@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} } @article {328, title = {Genomic and epigenetic alterations deregulate microRNA expression in human epithelial ovarian cancer.}, journal = {Proc Natl Acad Sci U S A}, volume = {105}, year = {2008}, month = {2008 May 13}, pages = {7004-9}, abstract = {

MicroRNAs (miRNAs) are an abundant class of small noncoding RNAs that function as negative gene regulators. miRNA deregulation is involved in the initiation and progression of human cancer; however, the underlying mechanism and its contributions to genome-wide transcriptional changes in cancer are still largely unknown. We studied miRNA deregulation in human epithelial ovarian cancer by integrative genomic approach, including miRNA microarray (n = 106), array-based comparative genomic hybridization (n = 109), cDNA microarray (n = 76), and tissue array (n = 504). miRNA expression is markedly down-regulated in malignant transformation and tumor progression. Genomic copy number loss and epigenetic silencing, respectively, may account for the down-regulation of approximately 15\% and at least approximately 36\% of miRNAs in advanced ovarian tumors and miRNA down-regulation contributes to a genome-wide transcriptional deregulation. Last, eight miRNAs located in the chromosome 14 miRNA cluster (Dlk1-Gtl2 domain) were identified as potential tumor suppressor genes. Therefore, our results suggest that miRNAs may offer new biomarkers and therapeutic targets in epithelial ovarian cancer.

}, keywords = {DNA, Neoplasm, Down-Regulation, Epigenesis, Genetic, Epithelial Cells, Female, Gene Expression Profiling, Gene Expression Regulation, Neoplastic, Genome, Human, Humans, MicroRNAs, Neoplasm Staging, Ovarian Neoplasms, Ribonuclease III, RNA, Messenger, Survival Analysis}, issn = {1091-6490}, doi = {10.1073/pnas.0801615105}, author = {Zhang, Lin and Volinia, Stefano and Bonome, Tomas and Calin, George Adrian and Greshock, Joel and Yang, Nuo and Liu, Chang-Gong and Giannakakis, Antonis and Alexiou, Pangiotis and Hasegawa, Kosei and Johnstone, Cameron N and Megraw, Molly S and Adams, Sarah and Lassus, Heini and Huang, Jia and Kaur, Sippy and Liang, Shun and Sethupathy, Praveen and Leminen, Arto and Simossis, Victor A and Sandaltzopoulos, Raphael and Naomoto, Yoshio and Katsaros, Dionyssios and Gimotty, Phyllis A and DeMichele, Angela and Huang, Qihong and B{\"u}tzow, Ralf and Rustgi, Anil K and Weber, Barbara L and Birrer, Michael J and Hatzigeorgiou, Artemis G and Croce, Carlo M and Coukos, George} } @article {332, title = {microRNAs exhibit high frequency genomic alterations in human cancer.}, journal = {Proc Natl Acad Sci U S A}, volume = {103}, year = {2006}, month = {2006 Jun 13}, pages = {9136-41}, abstract = {

MicroRNAs (miRNAs) are endogenous noncoding RNAs, which negatively regulate gene expression. To determine genomewide miRNA DNA copy number abnormalities in cancer, 283 known human miRNA genes were analyzed by high-resolution array-based comparative genomic hybridization in 227 human ovarian cancer, breast cancer, and melanoma specimens. A high proportion of genomic loci containing miRNA genes exhibited DNA copy number alterations in ovarian cancer (37.1\%), breast cancer (72.8\%), and melanoma (85.9\%), where copy number alterations observed in \>15\% tumors were considered significant for each miRNA gene. We identified 41 miRNA genes with gene copy number changes that were shared among the three cancer types (26 with gains and 15 with losses) as well as miRNA genes with copy number changes that were unique to each tumor type. Importantly, we show that miRNA copy changes correlate with miRNA expression. Finally, we identified high frequency copy number abnormalities of Dicer1, Argonaute2, and other miRNA-associated genes in breast and ovarian cancer as well as melanoma. These findings support the notion that copy number alterations of miRNAs and their regulatory genes are highly prevalent in cancer and may account partly for the frequent miRNA gene deregulation reported in several tumor types.

}, keywords = {Breast Neoplasms, Female, Gene Dosage, Gene Expression Profiling, Humans, MicroRNAs, Neoplasms, Nucleic Acid Hybridization, Oligonucleotide Array Sequence Analysis, Ovarian Neoplasms, Statistics as Topic}, issn = {0027-8424}, doi = {10.1073/pnas.0508889103}, author = {Zhang, Lin and Huang, Jia and Yang, Nuo and Greshock, Joel and Megraw, Molly S and Giannakakis, Antonis and Liang, Shun and Naylor, Tara L and Barchetti, Andrea and Ward, Michelle R and Yao, George and Medina, Angelica and O{\textquoteright}brien-Jenkins, Ann and Katsaros, Dionyssios and Hatzigeorgiou, Artemis and Gimotty, Phyllis A and Weber, Barbara L and Coukos, George} }