Multiparameter functional diversity of human C2H2 zinc finger proteins. Genome Research. Stem Cell Reports. Greenblatt J , et al. Proteome-wide dataset supporting the study of ancient metazoan macromolecular complexes. Data in Brief. Plos One.
Systems Analysis of Chromatin-Related Protein Complexes in Cancer
Panorama of ancient metazoan macromolecular complexes. Assessment of a method to characterize antibody selectivity and specificity for use in immunoprecipitation. Nature Methods.
Extracting high confidence protein interactions from affinity purification data: at the crossroads. Journal of Proteomics. C2H2 zinc finger proteins greatly expand the human regulatory lexicon. Nature Biotechnology. Bioinformatics Oxford, England. Human-chromatin-related protein interactions identify a demethylase complex required for chromosome segregation. Cell Reports. Quantitative genome-wide genetic interaction screens reveal global epistatic relationships of protein complexes in Escherichia coli. Plos Genetics.
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Journal of Virology. A unified model for yeast transcript definition. Histone methyltransferase complexes in transcription, development, and cancer Systems Analysis of Chromatin-Related Protein Complexes in Cancer. DOI: Networks of histone demethylases and their relevance to the regulation of chromatin structure and dynamics Systems Analysis of Chromatin-Related Protein Complexes in Cancer. Mapping the functional yeast ABC transporter interactome. Nature Chemical Biology. The carboxyl terminus of Rtt functions in chaperone control of histone acetylation.
Proteomics to study DNA-bound and chromatin-associated gene regulatory complexes
Nucleic Acids Research. Identification of protein complexes in Escherichia coli using sequential peptide affinity purification in combination with tandem mass spectrometry.
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Journal of Visualized Experiments : Jove. Mapping bacterial functional networks and pathways in Escherichia Coli using synthetic genetic arrays. Interaction landscape of membrane-protein complexes in Saccharomyces cerevisiae. Hsp is required for spindle length control.
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The Journal of Cell Biology. Genetic interaction maps in Escherichia coli reveal functional crosstalk among cell envelope biogenesis pathways. Identification of mammalian protein complexes by lentiviral-based affinity purification and mass spectrometry. Methods in Molecular Biology Clifton, N.
Systems Analysis of Chromatin-Related Protein Complexes in Cancer | Andrew Emili | Springer
Array-based synthetic genetic screens to map bacterial pathways and functional networks in Escherichia coli. Ribosome-dependent ATPase interacts with conserved membrane protein in Escherichia coli to modulate protein synthesis and oxidative phosphorylation. OrthoNets: simultaneous visual analysis of orthologs and their interaction neighborhoods across different organisms.
Molecular Microbiology. DAnCER: disease-annotated chromatin epigenetics resource. Defining the budding yeast chromatin-associated interactome. Molecular Systems Biology. Expanding the landscape of chromatin modification CM -related functional domains and genes in human. Structure London, England : Epistatic relationships reveal the functional organization of yeast transcription factors. Shuye Pu, Andrei L. Turinsky, Shoshana Wodak. Identification of Chromatin-Binding Protein Complexes. Mahadevan Lakshminarasimhan, Michael P.
Victoria M. Richon, Mikel P. Moyer, Robert A. Genome Organization in Cancer Cells. Histone Chaperones, Epigenetics, and Cancer. However, with continuous improvements in proteomics instrumentation and methods, near-complete analysis of protein complexes will be achieved in the near future. Compared with normal prostate, low-grade PCa tissue samples have 1 seven more abundant protein complexes, 2 higher assembly levels of 20 protein complexes including six spliceosome subcomplexes involved in RNA splicing, 3 decreased abundance of 47 protein complexes including 13 integrin protein complexes involved in cell adhesion, and 4 decreased assembly levels of eight protein complexes.
To our knowledge, this study represents the first comprehensive, albeit indirect, analysis of individual protein complexes in PCa tissue specimens. It may serve as a useful resource for better understanding the dysregulation of protein complexes in primary PCa. Global cancer statistics, CA Cancer J Clin. Cancer statistics, Recent advances in prostate cancer research: large-scale genomic analyses reveal novel driver mutations and DNA repair defects.
Roychowdhury S, Chinnaiyan AM. Translating cancer genomes and transcriptomes for precision oncology.
Of proteins and DNA—proteomic role in the field of chromatin research
Integrated classification of prostate cancer reveals a novel luminal subtype with poor outcome. Cancer Res. Systems pharmacology using mass spectrometry identifies critical response nodes in prostate cancer. Integrative proteomics in prostate cancer uncovers robustness against genomic and transcriptomic aberrations during disease progression.
Nat Commun. Proteogenomic characterization of human colon and rectal cancer. Harnessing the power of proteomics for identification of oncogenic, druggable signalling pathways in cancer.
Expert Opin Drug Discov. Tissue proteomics studies in the investigation of prostate cancer. Expert Rev Proteomics. The proteome of primary prostate cancer. Eur Urol. Pathology-driven comprehensive proteomic profiling of the prostate cancer tumor microenvironment. Mol Cancer Res. Proteomic characterization of prostate cancer to distinguish nonmetastasizing and metastasizing primary tumors and lymph node metastases. Multi-region proteome analysis quantifies spatial heterogeneity of prostate tissue biomarkers. Life Sci Alliance. The proteome of prostate cancer bone metastasis reveals heterogeneity with prognostic implications.
Clin Cancer Res. Alberts B. The cell as a collection of protein machines: preparing the next generation of molecular biologists. Protein complexes, big data, machine learning and integrative proteomics: lessons learned over a decade of systematic analysis of protein interaction networks.
J Proteomics. Relative and absolute quantitation in mass spectrometry—based proteomics. Annu Rev Anal Chem. Anal Chem. Increasing the multiplexing capacity of TMTs using reporter ion isotopologues with isobaric masses. MS3 eliminates ratio distortion in isobaric multiplexed quantitative proteomics. Nat Methods. MultiNotch MS3 enables accurate, sensitive, and multiplexed detection of differential expression across cancer cell line proteomes.
Detection of dysregulated protein-association networks by high-throughput proteomics predicts cancer vulnerabilities.