@article {318, title = {A comparative study of ripening among berries of the grape cluster reveals an altered transcriptional programme and enhanced ripening rate in delayed berries.}, journal = {J Exp Bot}, volume = {65}, year = {2014}, month = {2014 Nov}, pages = {5889-902}, abstract = {

Transcriptional studies in relation to fruit ripening generally aim to identify the transcriptional states associated with physiological ripening stages and the transcriptional changes between stages within the ripening programme. In non-climacteric fruits such as grape, all ripening-related genes involved in this programme have not been identified, mainly due to the lack of mutants for comparative transcriptomic studies. A feature in grape cluster ripening (Vitis vinifera cv. Pinot noir), where all berries do not initiate the ripening at the same time, was exploited to study their shifted ripening programmes in parallel. Berries that showed marked ripening state differences in a v{\'e}raison-stage cluster (ripening onset) ultimately reached similar ripeness states toward maturity, indicating the flexibility of the ripening programme. The expression variance between these v{\'e}raison-stage berry classes, where 11\% of the genes were found to be differentially expressed, was reduced significantly toward maturity, resulting in the synchronization of their transcriptional states. Defined quantitative expression changes (transcriptional distances) not only existed between the v{\'e}raison transitional stages, but also between the v{\'e}raison to maturity stages, regardless of the berry class. It was observed that lagging berries complete their transcriptional programme in a shorter time through altered gene expressions and ripening-related hormone dynamics, and enhance the rate of physiological ripening progression. Finally, the reduction in expression variance of genes can identify new genes directly associated with ripening and also assess the relevance of gene activity to the phase of the ripening programme.

}, keywords = {Fruit, Gene Expression Profiling, Gene Expression Regulation, Plant, Oligonucleotide Array Sequence Analysis, Plant Growth Regulators, Time Factors, Transcription, Genetic, Vitis}, issn = {1460-2431}, doi = {10.1093/jxb/eru329}, author = {Gouthu, Satyanarayana and O{\textquoteright}Neil, Shawn T and Di, Yanming and Ansarolia, Mitra and Megraw, Molly and Deluc, Laurent G} } @article {321, title = {The protein expression landscape of the Arabidopsis root.}, journal = {Proc Natl Acad Sci U S A}, volume = {109}, year = {2012}, month = {2012 May 1}, pages = {6811-8}, abstract = {

Because proteins are the major functional components of cells, knowledge of their cellular localization is crucial to gaining an understanding of the biology of multicellular organisms. We have generated a protein expression map of the Arabidopsis root providing the identity and cell type-specific localization of nearly 2,000 proteins. Grouping proteins into functional categories revealed unique cellular functions and identified cell type-specific biomarkers. Cellular colocalization provided support for numerous protein-protein interactions. With a binary comparison, we found that RNA and protein expression profiles are weakly correlated. We then performed peak integration at cell type-specific resolution and found an improved correlation with transcriptome data using continuous values. We performed GeLC-MS/MS (in-gel tryptic digestion followed by liquid chromatography-tandem mass spectrometry) proteomic experiments on mutants with ectopic and no root hairs, providing complementary proteomic data. Finally, among our root hair-specific proteins we identified two unique regulators of root hair development.

}, keywords = {Arabidopsis, Arabidopsis Proteins, Base Sequence, Chromatography, Liquid, DNA Primers, Gene Expression Profiling, Plant Roots, Plants, Genetically Modified, Protein Array Analysis, Protein Interaction Mapping, Proteome, Proteomics, RNA, Plant, Tandem Mass Spectrometry}, issn = {1091-6490}, doi = {10.1073/pnas.1202546109}, author = {Petricka, Jalean J and Schauer, Monica A and Megraw, Molly and Breakfield, Natalie W and Thompson, J Will and Georgiev, Stoyan and Soderblom, Erik J and Ohler, Uwe and Moseley, Martin Arthur and Grossniklaus, Ueli and Benfey, Philip N} } @article {322, title = {A stele-enriched gene regulatory network in the Arabidopsis root.}, journal = {Mol Syst Biol}, volume = {7}, year = {2011}, month = {2011 Jan 18}, pages = {459}, abstract = {

Tightly controlled gene expression is a hallmark of multicellular development and is accomplished by transcription factors (TFs) and microRNAs (miRNAs). Although many studies have focused on identifying downstream targets of these molecules, less is known about the factors that regulate their differential expression. We used data from high spatial resolution gene expression experiments and yeast one-hybrid (Y1H) and two-hybrid (Y2H) assays to delineate a subset of interactions occurring within a gene regulatory network (GRN) that determines tissue-specific TF and miRNA expression in plants. We find that upstream TFs are expressed in more diverse cell types than their targets and that promoters that are bound by a relatively large number of TFs correspond to key developmental regulators. The regulatory consequence of many TFs for their target was experimentally determined using genetic analysis. Remarkably, molecular phenotypes were identified for 65\% of the TFs, but morphological phenotypes were associated with only 16\%. This indicates that the GRN is robust, and that gene expression changes may be canalized or buffered.

}, keywords = {Arabidopsis, Arabidopsis Proteins, Gene Expression Profiling, Gene Regulatory Networks, MicroRNAs, Plant Roots, Reproducibility of Results, Systems Biology, Transcription Factors, Two-Hybrid System Techniques}, issn = {1744-4292}, doi = {10.1038/msb.2010.114}, author = {Brady, Siobhan M and Zhang, Lifang and Megraw, Molly and Martinez, Natalia J and Jiang, Eric and Yi, Charles S and Liu, Weilin and Zeng, Anna and Taylor-Teeples, Mallorie and Kim, Dahae and Ahnert, Sebastian and Ohler, Uwe and Ware, Doreen and Walhout, Albertha J M and Benfey, Philip N} }