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  • 1
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    Genome-scale proteomics reveals Arabidopsis thaliana gene models and proteome dynamics (2008)
    American Association for the Advancement of Science (AAAS)
    Details
    Publication Date: 2008-04-26
    Description: We have assembled a proteome map for Arabidopsis thaliana from high-density, organ-specific proteome catalogs that we generated for different organs, developmental stages, and undifferentiated cultured cells. We matched 86,456 unique peptides to 13,029 proteins and provide expression evidence for 57 gene models that are not represented in the TAIR7 protein database. Analysis of the proteome identified organ-specific biomarkers and allowed us to compile an organ-specific set of proteotypic peptides for 4105 proteins to facilitate targeted quantitative proteomics surveys. Quantitative information for the identified proteins was used to establish correlations between transcript and protein accumulation in different plant organs. The Arabidopsis proteome map provides information about genome activity and proteome assembly and is available as a resource for plant systems biology.〈br /〉〈span class="detail_caption"〉Notes: 〈/span〉Baerenfaller, Katja -- Grossmann, Jonas -- Grobei, Monica A -- Hull, Roger -- Hirsch-Hoffmann, Matthias -- Yalovsky, Shaul -- Zimmermann, Philip -- Grossniklaus, Ueli -- Gruissem, Wilhelm -- Baginsky, Sacha -- New York, N.Y. -- Science. 2008 May 16;320(5878):938-41. doi: 10.1126/science.1157956. Epub 2008 Apr 24.〈br /〉〈span class="detail_caption"〉Author address: 〈/span〉Institute of Plant Sciences, ETH (Swiss Federal Institute of Technology) Zurich, Universitatstrasse 2, 8092 Zurich, Switzerland. kbaerenfaller@ethz.ch〈br /〉〈span class="detail_caption"〉Record origin:〈/span〉 〈a href="http://www.ncbi.nlm.nih.gov/pubmed/18436743" target="_blank"〉PubMed〈/a〉
    Keywords: Algorithms ; Amino Acid Sequence ; Arabidopsis/*chemistry/cytology/*genetics/physiology ; Arabidopsis Proteins/*analysis/chemistry/genetics ; Base Sequence ; Biomarkers/analysis ; Cells, Cultured ; Computational Biology ; Databases, Genetic ; Flowers/chemistry/genetics ; Gene Expression Profiling ; Gene Expression Regulation, Plant ; *Genome, Plant ; Models, Genetic ; Molecular Sequence Data ; Peptides/analysis/chemistry ; Plant Roots/chemistry/genetics ; Proteome/*analysis ; *Proteomics ; Seeds/chemistry/genetics ; Transcription, Genetic
    Print ISSN: 0036-8075
    Electronic ISSN: 1095-9203
    Topics: Biology , Chemistry and Pharmacology , Computer Science , Medicine , Natural Sciences in General , Physics
    Published by American Association for the Advancement of Science (AAAS)
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  • 2
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    Genome-scale, single-cell-type resolution of microRNA activities within a whole plant organ (2019)
    Springer Nature
    Details
    Publication Date: 2019
    Description: 〈sec〉〈st〉Synopsis〈/st〉〈p〉〈textbox textbox-type="graphic"〉〈p〉〈inline-fig〉〈/inline-fig〉〈/p〉〈/textbox〉〈/p〉 〈p〉Spatial coordination of miRNA activity at a genome-wide level within and across the various cell types of an intact organ remains largely unexplored. The current study tackles this question in the 〈i〉Arabidopsis〈/i〉 root tip and offers novel insights into miRNA-mediated gene regulation in a complex organ.〈/p〉 〈p〉 〈l type="unord"〉〈li〉〈p〉Exhaustive, cell-type-specific repertoires of functional miRNAs ("miRNAomes") where acquired via cell-type-specific AGO1 immunoprecipitation.〈/p〉〈/li〉 〈li〉〈p〉Cell-type-specific translatomes obtained in WT versus miRNA-deficient roots allowed identification of cell-type-specific repertoires of miRNA target transcripts ("targetomes").〈/p〉〈/li〉 〈li〉〈p〉miRNAomes and targetomes were then integrated into the miRoot browser, allowing user-friendly data interrogation.〈/p〉〈/li〉 〈li〉〈p〉miRoot coupled to experimentation uncovered new modes of plant miRNA action, including via unexpectedly widespread, functional cell-to-cell movement of miRNA between root layers.〈/p〉〈/li〉〈/l〉 〈/p〉〈/sec〉
    Print ISSN: 0261-4189
    Electronic ISSN: 1460-2075
    Topics: Biology , Medicine
    Published by Springer Nature on behalf of The European Molecular Biology Organization (EMBO).
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