Research case studies Explore a selection of reports that spotlight particular areas of research at the Crick over the past five years.
Postdoctoral clinical fellows Opportunities for postdoctoral clinicians to consolidate their research experience.
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 published2024 (3)2023 (15)2022 (9)2021 (16)2020 (6)2019 (10)2018 (13)2017 (7)2015 (3)2013 (1) Facet Year publishedResearch topicsGenetics & Genomics (80)Biochemistry & Proteomics (79)Computational & Systems Biology (79)Gene Expression (79)Neurosciences (78)Stem Cells (78)Tumour Biology (27)Cell Biology (15)Chemical Biology & High Throughput (10)Model Organisms (6)Cell Cycle & Chromosomes (5)Genome Integrity & Repair (5)Structural Biology & Biophysics (5)Synthetic Biology (5)Developmental Biology (4)Metabolism (4)Signalling & Oncogenes (4)Human Biology & Physiology (3)Immunology (3)Infectious Disease (3)Imaging (2)Microfabrication & Bioengineering (2) Facet Research topicsPublication typeJournal article (83)Primary research (66)Review (10)Commentary (3)Method (3)Editorial (1) Facet Publication typeJournalMolecular Cell (9)Nature Communications (8)Nucleic Acids Research (6)Genome Biology (5)Nature (5)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)RNA Biology (2)Science advances (2)The EMBO Journal (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)Frontiers in Immunology (1)Genes & Development (1)Genome Research (1)Journal of Biological Chemistry (1)Life Science Alliance (1)Molecular Systems Biology (1)Molecular Therapy - Nucleic Acids (1)Nature Ecology & Evolution (1)Nature Protocols (1)Nature Reviews Molecular Cell Biology (1)Neuron (1)RNA (1)Science Translational Medicine (1)The Lancet (1) Facet Journal Publications Displaying 21 - 40 of 83Last updated : 20 April 2024 02:12 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)Mahmoud-Reza 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 McDonaldProteomicsLight MicroscopyFull details Metabolic turnover and dynamics of modified ribonucleosides by 13C labeling Authors (5)Paulo Gameiro 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 Acute depletion of METTL3 implicates N6-methyladenosine in alternative intron/exon inclusion in the nascent transcriptome Authors (7) Guifeng Wei Mafalda Almeida Greta Pintacuda Heather Coker Joseph S BownessJernej Ule Neil Brockdorff Genome Research Published 1 August 2021 Crick labsJernej UleFull details Ultraplex: A rapid, flexible, all-in-one fastq demultiplexer Authors (4)Oscar WilkinsCharlotte CapitanchikNicholas LuscombeJernej Ule Wellcome Open Research Published 7 June 2021 Crick labs/ facilitiesJernej UleNicholas LuscombeAdvanced SequencingFull details MIR-NATs repress MAPT translation and aid proteostasis in neurodegeneration Authors (34) Roberto Simone Faiza Javad Warren EmmettOscar Wilkins Filipa Lourenço Almeida Natalia Barahona-Torres[...] Per Svenningsson Thomas T Warner Vincent PlagnolJernej Ule Rohan de Silva Nature Published 3 June 2021 Crick labsJernej UleRickie PataniFull details Intergenic RNA mainly derives from nascent transcripts of known genes Authors (5) Federico AgostiniJulian ZagalakJan AttigJernej UleNicholas Luscombe Genome Biology Published 5 May 2021 Crick labsJernej UleNicholas LuscombeFull details Pagination First page First Previous page Previous Page 1 Current page 2 Page 3 Page 4 Page 5 Next page Next Last page Last Share the page Share on Twitter Share on Facebook Share on LinkedIn Share on Email
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)Mahmoud-Reza 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 McDonaldProteomicsLight MicroscopyFull details
Metabolic turnover and dynamics of modified ribonucleosides by 13C labeling Authors (5)Paulo Gameiro 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
Acute depletion of METTL3 implicates N6-methyladenosine in alternative intron/exon inclusion in the nascent transcriptome Authors (7) Guifeng Wei Mafalda Almeida Greta Pintacuda Heather Coker Joseph S BownessJernej Ule Neil Brockdorff Genome Research Published 1 August 2021 Crick labsJernej UleFull details
Ultraplex: A rapid, flexible, all-in-one fastq demultiplexer Authors (4)Oscar WilkinsCharlotte CapitanchikNicholas LuscombeJernej Ule Wellcome Open Research Published 7 June 2021 Crick labs/ facilitiesJernej UleNicholas LuscombeAdvanced SequencingFull details
MIR-NATs repress MAPT translation and aid proteostasis in neurodegeneration Authors (34) Roberto Simone Faiza Javad Warren EmmettOscar Wilkins Filipa Lourenço Almeida Natalia Barahona-Torres[...] Per Svenningsson Thomas T Warner Vincent PlagnolJernej Ule Rohan de Silva Nature Published 3 June 2021 Crick labsJernej UleRickie PataniFull details
Intergenic RNA mainly derives from nascent transcripts of known genes Authors (5) Federico AgostiniJulian ZagalakJan AttigJernej UleNicholas Luscombe Genome Biology Published 5 May 2021 Crick labsJernej UleNicholas LuscombeFull details
