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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 published (-)2021 (16) Facet Year publishedResearch topicsComputational & Systems Biology (16)Gene Expression (16)Genetics & Genomics (16)Biochemistry & Proteomics (15)Neurosciences (15)Stem Cells (15)Tumour Biology (8)Cell Biology (5)Chemical Biology & High Throughput (3)Cell Cycle & Chromosomes (2)Model Organisms (2)Signalling & Oncogenes (2)Developmental Biology (1)Human Biology & Physiology (1)Immunology (1)Metabolism (1)Structural Biology & Biophysics (1)Synthetic Biology (1) Facet Research topicsPublication typeJournal article (16)Primary research (14)Review (2) Facet Publication typeJournalNature Communications (3)Molecular Cell (2)Nature Reviews Methods Primers (2)Cell (1)Cell Death & Differentiation (1)Genome Biology (1)Genome Research (1)International Journal of Molecular Sciences (1)Journal of Biological Chemistry (1)Nature (1)Nucleic Acids Research (1)Wellcome Open Research (1) Facet Journal Publications Displaying 1 - 16 of 16Last updated : 23 April 2024 03:31 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 psiCLIP reveals dynamic RNA binding by DEAH-box helicases before and after exon ligation Authors (10) Lisa StrittmatterCharlotte Capitanchik Andrew NewmanMartina Hallegger Christine Norman Sebastian Fica Chris OubridgeNicholas LuscombeJernej Ule Kiyoshi Nagai Nature Communications Published 5 March 2021 Crick labsJernej UleNicholas LuscombeFull details CLIP and complementary methods Authors (8) Markus Hafner Maria Katsantoni Tino Köster James MarksJoyita Mukherjee Dorothee StaigerJernej Ule Mihaela Zavolan Nature Reviews Methods Primers Published 4 March 2021 Crick labsJernej UleFull details CLIP and complimentary methods Authors (8) Markus Hafner Maria Katsantoni Tino Köster James MarksJoyita Mukherjee Dorothee StaigerJernej Ule Mihaela Zavolan Nature Reviews Methods Primers Published 4 March 2021 Crick labsJernej UleFull details Share the page Share on Twitter Share on Facebook Share on LinkedIn Share on Email
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
psiCLIP reveals dynamic RNA binding by DEAH-box helicases before and after exon ligation Authors (10) Lisa StrittmatterCharlotte Capitanchik Andrew NewmanMartina Hallegger Christine Norman Sebastian Fica Chris OubridgeNicholas LuscombeJernej Ule Kiyoshi Nagai Nature Communications Published 5 March 2021 Crick labsJernej UleNicholas LuscombeFull details
CLIP and complementary methods Authors (8) Markus Hafner Maria Katsantoni Tino Köster James MarksJoyita Mukherjee Dorothee StaigerJernej Ule Mihaela Zavolan Nature Reviews Methods Primers Published 4 March 2021 Crick labsJernej UleFull details
CLIP and complimentary methods Authors (8) Markus Hafner Maria Katsantoni Tino Köster James MarksJoyita Mukherjee Dorothee StaigerJernej Ule Mihaela Zavolan Nature Reviews Methods Primers Published 4 March 2021 Crick labsJernej UleFull details
