Browsing ICR Divisions by author "Choudhary, Jyoti"
Now showing items 41-60 of 86
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A HUWE1 defect causes PARP inhibitor resistance by modulating the BRCA1-∆11q splice variant.
Pettitt, SJ; Shao, N; Zatreanu, D; Frankum, J; Bajrami, I; et al. (SPRINGERNATURE, 2023-09-01)Although PARP inhibitors (PARPi) now form part of the standard-of-care for the treatment of homologous recombination defective cancers, de novo and acquired resistance limits their overall effectiveness. Previously, ... -
Identification of protein complexes that bind to histone H3 combinatorial modifications using super-SILAC and weighted correlation network analysis.
Kunowska, N; Rotival, M; Yu, L; Choudhary, J; Dillon, N (OXFORD UNIV PRESS, 2015-02-18)The large number of chemical modifications that are found on the histone proteins of eukaryotic cells form multiple complex combinations, which can act as recognition signals for reader proteins. We have used peptide capture ... -
Identifying and characterising Thrap3, Bclaf1 and Erh interactions using cross-linking mass spectrometry
Shcherbakova, L; Pardo, M; Roumeliotis, T; Choudhary, J (F1000 Research Ltd, 2023-01-06)<ns3:p><ns3:bold>Background: </ns3:bold>Cross-linking mass spectrometry (XL-MS) is a powerful technology capable of yielding structural insights across the complex cellular protein interaction network. However, up to date ... -
Identifying and characterising Thrap3, Bclaf1 and Erh interactions using cross-linking mass spectrometry.
Shcherbakova, L; Pardo, M; Roumeliotis, T; Choudhary, J (F1000 Research Ltd, 2021-01-01)Background: Cross-linking mass spectrometry (XL-MS) is a powerful technology capable of yielding structural insights across the complex cellular protein interaction network. However, up to date most of the studies utilising ... -
Improving GENCODE reference gene annotation using a high-stringency proteogenomics workflow.
Wright, JC; Mudge, J; Weisser, H; Barzine, MP; Gonzalez, JM; et al. (NATURE PORTFOLIO, 2016-06-02)Complete annotation of the human genome is indispensable for medical research. The GENCODE consortium strives to provide this, augmenting computational and experimental evidence with manual annotation. The rapidly developing ... -
Integrative epigenomics, transcriptomics and proteomics of patient chondrocytes reveal genes and pathways involved in osteoarthritis.
Steinberg, J; Ritchie, GRS; Roumeliotis, TI; Jayasuriya, RL; Clark, MJ; et al. (NATURE PORTFOLIO, 2017-08-21)Osteoarthritis (OA) is a common disease characterized by cartilage degeneration and joint remodeling. The underlying molecular changes underpinning disease progression are incompletely understood. We investigated genes and ... -
Interferon-driven alterations of the host's amino acid metabolism in the pathogenesis of typhoid fever.
Blohmke, CJ; Darton, TC; Jones, C; Suarez, NM; Waddington, CS; et al. (ROCKEFELLER UNIV PRESS, 2016-05-30)Enteric fever, caused by Salmonella enterica serovar Typhi, is an important public health problem in resource-limited settings and, despite decades of research, human responses to the infection are poorly understood. In ... -
Intestinal Epithelial Cells and the Microbiome Undergo Swift Reprogramming at the Inception of Colonic Citrobacter rodentium Infection.
Hopkins, EGD; Roumeliotis, TI; Mullineaux-Sanders, C; Choudhary, JS; Frankel, G (AMER SOC MICROBIOLOGY, 2019-04-02)We used the mouse attaching and effacing (A/E) pathogen Citrobacter rodentium, which models the human A/E pathogens enteropathogenic Escherichia coli and enterohemorrhagic E. coli (EPEC and EHEC), to temporally resolve ... -
Landscape of the Plasmodium Interactome Reveals Both Conserved and Species-Specific Functionality.
Hillier, C; Pardo, M; Yu, L; Bushell, E; Sanderson, T; et al. (CELL PRESS, 2019-08-06)Malaria represents a major global health issue, and the identification of new intervention targets remains an urgent priority. This search is hampered by more than one-third of the genes of malaria-causing Plasmodium ... -
Mechanism of assembly, activation and lysine selection by the SIN3B histone deacetylase complex.
Wan, MSM; Muhammad, R; Koliopoulos, MG; Roumeliotis, TI; Choudhary, JS; et al. (NATURE PORTFOLIO, 2023-05-03)Lysine acetylation in histone tails is a key post-translational modification that controls transcription activation. Histone deacetylase complexes remove histone acetylation, thereby repressing transcription and regulating ... -
Multiple short windows of calcium-dependent protein kinase 4 activity coordinate distinct cell cycle events during Plasmodium gametogenesis.
Fang, H; Klages, N; Baechler, B; Hillner, E; Yu, L; et al. (ELIFE SCIENCES PUBLICATIONS LTD, 2017-05-08)Malaria transmission relies on the production of gametes following ingestion by a mosquito. Here, we show that Ca2+-dependent protein kinase 4 controls three processes essential to progress from a single haploid microgametocyte ... -
Mutations in FAM50A suggest that Armfield XLID syndrome is a spliceosomopathy.
Lee, Y-R; Khan, K; Armfield-Uhas, K; Srikanth, S; Thompson, NA; et al. (NATURE PORTFOLIO, 2020-07-23)Intellectual disability (ID) is a heterogeneous clinical entity and includes an excess of males who harbor variants on the X-chromosome (XLID). We report rare FAM50A missense variants in the original Armfield XLID syndrome ... -
Myst2/Kat7 histone acetyltransferase interaction proteomics reveals tumour-suppressor Niam as a novel binding partner in embryonic stem cells.
Pardo, M; Yu, L; Shen, S; Tate, P; Bode, D; et al. (NATURE PORTFOLIO, 2017-08-15)MYST histone acetyltransferases have crucial functions in transcription, replication and DNA repair and are hence implicated in development and cancer. Here we characterise Myst2/Kat7/Hbo1 protein interactions in mouse ... -
Nbeal2 interacts with Dock7, Sec16a, and Vac14.
Mayer, L; Jasztal, M; Pardo, M; Aguera de Haro, S; Collins, J; et al. (AMER SOC HEMATOLOGY, 2018-03-01)Mutations in NBEAL2, the gene encoding the scaffolding protein Nbeal2, are causal of gray platelet syndrome (GPS), a rare recessive bleeding disorder characterized by platelets lacking α-granules and progressive marrow ... -
OpenMS: a flexible open-source software platform for mass spectrometry data analysis.
Röst, HL; Sachsenberg, T; Aiche, S; Bielow, C; Weisser, H; et al. (NATURE PORTFOLIO, 2016-08-30)High-resolution mass spectrometry (MS) has become an important tool in the life sciences, contributing to the diagnosis and understanding of human diseases, elucidating biomolecular structural information and characterizing ... -
Overexpression of Claspin and Timeless protects cancer cells from replication stress in a checkpoint-independent manner.
Bianco, JN; Bergoglio, V; Lin, Y-L; Pillaire, M-J; Schmitz, A-L; et al. (NATURE PUBLISHING GROUP, 2019-02-22)Oncogene-induced replication stress (RS) promotes cancer development but also impedes tumor growth by activating anti-cancer barriers. To determine how cancer cells adapt to RS, we have monitored the expression of different ... -
PBAF loss leads to DNA damage-induced inflammatory signaling through defective G2/M checkpoint maintenance.
Feng, H; Lane, KA; Roumeliotis, TI; Jeggo, PA; Somaiah, N; et al. (COLD SPRING HARBOR LAB PRESS, PUBLICATIONS DEPT, 2022-07-28)The PBRM1 subunit of the PBAF (SWI/SNF) chromatin remodeling complex is mutated in ∼40% of clear cell renal cancers. PBRM1 loss has been implicated in responses to immunotherapy in renal cancer, but the mechanism is unclear. ... -
Perspectives on ENCODE.
ENCODE Project Consortium,; Snyder, MP; Gingeras, TR; Moore, JE; Weng, Z; et al. (NATURE RESEARCH, 2020-07-30)The Encylopedia of DNA Elements (ENCODE) Project launched in 2003 with the long-term goal of developing a comprehensive map of functional elements in the human genome. These included genes, biochemical regions associated ... -
Phosphorylation-Dependent Assembly of a 14-3-3 Mediated Signaling Complex during Red Blood Cell Invasion by Plasmodium falciparum Merozoites.
More, KR; Kaur, I; Giai Gianetto, Q; Invergo, BM; Chaze, T; et al. (AMER SOC MICROBIOLOGY, 2020-08-18)Red blood cell (RBC) invasion by Plasmodium merozoites requires multiple steps that are regulated by signaling pathways. Exposure of P. falciparum merozoites to the physiological signal of low K+, as found in blood plasma, ... -
Precision Medicine in Pancreatic Disease-Knowledge Gaps and Research Opportunities: Summary of a National Institute of Diabetes and Digestive and Kidney Diseases Workshop.
Lowe, ME; Andersen, DK; Caprioli, RM; Choudhary, J; Cruz-Monserrate, Z; et al. (2019-11)A workshop on research gaps and opportunities for Precision Medicine in Pancreatic Disease was sponsored by the National Institute of Diabetes and Digestive Kidney Diseases on July 24, 2019, in Pittsburgh. The workshop ...