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Biotin proximity tagging favours unfolded proteins and enables the study of intrinsically disordered regions
Abstract: Intrinsically Disordered Regions (IDRs) are enriched in disease-linked proteins known to have multiple post-translational modifications, but there is limited in vivo information about how locally unfolded protein...
Biotin proximity tagging favours unfolded proteins and enables the study of intrinsically disordered regions
Abstract: Intrinsically Disordered Regions (IDRs) are enriched in disease-linked proteins known to have multiple post-translational modifications, but there is limited in vivo information about how locally unfolded protein...
Biotin proximity tagging favours unfolded proteins and enables the study of intrinsically disordered regions.
Intrinsically Disordered Regions (IDRs) are enriched in disease-linked proteins known to have multiple post-translational modifications, but there is limited in vivo information about how locally unfolded protein regions...
Published by: Communications biology
Trans-acting translational regulatory RNA binding proteins.
Robert F Harvey, Tom S Smith, Thomas Mulroney, Rayner ML Queiroz, Mariavittoria Pizzinga, Veronica Dezi, Eneko Villenueva, Manasa Ramakrishna, Kathryn S Lilley, Anne E Willis
Jun 25, 2018
The canonical molecular machinery required for global mRNA translation and its control has been well defined, with distinct sets of proteins involved in the processes of translation initiation, elongation and termination....
The cell stress response
Mariavittoria Pizzinga, Robert F Harvey, Gavin D Garland, Ryan Mordue, Veronica Dezi, Manasa Ramakrishna, Aristeidis Sfakianos, Mie Monti, Thomas E Mulroney, Tuija Poyry, Anne E Willis
Nov 28, 2019
Following cell stress, a wide range of molecular pathways are initiated to orchestrate the stress response and enable adaptation to an environmental or intracellular perturbation. The post-transcriptional regulation strategies...
Identification of the RNA polymerase I-RNA interactome.
David Piñeiro, Mark Stoneley, Manasa Ramakrishna, Jana Alexandrova, Veronica Dezi, Rebekha Juke-Jones, Kathryn S Lilley, Kelvin Cain, Anne E Willis
Mar 21, 2019
Ribosome biogenesis is a complex process orchestrated by a host of ribosome assembly factors. Although it is known that many of the proteins involved in this process have RNA binding activity, the full repertoire of proteins...
Comprehensive identification of RNA-protein interactions in any organism using orthogonal organic phase separation (OOPS).
Rayner ML Queiroz, Tom Smith, Eneko Villanueva, Maria Marti-Solano, Mie Monti, Mariavittoria Pizzinga, Dan-Mircea Mirea, Manasa Ramakrishna, Robert F Harvey, Veronica Dezi, Gavin H Thomas, Anne E Willis, Kathryn S Lilley
Jan 07, 2019
Existing high-throughput methods to identify RNA-binding proteins (RBPs) are based on capture of polyadenylated RNAs and cannot recover proteins that interact with nonadenylated RNAs, including long noncoding RNA, pre-mRNAs and...
Association of a germline copy number polymorphism of APOBEC3A and APOBEC3B with burden of putative APOBEC-dependent mutations in breast cancer.
Partially methylated domains are hypervariable in breast cancer and fuel widespread CpG island hypermethylation.
Arie B Brinkman, Serena Nik-Zainal, Femke Simmer, F Germán Rodríguez-González, Marcel Smid, Ludmil B Alexandrov, Adam Butler, Sancha Martin, Helen Davies, Dominik Glodzik, Xueqing Zou, Manasa Ramakrishna, Johan Staaf, Markus Ringnér, Anieta Sieuwerts, Anthony Ferrari, Sandro Morganella, Thomas Fleischer, Vessela Kristensen, Marta Gut, Marc J van de Vijver, Anne-Lise Børresen-Dale, Andrea L Richardson, GIlles Thomas, Ivo G Gut, John WM Martens, John A Foekens, Michael R Stratton, Hendrik G Stunnenberg
May 03, 2019
Global loss of DNA methylation and CpG island (CGI) hypermethylation are key epigenomic aberrations in cancer. Global loss manifests itself in partially methylated domains (PMDs) which extend up to megabases. However, the...
Interplay between spherical confinement and particle shape on the self-assembly of rounded cubes.
Da Wang, Michiel Hermes, Ramakrishna Kotni, Yaoting Wu, Nikos Tasios, Yang Liu, Bart de Nijs, Ernest B van der Wee, Christopher B Murray, Marjolein Dijkstra, Alfons van Blaaderen
Sep 08, 2018
Self-assembly of nanoparticles (NPs) inside drying emulsion droplets provides a general strategy for hierarchical structuring of matter at different length scales. The local orientation of neighboring crystalline NPs can be...
Epigenetic resetting in the human germ line entails histone modification remodeling.
Wolfram H Gruhn, Walfred WC Tang, Sabine Dietmann, João P Alves-Lopes, Christopher A Penfold, Frederick CK Wong, Navin B Ramakrishna, M Azim Surani
Feb 19, 2023
Epigenetic resetting in the mammalian germ line entails acute DNA demethylation, which lays the foundation for gametogenesis, totipotency, and embryonic development. We characterize the epigenome of hypomethylated human...
Somatic mutations reveal asymmetric cellular dynamics in the early human embryo.
Young Seok Ju, Inigo Martincorena, Moritz Gerstung, Mia Petljak, Ludmil B Alexandrov, Raheleh Rahbari, David C Wedge, Helen R Davies, Manasa Ramakrishna, Anthony Fullam, Sancha Martin, Christopher Alder, Nikita Patel, Steve Gamble, Sarah O'Meara, Dilip D Giri, Torril Sauer, Sarah E Pinder, Colin A Purdie, Åke Borg, Henk Stunnenberg, Marc van de Vijver, Benita KT Tan, Carlos Caldas, Andrew Tutt, Naoto T Ueno, Laura J van 't Veer, John WM Martens, Christos Sotiriou, Stian Knappskog, Paul N Span, Sunil R Lakhani, Jórunn Erla Eyfjörd, Anne-Lise Børresen-Dale, Andrea Richardson, Alastair M Thompson, Alain Viari, Matthew E Hurles, Serena Nik-Zainal, Peter J Campbell, Michael R Stratton
May 07, 2019
Somatic cells acquire mutations throughout the course of an individual's life. Mutations occurring early in embryogenesis are often present in a substantial proportion of, but not all, cells in postnatal humans and thus have...
Processed pseudogenes acquired somatically during cancer development.
Susanna L Cooke, Adam Shlien, John Marshall, Christodoulos P Pipinikas, Inigo Martincorena, Jose MC Tubio, Yilong Li, Andrew Menzies, Laura Mudie, Manasa Ramakrishna, Lucy Yates, Helen Davies, Niccolo Bolli, Graham R Bignell, Patrick S Tarpey, Sam Behjati, Serena Nik-Zainal, Elli Papaemmanuil, Vitor H Teixeira, Keiran Raine, Sarah O'Meara, Maryam S Dodoran, Jon W Teague, Adam P Butler, Christine Iacobuzio-Donahue, Thomas Santarius, Richard G Grundy, David Malkin, Mel Greaves, Nikhil Munshi, Adrienne M Flanagan, David Bowtell, Sancha Martin, Denis Larsimont, Jorge S Reis-Filho, Alex Boussioutas, Jack A Taylor, Neil D Hayes, Sam M Janes, P Andrew Futreal, Michael R Stratton, Ultan McDermott, Peter J Campbell, ICGC Breast Cancer Group
Nov 01, 2018
Cancer evolves by mutation, with somatic reactivation of retrotransposons being one such mutational process. Germline retrotransposition can cause processed pseudogenes, but whether this occurs somatically has not been...
HRDetect is a predictor of BRCA1 and BRCA2 deficiency based on mutational signatures.
Helen Davies, Dominik Glodzik, Sandro Morganella, Lucy R Yates, Johan Staaf, Xueqing Zou, Manasa Ramakrishna, Sancha Martin, Sandrine Boyault, Anieta M Sieuwerts, Peter T Simpson, Tari A King, Keiran Raine, Jorunn E Eyfjord, Gu Kong, Åke Borg, Ewan Birney, Hendrik G Stunnenberg, Marc J van de Vijver, Anne-Lise Børresen-Dale, John WM Martens, Paul N Span, Sunil R Lakhani, Anne Vincent-Salomon, Christos Sotiriou, Andrew Tutt, Alastair M Thompson, Steven Van Laere, Andrea L Richardson, Alain Viari, Peter J Campbell, Michael R Stratton, Serena Nik-Zainal
Dec 07, 2020
Approximately 1-5% of breast cancers are attributed to inherited mutations in BRCA1 or BRCA2 and are selectively sensitive to poly(ADP-ribose) polymerase (PARP) inhibitors. In other cancer types, germline and/or somatic...
The topography of mutational processes in breast cancer genomes.
Sandro Morganella, Ludmil B Alexandrov, Dominik Glodzik, Xueqing Zou, Helen Davies, Johan Staaf, Anieta M Sieuwerts, Arie B Brinkman, Sancha Martin, Manasa Ramakrishna, Adam Butler, Hyung-Yong Kim, Åke Borg, Christos Sotiriou, P Andrew Futreal, Peter J Campbell, Paul N Span, Steven Van Laere, Sunil R Lakhani, Jorunn E Eyfjord, Alastair M Thompson, Hendrik G Stunnenberg, Marc J van de Vijver, John WM Martens, Anne-Lise Børresen-Dale, Andrea L Richardson, Gu Kong, GIlles Thomas, Julian Sale, Cristina Rada, Michael R Stratton, Ewan Birney, Serena Nik-Zainal
Nov 01, 2018
Somatic mutations in human cancers show unevenness in genomic distribution that correlate with aspects of genome structure and function. These mutations are, however, generated by multiple mutational processes operating through...
Subclonal diversification of primary breast cancer revealed by multiregion sequencing.
Lucy R Yates, Moritz Gerstung, Stian Knappskog, Christine Desmedt, Gunes Gundem, Peter Van Loo, Turid Aas, Ludmil B Alexandrov, Denis Larsimont, Helen Davies, Yilong Li, Young Seok Ju, Manasa Ramakrishna, Hans Kristian Haugland, Peer Kaare Lilleng, Serena Nik-Zainal, Stuart McLaren, Adam Butler, Sancha Martin, Dominic Glodzik, Andrew Menzies, Keiran Raine, Jonathan Hinton, David Jones, Laura J Mudie, Bing Jiang, Delphine Vincent, April Greene-Colozzi, Pierre-Yves Adnet, Aquila Fatima, Marion Maetens, Michail Ignatiadis, Michael R Stratton, Christos Sotiriou, Andrea L Richardson, Per Eystein Lønning, David C Wedge, Peter J Campbell
Nov 01, 2018
The sequencing of cancer genomes may enable tailoring of therapeutics to the underlying biological abnormalities driving a particular patient's tumor. However, sequencing-based strategies rely heavily on representative sampling...
The genetic heterogeneity and mutational burden of engineered melanomas in zebrafish models.
Jennifer Yen, Richard M White, David C Wedge, Peter Van Loo, Jeroen de Ridder, Amy Capper, Jennifer Richardson, David Jones, Keiran Raine, Ian R Watson, Chang-Jiun Wu, Jiqiu Cheng, Iñigo Martincorena, Serena Nik-Zainal, Laura Mudie, Yves Moreau, John Marshall, Manasa Ramakrishna, Patrick Tarpey, Adam Shlien, Ian Whitmore, Steve Gamble, Calli Latimer, Erin Langdon, Charles Kaufman, Mike Dovey, Alison Taylor, Andy Menzies, Stuart McLaren, Sarah O'Meara, Adam Butler, Jon Teague, James Lister, Lynda Chin, Peter Campbell, David J Adams, Leonard I Zon, E Elizabeth Patton, Derek L Stemple, P Andy Futreal
Nov 29, 2018
BACKGROUND: Melanoma is the most deadly form of skin cancer. Expression of oncogenic BRAF or NRAS, which are frequently mutated in human melanomas, promote the formation of nevi but are not sufficient for tumorigenesis. Even...
Mutational processes molding the genomes of 21 breast cancers.
Serena Nik-Zainal, Ludmil B Alexandrov, David C Wedge, Peter Van Loo, Christopher D Greenman, Keiran Raine, David Jones, Jonathan Hinton, John Marshall, Lucy A Stebbings, Andrew Menzies, Sancha Martin, Kenric Leung, Lina Chen, Catherine Leroy, Manasa Ramakrishna, Richard Rance, King Wai Lau, Laura J Mudie, Ignacio Varela, David J McBride, Graham R Bignell, Susanna L Cooke, Adam Shlien, John Gamble, Ian Whitmore, Mark Maddison, Patrick S Tarpey, Helen R Davies, Elli Papaemmanuil, Philip J Stephens, Stuart McLaren, Adam P Butler, Jon W Teague, Göran Jönsson, Judy E Garber, Daniel Silver, Penelope Miron, Aquila Fatima, Sandrine Boyault, Anita Langerød, Andrew Tutt, John WM Martens, Samuel AJR Aparicio, Åke Borg, Anne Vincent Salomon, GIlles Thomas, Anne-Lise Børresen-Dale, Andrea L Richardson, Michael S Neuberger, P Andrew Futreal, Peter J Campbell, Michael R Stratton, Breast Cancer Working Group of the International Cancer Genome Consortium
Aug 27, 2020
All cancers carry somatic mutations. The patterns of mutation in cancer genomes reflect the DNA damage and repair processes to which cancer cells and their precursors have been exposed. To explore these mechanisms further, we...
Transcriptional activity and epigenetic regulation of transposable elements in the symbiotic fungus Rhizophagus irregularis.
Direct Transcriptional Consequences of Somatic Mutation in Breast Cancer.
Adam Shlien, Keiran Raine, Fabio Fuligni, Roland Arnold, Serena Nik-Zainal, Serge Dronov, Lira Mamanova, Andrej Rosic, Young Seok Ju, Susanna L Cooke, Manasa Ramakrishna, Elli Papaemmanuil, Helen R Davies, Patrick S Tarpey, Peter Van Loo, David C Wedge, David R Jones, Sancha Martin, John Marshall, Elizabeth Anderson, Claire Hardy, Oslo Breast Cancer Research Consortium ICGC Breast Cancer Working Group, Violetta Barbashina, Samuel AJR Aparicio, Torill Sauer, Øystein Garred, Anne Vincent-Salomon, Odette Mariani, Sandrine Boyault, Aquila Fatima, Anita Langerød, Åke Borg, GIlles Thomas, Andrea L Richardson, Anne-Lise Børresen-Dale, Kornelia Polyak, Michael R Stratton, Peter J Campbell
Nov 01, 2018
Disordered transcriptomes of cancer encompass direct effects of somatic mutation on transcription, coordinated secondary pathway alterations, and increased transcriptional noise. To catalog the rules governing how somatic...
The life history of 21 breast cancers.
Serena Nik-Zainal, Peter Van Loo, David C Wedge, Ludmil B Alexandrov, Christopher D Greenman, King Wai Lau, Keiran Raine, David Jones, John Marshall, Manasa Ramakrishna, Adam Shlien, Susanna L Cooke, Jonathan Hinton, Andrew Menzies, Lucy A Stebbings, Catherine Leroy, Mingming Jia, Richard Rance, Laura J Mudie, Stephen J Gamble, Philip J Stephens, Stuart McLaren, Patrick S Tarpey, Elli Papaemmanuil, Helen R Davies, Ignacio Varela, David J McBride, Graham R Bignell, Kenric Leung, Adam P Butler, Jon W Teague, Sancha Martin, Goran Jönsson, Odette Mariani, Sandrine Boyault, Penelope Miron, Aquila Fatima, Anita Langerød, Samuel AJR Aparicio, Andrew Tutt, Anieta M Sieuwerts, Åke Borg, GIlles Thomas, Anne Vincent Salomon, Andrea L Richardson, Anne-Lise Børresen-Dale, P Andrew Futreal, Michael R Stratton, Peter J Campbell, Breast Cancer Working Group of the International Cancer Genome Consortium
Aug 27, 2020
Cancer evolves dynamically as clonal expansions supersede one another driven by shifting selective pressures, mutational processes, and disrupted cancer genes. These processes mark the genome, such that a cancer's life history...
Origins and functional consequences of somatic mitochondrial DNA mutations in human cancer.
Young Seok Ju, Ludmil B Alexandrov, Moritz Gerstung, Inigo Martincorena, Serena Nik-Zainal, Manasa Ramakrishna, Helen R Davies, Elli Papaemmanuil, Gunes Gundem, Adam Shlien, Niccolo Bolli, Sam Behjati, Patrick S Tarpey, Jyoti Nangalia, Charles E Massie, Adam P Butler, Jon W Teague, George S Vassiliou, Anthony R Green, Ming-Qing Du, Ashwin Unnikrishnan, John E Pimanda, Bin Tean Teh, Nikhil Munshi, Mel Greaves, Paresh Vyas, Adel K El-Naggar, Tom Santarius, V Peter Collins, Richard Grundy, Jack A Taylor, D Neil Hayes, David Malkin, ICGC Breast Cancer Group, ICGC Chronic Myeloid Disorders Group, ICGC Prostate Cancer Group, Christopher S Foster, Anne Y Warren, Hayley C Whitaker, Daniel Brewer, Rosalind Eeles, Colin Cooper, David Neal, Tapio Visakorpi, William B Isaacs, G Steven Bova, Adrienne M Flanagan, P Andrew Futreal, Andy G Lynch, Patrick F Chinnery, Ultan McDermott, Michael R Stratton, Peter J Campbell
Nov 01, 2018
Recent sequencing studies have extensively explored the somatic alterations present in the nuclear genomes of cancers. Although mitochondria control energy metabolism and apoptosis, the origins and impact of cancer-associated...
cancer genome evolution evolutionary biology Genomics human Mitochondrial DNA mutational signature SEQUENCING Somatic mutation Animals Base Composition DNA DNA Replication DNA Mitochondrial DNA Neoplasm Data Mining evolution Molecular Genome Mitochondrial High-Throughput Nucleotide Sequencing Humans Mitochondria Mutation Neoplasms Polymorphism Single Nucleotide
Mutational signatures of ionizing radiation in second malignancies
S Behjati, G Gundem, DC Wedge, ND Roberts, PS Tarpey, SL Cooke, P Van Loo, LB Alexandrov, M Ramakrishna, H Davies, S Nik-Zainal, C Hardy, C Latimer, KM Raine, L Stebbings, A Menzies, D Jones, R Shepherd, AP Butler, JW Teague, M Jorgensen, B Khatri, N Pillay, A Shlien, PA Futreal, C Badie, ICGC Prostate Group, U McDermott, GS Bova, AL Richardson, AM Flanagan, MR Stratton, PJ Campbell
Mar 31, 2017
Zfp503/Nlz2 Is Required for RPE Differentiation and Optic Fissure Closure.
Elangovan Boobalan, Amy H Thompson, Ramakrishna P Alur, David M McGaughey, Lijin Dong, Grace Shih, Emile R Vieta-Ferrer, Ighovie F Onojafe, Vijay K Kalaskar, Gavin Arno, Andrew J Lotery, Bin Guan, Chelsea Bender, Omar Memon, Lauren Brinster, Clement Soleilhavoup, Lia Panman, Tudor C Badea, Andrea Minella, Antonio Jacobo Lopez, Sara M Thomasy, Ala Moshiri, Delphine Blain, Robert B Hufnagel, Tiziana Cogliati, Kapil Bharti, Brian P Brooks
Dec 08, 2022
Development of a sensitive trial-ready poly(GP) CSF biomarker assay for C9orf72-associated frontotemporal dementia and amyotrophic lateral sclerosis.
Katherine M Wilson, Eszter Katona, Idoia Glaria, Mireia Carcolé, Imogen J Swift, Aitana Sogorb-Esteve, Carolin Heller, Arabella Bouzigues, Amanda J Heslegrave, Ashvini Keshavan, Kathryn Knowles, Saurabh Patil, Susovan Mohapatra, Yuanjing Liu, Jaya Goyal, Raquel Sanchez-Valle, Robert Jr Laforce, Matthis Synofzik, James B Rowe, Elizabeth Finger, Rik Vandenberghe, Christopher R Butler, Alexander Gerhard, John C van Swieten, Harro Seelaar, Barbara Borroni, Daniela Galimberti, Alexandre de Mendonça, Mario Masellis, M Carmela Tartaglia, Markus Otto, Caroline Graff, Simon Ducharme, Jonathan M Schott, Andrea Malaspina, Henrik Zetterberg, Ramakrishna Boyanapalli, Jonathan D Rohrer, Adrian M Isaacs, Genetic FTD Initiative (GENFI)
Apr 07, 2022
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