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Results: 25
Analysis of CLIP and iCLIP methods for nucleotide-resolution studies of protein-RNA interactions.
Yoichiro Sugimoto, Julian König, Shobbir Hussain, Blaž Zupan, Tomaž Curk, Michaela Frye, Jernej Ule
Jan 02, 2013
Animals Antigens Neoplasm COS Cells Chlorocebus aethiops Gene Library HeLa Cells High-Throughput Nucleotide Sequencing Humans Immunoprecipitation Methyltransferases Mice Molecular Sequence Annotation Nerve Tissue Proteins Neuro-Oncological Ventral Antigen RNA RNA-Binding Proteins Sequence Analysis DNA Sequence Deletion
Analysis of CLIP and iCLIP methods for nucleotide-resolution studies of protein-RNA interactions
Yoichiro Sugimoto, Julian König, Shobbir Hussain, Blaž Zupan, Tomaž Curk, Michaela Frye, Jernej Ule
Jan 01, 0001
UV cross-linking and immunoprecipitation (CLIP) and individual-nucleotide resolution CLIP (iCLIP) are methods to study protein-RNA interactions in untreated cells and tissues. Here, we analyzed six published and two novel data...
Analysis of CLIP and iCLIP methods for nucleotide-resolution studies of protein-RNA interactions
Yoichiro Sugimoto, Julian König, Shobbir Hussain, Blaž Zupan, Tomaž Curk, Michaela Frye, Jernej Ule
Jan 01, 0001
UV cross-linking and immunoprecipitation (CLIP) and individual-nucleotide resolution CLIP (iCLIP) are methods to study protein-RNA interactions in untreated cells and tissues. Here, we analyzed six published and two novel data...
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.
Jason Iles, Raminta Zmuidinaite, Christoph Sadee, Anna Gardiner, Jonathan Lacey, Stephen Harding, Jernej Ule, Debra Roblett, Jonathan Heeney, Helen Baxendale, Ray K Iles
Apr 09, 2022
The immune response to SARS-CoV-2 infection requires antibody recognition of the spike protein. In a study designed to examine the molecular features of anti-spike and anti-nucleocapsid antibodies, patient plasma proteins...
The alternative splicing program of differentiated smooth muscle cells involves concerted non-productive splicing of post-transcriptional regulators
Regulation of constitutive and alternative mRNA splicing across the human transcriptome by PRPF8 is determined by 5' splice site strength.
Vihandha O Wickramasinghe, Mar Gonzàlez-Porta, David Perera, Arthur R Bartolozzi, Christopher R Sibley, Martina Hallegger, Jernej Ule, John C Marioni, Ashok R Venkitaraman
Feb 18, 2020
BACKGROUND: Sequential assembly of the human spliceosome on RNA transcripts regulates splicing across the human transcriptome. The core spliceosome component PRPF8 is essential for spliceosome assembly through its participation...
Nuclear matrix protein Matrin3 regulates alternative splicing and forms overlapping regulatory networks with PTB.
Miguel B Coelho, Jan Attig, Nicolás Bellora, Julian König, Martina Hallegger, Melis Kayikci, Eduardo Eyras, Jernej Ule, Christopher WJ Smith
Feb 19, 2015
Matrin3 PTB Alternative Splicing Alternative Splicing Computational Biology DNA Primers Electrophoresis Polyacrylamide Gel Gene Expression Profiling Gene Regulatory Networks HEK293 Cells HeLa Cells Humans Microarray Analysis Nuclear Matrix-Associated Proteins Polypyrimidine Tract-Binding Protein RNA Interference RNA Small Interfering RNA-Binding Proteins Reverse Transcriptase Polymerase Chain Reaction
Tia1 dependent regulation of mRNA subcellular location and translation controls p53 expression in B cells.
Manuel D Díaz-Muñoz, Vladimir Yu Kiselev, Nicolas Le Novère, Tomaz Curk, Jernej Ule, Martin Turner
Jun 24, 2019
Post-transcriptional regulation of cellular mRNA is essential for protein synthesis. Here we describe the importance of mRNA translational repression and mRNA subcellular location for protein expression during B lymphocyte...
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.
Jason Iles, Raminta Zmuidinaite, Christoph Sadee, Anna Gardiner, Jonathan Lacey, Stephen Harding, Jernej Ule, Debra Roblett, Jonathan Heeney, Helen Baxendale, Ray K Iles
May 24, 2022
The immune response to SARS-CoV-2 infection requires antibody recognition of the spike protein. In a study designed to examine the molecular features of anti-spike and anti-nucleocapsid antibodies, patient plasma proteins...
Cytotoxic T-cells mediate exercise-induced reductions in tumor growth
Helene Rundqvist, Pedro Veliça, Laura Barbieri, Paulo A Gameiro, David Bargiela, Milos Gojkovic, Sara Mijwel, Stefan Markus Reitzner, David Wulliman, Emil Ahlstedt, Jernej Ule, Arne Östman, Randall S Johnson
Oct 24, 2020
SRSF3 maintains transcriptome integrity in oocytes by regulation of alternative splicing and transposable elements
Vinh Dang Do, Bernhard Strauss, Engin Cukuroglu, Iain Macaulay, Keng Boon Wee, Tim Xiamoming, Igor Ruiz De Los Mozos, Caroline Lee, Andrew Harrison, Richard Butler, Sabine Dietmann, Ule Jernej, John Marioni, Christopher WJ Smith, Jonathan Goke, Azim M Surani
Sep 05, 2018
The RNA-binding protein SRSF3 (also known as SRp20) has critical roles in the regulation of pre-mRNA splicing. Zygotic knockout of Srsf3 results in embryo arrest at the blastocyst stage.
However, SRSF3 is also present in...
The alternative splicing program of differentiated smooth muscle cells involves concerted non-productive splicing of post-transcriptional regulators.
Miriam Llorian, Clare Gooding, Nicolas Bellora, Martina Hallegger, Adrian Buckroyd, Xiao Wang, Dipen Rajgor, Melis Kayikci, Jack Feltham, Jernej Ule, Eduardo Eyras, Christopher WJ Smith
Aug 15, 2017
Cytotoxic T-cells mediate an exercise-induced reduction in tumor growth
Randall Johnson, Helene Rundqvist, Pedro Velica, Laura Barbieri, Paulo Gameiro, David Bargiela, Milos Gojkovic, Sara Mijwel, Stefan Reitzner, David Wulliman, Emil Ahlstedt, Jernej Ule, Arne Östman
Oct 20, 2020
Heteromeric RNP Assembly at LINEs Controls Lineage-Specific RNA Processing.
Jan Attig, Federico Agostini, Clare Gooding, Anob M Chakrabarti, Aarti Singh, Nejc Haberman, Julian A Zagalak, Warren Emmett, Christopher WJ Smith, Nicholas M Luscombe, Jernej Ule
Sep 18, 2019
Long mammalian introns make it challenging for the RNA processing machinery to identify exons accurately. We find that LINE-derived sequences (LINEs) contribute to this selection by recruiting dozens of RNA-binding proteins...
CLIP LINE repeats MATR3 PTBP1 alternative polyadenylation cryptic exons evolution exonogenesis multivalency splicing Alternative Splicing Animals Binding Sites Exons HeLa Cells Heterogeneous-Nuclear Ribonucleoproteins Humans Introns Long Interspersed Nucleotide Elements Mice Mutation Nuclear Matrix-Associated Proteins Nucleotide Motifs Phylogeny Polyadenylation Polypyrimidine Tract-Binding Protein Protein Binding Protein Interaction Mapping RNA RNA Splicing RNA-Binding Proteins
A systems view of spliceosomal assembly and branchpoints with iCLIP.
Michael Briese, Nejc Haberman, Christopher R Sibley, Rupert Faraway, Andrea S Elser, Anob M Chakrabarti, Zhen Wang, Julian König, David Perera, Vihandha O Wickramasinghe, Ashok R Venkitaraman, Nicholas M Luscombe, Luciano Saieva, Livio Pellizzoni, Christopher WJ Smith, Tomaž Curk, Jernej Ule
Apr 22, 2020
Studies of spliceosomal interactions are challenging due to their dynamic nature. Here we used spliceosome iCLIP, which immunoprecipitates SmB along with small nuclear ribonucleoprotein particles and auxiliary RNA binding...
The SMAD2/3 interactome reveals that TGFβ controls m6A mRNA methylation in pluripotency.
Alessandro Bertero, Stephanie Brown, Pedro Madrigal, Anna Osnato, Daniel Ortmann, Loukia Yiangou, Juned Kadiwala, Nina C Hubner, Igor Ruiz de Los Mozos, Christoph Sadée, An-Sofie Lenaerts, Shota Nakanoh, Rodrigo Grandy, Edward Farnell, Jernej Ule, Hendrik G Stunnenberg, Sasha Mendjan, Ludovic Vallier
May 15, 2018
Activins Adenosine Animals Cell Cycle Proteins Cell Differentiation Epigenesis Genetic Humans Methylation Methyltransferases Multiprotein Complexes Nanog Homeobox Protein Nodal Protein Nuclear Proteins Pluripotent Stem Cells Protein Binding RNA Splicing Factors RNA Messenger Signal Transduction Smad2 Protein Smad3 Protein Transcriptome Transforming Growth Factor beta
The RNA-binding protein HuR is essential for the B cell antibody response.
Manuel D Diaz-Muñoz, Sarah E Bell, Kirsten Fairfax, Elisa Monzon-Casanova, Adam F Cunningham, Mar Gonzalez-Porta, Simon R Andrews, Victoria I Bunik, Kathi Zarnack, Tomaž Curk, Ward A Heggermont, Stephane Heymans, Gary E Gibson, Dimitris L Kontoyiannis, Jernej Ule, Martin Turner
Jun 24, 2019
Post-transcriptional regulation of mRNA by the RNA-binding protein HuR (encoded by Elavl1) is required in B cells for the germinal center reaction and for the production of class-switched antibodies in response to...
Acyltransferases Alternative Splicing Animals Antigens B-Lymphocytes Cell Death Cell Differentiation Cell Proliferation ELAV Proteins Erythrocytes Germinal Center Immunity Humoral Immunization Immunoglobulin Class Switching Immunoglobulins Lipopolysaccharides Mice Mice Inbred C57BL Mice Knockout Mitochondria RNA Messenger Reactive Oxygen Species Sheep
RNA modifications detection by comparative Nanopore direct RNA sequencing.
Adrien Leger, Paulo P Amaral, Luca Pandolfini, Charlotte Capitanchik, Federica Capraro, Valentina Miano, Valentina Migliori, Patrick Toolan-Kerr, Theodora Sideri, Anton J Enright, Konstantinos Tzelepis, Folkert J van Werven, Nicholas M Luscombe, Isaia Barbieri, Jernej Ule, Tomas Fitzgerald, Ewan Birney, Tommaso Leonardi, Tony Kouzarides
Jan 04, 2022
Progressive Motor Neuron Pathology and the Role of Astrocytes in a Human Stem Cell Model of VCP-Related ALS.
Claire E Hall, Zhi Yao, Minee Choi, Giulia E Tyzack, Andrea Serio, Raphaelle Luisier, Jasmine Harley, Elisavet Preza, Charlie Arber, Sarah J Crisp, P Marc D Watson, Dimitri M Kullmann, Andrey Y Abramov, Selina Wray, Russell Burley, Samantha HY Loh, L Miguel Martins, Molly M Stevens, Nicholas M Luscombe, Christopher R Sibley, Andras Lakatos, Jernej Ule, Sonia Gandhi, Rickie Patani
Nov 29, 2018
Motor neurons (MNs) and astrocytes (ACs) are implicated in the pathogenesis of amyotrophic lateral sclerosis (ALS), but their interaction and the sequence of molecular events leading to MN death remain unresolved. Here, we...
amyotrophic lateral sclerosis (ALS) astrocytes (ACs) Disease Modeling induced pluripotent stem cells (iPSCs) motor neurons (MNs) Amyotrophic Lateral Sclerosis Astrocytes Cell Survival DNA-Binding Proteins Endoplasmic Reticulum Endoplasmic reticulum stress Humans Induced Pluripotent Stem Cells Membrane potential Mitochondrial Mitochondria Models Biological Motor Neurons Mutation Nerve Degeneration Neurogenesis Oxidative Stress Phenotype Synapses Valosin Containing Protein
Aberrant methylation of tRNAs links cellular stress to neuro-developmental disorders.
Sandra Blanco, Sabine Dietmann, Joana V Flores, Shobbir Hussain, Claudia Kutter, Peter Humphreys, Margus Lukk, Patrick Lombard, Lucas Treps, Martyna Popis, Stefanie Kellner, Sabine M Hölter, Lillian Garrett, Wolfgang Wurst, Lore Becker, Thomas Klopstock, Helmut Fuchs, Valerie Gailus-Durner, Martin Hrabĕ de Angelis, Ragnhildur T Káradóttir, Mark Helm, Jernej Ule, Joseph G Gleeson, Duncan T Odom, Michaela Frye
Jan 31, 2020
Mutations in the cytosine-5 RNA methyltransferase NSun2 cause microcephaly and other neurological abnormalities in mice and human. How post-transcriptional methylation contributes to the human disease is currently unknown. By...
Sequential inverse dysregulation of the RNA helicases DDX3X and DDX3Y facilitates MYC-driven lymphomagenesis.
Chun Gong, Joanna A Krupka, Jie Gao, Nicholas F Grigoropoulos, George Giotopoulos, Ryan Asby, Michael Screen, Zelvera Usheva, Francesco Cucco, Sharon Barrans, Daniel Painter, Nurmahirah Binte Mohammed Zaini, Björn Haupl, Susanne Bornelöv, Igor Ruiz De Los Mozos, Wei Meng, Peixun Zhou, Alex E Blain, Sorcha Forde, Jamie Matthews, Michelle Guet Khim Tan, GA Amos Burke, Siu Kwan Sze, Philip Beer, Cathy Burton, Peter Campbell, Vikki Rand, Suzanne D Turner, Jernej Ule, Eve Roman, Reuben Tooze, Thomas Oellerich, Brian J Huntly, Martin Turner, Ming-Qing Du, Shamith A Samarajiwa, Daniel J Hodson
Jul 30, 2021
DDX3X is a ubiquitously expressed RNA helicase involved in multiple stages of RNA biogenesis. DDX3X is frequently mutated in Burkitt lymphoma, but the functional basis for this is unknown. Here, we show that loss-of-function...
Burkitt lymphoma DDX3X Myc RNA helicase Germinal Center proteotoxic stress Translation Adolescent Adult Aged Aged 80 and over Animals B-Lymphocytes Cell Line Tumor Child Child Preschool DEAD-box RNA Helicases Endoplasmic reticulum stress Female Gene Expression Regulation Enzymologic Gene Expression Regulation Neoplastic Humans Loss of Function Mutation Lymphoma B-Cell Male Mice Transgenic Middle Aged Minor Histocompatibility Antigens Neoplasm Proteins Protein Biosynthesis Proteome Proteostasis Proto-Oncogene Proteins c-myc Young Adult
Genetic tool development in marine protists
Drahomíra Faktorová, R Ellen R Nisbet, José A Fernández Robledo, Elena Casacuberta, Lisa Sudek, Andrew E Allen, Manuel Ares, Cristina Aresté, Cecilia Balestreri, Adrian C Barbrook, Patrick Beardslee, Sara Bender, David S Booth, François-Yves Bouget, Chris Bowler, Susana A Breglia, Colin Brownlee, Gertraud Burger, Heriberto Cerutti, Rachele Cesaroni, Miguel A Chiurillo, Thomas Clemente, Duncan B Coles, Jackie L Collier, Elizabeth C Cooney, Kathryn Coyne, Roberto Docampo, Christopher L Dupont, Virginia Edgcomb, Elin Einarsson, Pía A Elustondo, Fernan Federici, Veronica Freire-Beneitez, Nastasia J Freyria, Kodai Fukuda, Paulo A García, Peter R Girguis, Fatma Gomaa, Sebastian G Gornik, Jian Guo, Vladimír Hampl, Yutaka Hanawa, Esteban R Haro-Contreras, Elisabeth Hehenberger, Andrea Highfield, Yoshihisa Hirakawa, Amanda Hopes, Christopher J Howe, Ian Hu, Jorge Ibañez, Nicholas AT Irwin, Yuu Ishii, Natalia Ewa Janowicz, Adam C Jones, Ambar Kachale, Konomi Fujimura-Kamada, Binnypreet Kaur, Jonathan Z Kaye, Eleanna Kazana, Patrick J Keeling, Nicole King, Lawrence A Klobutcher, Noelia Lander, Imen Lassadi, Zhuhong Li, Senjie Lin, Jean-Claude Lozano, Fulei Luan, Shinichiro Maruyama, Tamara Matute, Cristina Miceli, Jun Minagawa, Mark Moosburner, Sebastián R Najle, Deepak Nanjappa, Isabel C Nimmo, Luke Noble, Anna MG Novák Vanclová, Mariusz Nowacki, Isaac Nuñez, Arnab Pain, Angela Piersanti, Sandra Pucciarelli, Jan Pyrih, Joshua S Rest, Mariana Rius, Deborah Robertson, Albane Ruaud, Iñaki Ruiz-Trillo, Monika A Sigg, Pamela A Silver, Claudio H Slamovits, G Jason Smith, Brittany N Sprecher, Rowena Stern, Estienne C Swart, Anastasios D Tsaousis, Lev Tsypin, Aaron Turkewitz, Jernej Turnšek, Matus Valach, Valérie Vergé, Peter von Dassow, Tobias von der Haar, Ross F Waller, Lu Wang, Xiaoxue Wen, Glen Wheeler, April Woods, Huan Zhang, Thomas Mock, Alexandra Z Worden, Julius Lukeš
Jun 01, 2020
Diverse microbial ecosystems underpin life in the sea. Among these microbes are many unicellular eukaryotes that span the diversity of the eukaryotic tree of life. However, genetic tractability has been limited to a few species...
Genetic tool development in marine protists
Drahomíra Faktorová, R. Ellen R. Nisbet, José A. Fernández Robledo, Elena Casacuberta, Lisa Sudek, Andrew E. Allen, Manuel, Jr Ares, Cristina Aresté, Cecilia Balestreri, Adrian C. Barbrook, Patrick Beardslee, Sara Bender, David S. Booth, François-Yves Bouget, Chris Bowler, Susana A. Breglia, Colin Brownlee, Gertraud Burger, Heriberto Cerutti, Rachele Cesaroni, Miguel A. Chiurillo, Thomas Clemente, Duncan B. Coles, Jackie L. Collier, Elizabeth C. Cooney, Kathryn Coyne, Roberto Docampo, Christopher L. Dupont, Virginia Edgcomb, Elin Einarsson, Pía A. Elustondo, Fernan Federici, Veronica Freire-Beneitez, Nastasia J. Freyria, Kodai Fukuda, Paulo A. García, Peter R. Girguis, Fatma Gomaa, Sebastian G. Gornik, Jian Guo, Vladimír Hampl, Yutaka Hanawa, Esteban R. Haro-Contreras, Elisabeth Hehenberger, Andrea Highfield, Yoshihisa Hirakawa, Amanda Hopes, Christopher J. Howe, Ian Hu, Jorge Ibañez, Nicholas A. T. Irwin, Yuu Ishii, Natalia Ewa Janowicz, Adam C. Jones, Ambar Kachale, Konomi Fujimura-Kamada, Binnypreet Kaur, Jonathan Z. Kaye, Eleanna Kazana, Patrick J. Keeling, Nicole King, Lawrence A. Klobutcher, Noelia Lander, Imen Lassadi, Zhuhong Li, Senjie Lin, Jean-Claude Lozano, Fulei Luan, Shinichiro Maruyama, Tamara Matute, Cristina Miceli, Jun Minagawa, Mark Moosburner, Sebastián R. Najle, Deepak Nanjappa, Isabel C. Nimmo, Luke Noble, Anna M. G. Novák Vanclová, Mariusz Nowacki, Isaac Nuñez, Arnab Pain, Angela Piersanti, Sandra Pucciarelli, Jan Pyrih, Joshua S. Rest, Mariana Rius, Deborah Robertson, Albane Ruaud, Iñaki Ruiz-Trillo, Monika A. Sigg, Pamela A. Silver, Claudio H. Slamovits, G. Jason Smith, Brittany N. Sprecher, Rowena Stern, Estienne C. Swart, Anastasios D. Tsaousis, Lev Tsypin, Aaron Turkewitz, Jernej Turnšek, Matus Valach, Valérie Vergé, Peter von Dassow, Tobias von der Haar, Ross F. Waller, Lu Wang, Xiaoxue Wen, Glen Wheeler, April Woods, Huan Zhang, Thomas Mock, Alexandra Z. Worden, Julius Lukeš
Jul 30, 2021
Abstract: Diverse microbial ecosystems underpin life in the sea. Among these microbes are many unicellular eukaryotes that span the diversity of the eukaryotic tree of life. However, genetic tractability has been limited to a...
Genetic tool development in marine protists
Drahomíra Faktorová, R. Ellen R. Nisbet, José A. Fernández Robledo, Elena Casacuberta, Lisa Sudek, Andrew E. Allen, Manuel, Jr Ares, Cristina Aresté, Cecilia Balestreri, Adrian C. Barbrook, Patrick Beardslee, Sara Bender, David S. Booth, François-Yves Bouget, Chris Bowler, Susana A. Breglia, Colin Brownlee, Gertraud Burger, Heriberto Cerutti, Rachele Cesaroni, Miguel A. Chiurillo, Thomas Clemente, Duncan B. Coles, Jackie L. Collier, Elizabeth C. Cooney, Kathryn Coyne, Roberto Docampo, Christopher L. Dupont, Virginia Edgcomb, Elin Einarsson, Pía A. Elustondo, Fernan Federici, Veronica Freire-Beneitez, Nastasia J. Freyria, Kodai Fukuda, Paulo A. García, Peter R. Girguis, Fatma Gomaa, Sebastian G. Gornik, Jian Guo, Vladimír Hampl, Yutaka Hanawa, Esteban R. Haro-Contreras, Elisabeth Hehenberger, Andrea Highfield, Yoshihisa Hirakawa, Amanda Hopes, Christopher J. Howe, Ian Hu, Jorge Ibañez, Nicholas A. T. Irwin, Yuu Ishii, Natalia Ewa Janowicz, Adam C. Jones, Ambar Kachale, Konomi Fujimura-Kamada, Binnypreet Kaur, Jonathan Z. Kaye, Eleanna Kazana, Patrick J. Keeling, Nicole King, Lawrence A. Klobutcher, Noelia Lander, Imen Lassadi, Zhuhong Li, Senjie Lin, Jean-Claude Lozano, Fulei Luan, Shinichiro Maruyama, Tamara Matute, Cristina Miceli, Jun Minagawa, Mark Moosburner, Sebastián R. Najle, Deepak Nanjappa, Isabel C. Nimmo, Luke Noble, Anna M. G. Novák Vanclová, Mariusz Nowacki, Isaac Nuñez, Arnab Pain, Angela Piersanti, Sandra Pucciarelli, Jan Pyrih, Joshua S. Rest, Mariana Rius, Deborah Robertson, Albane Ruaud, Iñaki Ruiz-Trillo, Monika A. Sigg, Pamela A. Silver, Claudio H. Slamovits, G. Jason Smith, Brittany N. Sprecher, Rowena Stern, Estienne C. Swart, Anastasios D. Tsaousis, Lev Tsypin, Aaron Turkewitz, Jernej Turnšek, Matus Valach, Valérie Vergé, Peter von Dassow, Tobias von der Haar, Ross F. Waller, Lu Wang, Xiaoxue Wen, Glen Wheeler, April Woods, Huan Zhang, Thomas Mock, Alexandra Z. Worden, Julius Lukeš
Apr 06, 2021
Abstract: Diverse microbial ecosystems underpin life in the sea. Among these microbes are many unicellular eukaryotes that span the diversity of the eukaryotic tree of life. However, genetic tractability has been limited to a...