Weaverly Colleen Lee[...]Jernej Ule Emanuele Buratti Jack Humphrey Michael E Ward Pietro Fratta Nature Published 3 March 2022 Crick labs/ facilitiesJernej UleStructural BiologyFull details RNA modifications detection by comparative Nanopore direct RNA sequencing Authors (19) Adrien Leger Paulo P Amaral Luca PandolfiniCharlotte CapitanchikFederica Capraro Valentina Miano[...]Jernej Ule Tomas Fitzgerald Ewan Birney Tommaso Leonardi Tony Kouzarides Nature Communications Published 10 December 2021 Crick labsFolkert van WervenJernej UleNicholas LuscombeFull details Chromatin-contact atlas reveals disorder-mediated protein interactions and moonlighting chromatin-associated RBPs Authors (7)Sina RafieeJulian Zagalak Sviatoslav Sidorov Sebastian Steinhauser Karen DaveyJernej UleNicholas Luscombe Nucleic Acids Research Published 16 December 2021 Crick labsJernej UleNicholas LuscombeFull details RGS4 RNA secondary structure mediates staufen2 RNP assembly in neurons Authors (11) Sandra M Fernández-Moya Janina Ehses Karl E Bauer Rico SchieweckAnob ChakrabartiFlora Lee Christin IlligNicholas Luscombe Max HarnerJernej Ule Michael A Kiebler International Journal of Molecular Sciences Published 1 December 2021 Crick labsJernej UleNicholas LuscombeFull details A genetically-encoded crosslinker screen identifies SERBP1 as a PKCε substrate influencing translation and cell division Authors (12)Silvia MartiniKhalil DavisRupert Faraway Lisa ElzeNicola LockwoodAndrew Jones[...]Neil McDonald David J Mann Alan ArmstrongJernej UlePeter Parker Nature Communications Published 26 November 2021 Crick labs/ facilitiesJernej UlePeter ParkerPaul NurseNeil McDonaldProteomicsPeptide ChemistryLight MicroscopyFull details Metabolic turnover and dynamics of modified ribonucleosides by 13C labeling Authors (5)Paulo Da Costa Gameiro Guerreiro Vesela EnchevaMariana Silva Dos SantosJames MacraeJernej Ule Journal of Biological Chemistry Published 1 November 2021 Crick labs/ facilitiesJernej UleProteomicsMetabolomicsFull details Sequential inverse dysregulation of the RNA helicases DDX3X and DDX3Y facilitates MYC-driven lymphomagenesis Authors (37) Chun Gong Joanna A Krupka Jie Gao Nicholas F Grigoropoulos George Giotopoulos Ryan Asby[...] Brian J Huntly Martin Turner Ming-Qing Du Shamith A Samarajiwa Daniel J Hodson Molecular Cell Published 7 October 2021 Crick labsJernej UleFull details TDP-43 condensation properties specify its RNA-binding and regulatory repertoire Authors (17)Martina HalleggerAnob ChakrabartiFlora Lee Bo Lim Lee Aram G Amalietti Hana M Odeh[...]Rickie Patani Nicolas L Fawzi James ShorterNicholas LuscombeJernej Ule Cell Published 2 September 2021 Crick labs/ facilitiesJernej UleRickie PataniNicholas LuscombeLight MicroscopyAdvanced SequencingFull details Nascent RNA antagonizes the interaction of a set of regulatory proteins with chromatin Authors (17) Lenka Skalska Victoria Begley Manuel Beltran Saulius Lukauskas Garima KhandelwalPeter Faull[...] Javier Herrero Silvia SurinovaBram Snijders Till Bartke Richard G Jenner Molecular Cell Published 15 July 2021 Crick labs/ facilitiesJernej UleProteomicsFull details eIF4A3 regulates the TFEB-mediated transcriptional response via GSK3B to control autophagy Authors (10) Despoina Sakellariou Matteo Tiberti Thomas H Kleiber Lorea Blazquez Aida Rodríguez López Marie Holm Abildgaard Michal Lubas Jiri Bartek Elena Papaleo Lisa B Frankel Cell Death & Differentiation Published 1 December 2021 Crick labsJernej UleFull details Pagination Current page 1 Page 2 Page 3 Page 4 Next page Next Last page Last Share the page Share on Twitter Share on Facebook Share on LinkedIn Share on Email
clipplotr - a comparative visualisation and analysis tool for CLIP data Authors (4)Anob ChakrabartiCharlotte CapitanchikJernej UleNicholas Luscombe RNA Published 9 March 2023 Crick labsJernej UleNicholas LuscombeFull details
RNA polymerase II-associated proteins reveal pathways affected in VCP-related amyotrophic lateral sclerosis Authors (5)Sina Rafiee Sara Rohban Karen DaveyJernej UleNicholas Luscombe Brain Published 15 February 2023 Crick labsJernej UleNicholas LuscombeFull details
N6-methyladenosine (m6A) reader Pho92 is recruited co-transcriptionally and couples translation to mRNA decay to promote meiotic fitness in yeast Authors (18) Radhika A VarierTheodora SideriCharlotte CapitanchikZornitsa ManovaEnrica CalvaniAlice Rossi[...] Michiel VermeulenMarkus RalserJernej UleNicholas LuscombeFolkert Van Werven eLife Published 24 November 2022 Crick labs/ facilitiesFolkert van WervenJernej UleMarkus RalserNicholas LuscombeProteomicsMetabolomicsBioinformatics and BiostatisticsGenomics/Equipment ParkFermentationAdvanced SequencingFull details
Cell-specific bioorthogonal tagging of glycoproteins Authors (31)Anna CioceBea CalleTatiana Rizou Sarah C LoweryVicky Bridgeman Keira E Mahoney[...] Stuart M Haslam Sabine L Flitsch Stacy A MalakerIlaria MalanchiBen Schumann Nature Communications Published 25 October 2022 Crick labs/ facilitiesJernej UleBen SchumannIlaria MalanchiLuiz Pedro CarvalhoStructural BiologyProteomicsBioinformatics and BiostatisticsPeptide ChemistryLight MicroscopyCell ServicesBiological Research FacilityAdvanced SequencingFull details
CDK11 regulates pre-mRNA splicing by phosphorylation of SF3B1 Authors (15) Milan Hluchý Pavla GajduškováIgor Ruiz De Los Mozos Michal Rájecký Michael Kluge Benedict-Tilman Berger[...] Zbyněk Zdráhal Stefan Knapp Kamil Paruch Caroline C Friedel Dalibor Blazek Nature Published 22 September 2022 Crick labsJernej UleFull details
Positional motif analysis reveals the extent of specificity of protein-RNA interactions observed by CLIP Authors (5) Klara Kuret Aram Gustav Amalietti D Marc JonesCharlotte CapitanchikJernej Ule Genome Biology Published 9 September 2022 Crick labsJernej UleFull details
Identifying ribosome heterogeneity using ribosome profiling Authors (7) Ferhat AlkanOscar Wilkins Santiago Hernández-Pérez Sofia Ramalho Joana SilvaJernej Ule William J Faller Nucleic Acids Research Published 9 September 2022 Crick labsJernej UleFull details
Determination of IgG1 and IgG3 SARS-CoV-2 spike protein and nucleocapsid binding-who is binding who and why? Authors (12) Jason K Iles Raminta Zmuidinaite Christoph Sadee Anna Gardiner Jonathan Lacey Stephen Harding[...] Roshani Patel Debra Roblett Jonathan Heeney Helen Baxendale Ray Kruse Iles International Journal of Molecular Sciences Published 27 May 2022 Crick labsJernej UleFull details
U1A is a positive regulator of the expression of heterologous and cellular genes involved in cell proliferation and migration Authors (11) Eric Rovira Beatriz Moreno Nerea Razquin Roland Hjerpe Monika Gonzalez-Lopez Rosa Barrio Igor Ruiz De Los MozosJernej Ule Fernando Pastor Lorea Blazquez Puri Fortes Molecular Therapy - Nucleic Acids Published 14 June 2022 Crick labsJernej UleFull details
SARS‐CoV‐2 spike protein binding of glycated serum albumin—its potential role in the pathogenesis of the COVID‐19 clinical syndromes and bias towards individuals with pre‐diabetes/type 2 diabetes and metabolic diseases Authors (11) Jason Iles Raminta Zmuidinaite Christoph Sadée Anna Gardiner Jonathan Lacey Stephen HardingJernej Ule Debra Roblett Jonathan Heeney Helen Baxendale Ray K Iles International Journal of Molecular Sciences Published 8 April 2022 Crick labsJernej UleFull details
TDP-43 loss and ALS-risk SNPs drive mis-splicing and depletion of UNC13A Authors (32) Anna-Leigh BrownOscar Wilkins Matthew J Keuss Sarah E Hill Matteo Zanovello Weaverly Colleen Lee[...]Jernej Ule Emanuele Buratti Jack Humphrey Michael E Ward Pietro Fratta Nature Published 3 March 2022 Crick labs/ facilitiesJernej UleStructural BiologyFull details
RNA modifications detection by comparative Nanopore direct RNA sequencing Authors (19) Adrien Leger Paulo P Amaral Luca PandolfiniCharlotte CapitanchikFederica Capraro Valentina Miano[...]Jernej Ule Tomas Fitzgerald Ewan Birney Tommaso Leonardi Tony Kouzarides Nature Communications Published 10 December 2021 Crick labsFolkert van WervenJernej UleNicholas LuscombeFull details
Chromatin-contact atlas reveals disorder-mediated protein interactions and moonlighting chromatin-associated RBPs Authors (7)Sina RafieeJulian Zagalak Sviatoslav Sidorov Sebastian Steinhauser Karen DaveyJernej UleNicholas Luscombe Nucleic Acids Research Published 16 December 2021 Crick labsJernej UleNicholas LuscombeFull details
RGS4 RNA secondary structure mediates staufen2 RNP assembly in neurons Authors (11) Sandra M Fernández-Moya Janina Ehses Karl E Bauer Rico SchieweckAnob ChakrabartiFlora Lee Christin IlligNicholas Luscombe Max HarnerJernej Ule Michael A Kiebler International Journal of Molecular Sciences Published 1 December 2021 Crick labsJernej UleNicholas LuscombeFull details
A genetically-encoded crosslinker screen identifies SERBP1 as a PKCε substrate influencing translation and cell division Authors (12)Silvia MartiniKhalil DavisRupert Faraway Lisa ElzeNicola LockwoodAndrew Jones[...]Neil McDonald David J Mann Alan ArmstrongJernej UlePeter Parker Nature Communications Published 26 November 2021 Crick labs/ facilitiesJernej UlePeter ParkerPaul NurseNeil McDonaldProteomicsPeptide ChemistryLight MicroscopyFull details
Metabolic turnover and dynamics of modified ribonucleosides by 13C labeling Authors (5)Paulo Da Costa Gameiro Guerreiro Vesela EnchevaMariana Silva Dos SantosJames MacraeJernej Ule Journal of Biological Chemistry Published 1 November 2021 Crick labs/ facilitiesJernej UleProteomicsMetabolomicsFull details
Sequential inverse dysregulation of the RNA helicases DDX3X and DDX3Y facilitates MYC-driven lymphomagenesis Authors (37) Chun Gong Joanna A Krupka Jie Gao Nicholas F Grigoropoulos George Giotopoulos Ryan Asby[...] Brian J Huntly Martin Turner Ming-Qing Du Shamith A Samarajiwa Daniel J Hodson Molecular Cell Published 7 October 2021 Crick labsJernej UleFull details
TDP-43 condensation properties specify its RNA-binding and regulatory repertoire Authors (17)Martina HalleggerAnob ChakrabartiFlora Lee Bo Lim Lee Aram G Amalietti Hana M Odeh[...]Rickie Patani Nicolas L Fawzi James ShorterNicholas LuscombeJernej Ule Cell Published 2 September 2021 Crick labs/ facilitiesJernej UleRickie PataniNicholas LuscombeLight MicroscopyAdvanced SequencingFull details
Nascent RNA antagonizes the interaction of a set of regulatory proteins with chromatin Authors (17) Lenka Skalska Victoria Begley Manuel Beltran Saulius Lukauskas Garima KhandelwalPeter Faull[...] Javier Herrero Silvia SurinovaBram Snijders Till Bartke Richard G Jenner Molecular Cell Published 15 July 2021 Crick labs/ facilitiesJernej UleProteomicsFull details
eIF4A3 regulates the TFEB-mediated transcriptional response via GSK3B to control autophagy Authors (10) Despoina Sakellariou Matteo Tiberti Thomas H Kleiber Lorea Blazquez Aida Rodríguez López Marie Holm Abildgaard Michal Lubas Jiri Bartek Elena Papaleo Lisa B Frankel Cell Death & Differentiation Published 1 December 2021 Crick labsJernej UleFull details
