Literature DB >> 31933212

An Integrated Strategy for Identifying Targets of Ubiquitin-Mediated Degradation in CD4+ T Cells.

Natania S Field1,2, Claire E O'Leary3, Joseph M Dybas1,2, Hua Ding4, Paula M Oliver5,6.   

Abstract

Ubiquitination is a crucial component of many immune processes. While ubiquitin-mediated degradation is essential to T cell activation via T cell receptor signaling, the specific E3 ligases and substrates involved are not well-understood. Here, we describe a strategy integrating RNA, protein, and posttranslational modification datasets to identify targets of ubiquitin-mediated degradation. When integrated, these assays can provide broad insight into how this posttranslational modification regulates protein function and influences T cell biology.

Entities:  

Keywords:  Diglycine remnant profiling; Lymphocyte; Signaling; T cell; Ubiquitin

Mesh:

Substances:

Year:  2020        PMID: 31933212      PMCID: PMC7549384          DOI: 10.1007/978-1-0716-0266-9_19

Source DB:  PubMed          Journal:  Methods Mol Biol        ISSN: 1064-3745


  15 in total

1.  In-gel digestion for mass spectrometric characterization of proteins and proteomes.

Authors:  Andrej Shevchenko; Henrik Tomas; Jan Havlis; Jesper V Olsen; Matthias Mann
Journal:  Nat Protoc       Date:  2006       Impact factor: 13.491

2.  Integrative proteomics reveals an increase in non-degradative ubiquitylation in activated CD4+ T cells.

Authors:  Joseph M Dybas; Claire E O'Leary; Hua Ding; Lynn A Spruce; Steven H Seeholzer; Paula M Oliver
Journal:  Nat Immunol       Date:  2019-05-06       Impact factor: 25.606

3.  The MaxQuant computational platform for mass spectrometry-based shotgun proteomics.

Authors:  Stefka Tyanova; Tikira Temu; Juergen Cox
Journal:  Nat Protoc       Date:  2016-10-27       Impact factor: 13.491

4.  STAR: ultrafast universal RNA-seq aligner.

Authors:  Alexander Dobin; Carrie A Davis; Felix Schlesinger; Jorg Drenkow; Chris Zaleski; Sonali Jha; Philippe Batut; Mark Chaisson; Thomas R Gingeras
Journal:  Bioinformatics       Date:  2012-10-25       Impact factor: 6.937

5.  Dysregulation of T lymphocyte function in itchy mice: a role for Itch in TH2 differentiation.

Authors:  Deyu Fang; Chris Elly; Baixue Gao; Nan Fang; Yoav Altman; Claudio Joazeiro; Tony Hunter; Neal Copeland; Nancy Jenkins; Yun-Cai Liu
Journal:  Nat Immunol       Date:  2002-02-04       Impact factor: 25.606

6.  Multiple testing corrections in quantitative proteomics: A useful but blunt tool.

Authors:  Dana Pascovici; David C L Handler; Jemma X Wu; Paul A Haynes
Journal:  Proteomics       Date:  2016-09       Impact factor: 3.984

7.  Integrative Proteomics and Phosphoproteomics Profiling Reveals Dynamic Signaling Networks and Bioenergetics Pathways Underlying T Cell Activation.

Authors:  Haiyan Tan; Kai Yang; Yuxin Li; Timothy I Shaw; Yanyan Wang; Daniel Bastardo Blanco; Xusheng Wang; Ji-Hoon Cho; Hong Wang; Sherri Rankin; Cliff Guy; Junmin Peng; Hongbo Chi
Journal:  Immunity       Date:  2017-03-09       Impact factor: 31.745

8.  Fast and sensitive colloidal coomassie G-250 staining for proteins in polyacrylamide gels.

Authors:  Nadine Dyballa; Sabine Metzger
Journal:  J Vis Exp       Date:  2009-08-03       Impact factor: 1.355

9.  Refined preparation and use of anti-diglycine remnant (K-ε-GG) antibody enables routine quantification of 10,000s of ubiquitination sites in single proteomics experiments.

Authors:  Namrata D Udeshi; Tanya Svinkina; Philipp Mertins; Eric Kuhn; D R Mani; Jana W Qiao; Steven A Carr
Journal:  Mol Cell Proteomics       Date:  2012-12-24       Impact factor: 5.911

10.  Targeted analysis of nucleotide and copy number variation by exon capture in allotetraploid wheat genome.

Authors:  Cyrille Saintenac; Dayou Jiang; Eduard D Akhunov
Journal:  Genome Biol       Date:  2011-09-14       Impact factor: 13.583

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  1 in total

1.  Itch attenuates CD4 T-cell proliferation in mice by limiting WBP2 protein stability.

Authors:  Natania S Field; Omar A Elbulok; Joseph M Dybas; Emily K Moser; Asif A Dar; Lynn A Spruce; Hossein Fazelinia; Steven H Seeholzer; Paula M Oliver
Journal:  Eur J Immunol       Date:  2020-06-09       Impact factor: 5.532

  1 in total

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