TY - JOUR T1 - A comparative study of ripening among berries of the grape cluster reveals an altered transcriptional programme and enhanced ripening rate in delayed berries. JF - J Exp Bot Y1 - 2014 A1 - Gouthu, Satyanarayana A1 - O'Neil, Shawn T A1 - Di, Yanming A1 - Ansarolia, Mitra A1 - Megraw, Molly A1 - Deluc, Laurent G KW - Fruit KW - Gene Expression Profiling KW - Gene Expression Regulation, Plant KW - Oligonucleotide Array Sequence Analysis KW - Plant Growth Regulators KW - Time Factors KW - Transcription, Genetic KW - Vitis AB -

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 véraison-stage cluster (ripening onset) ultimately reached similar ripeness states toward maturity, indicating the flexibility of the ripening programme. The expression variance between these véraison-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 véraison transitional stages, but also between the véraison 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.

VL - 65 IS - 20 ER - TY - JOUR T1 - The protein expression landscape of the Arabidopsis root. JF - Proc Natl Acad Sci U S A Y1 - 2012 A1 - Petricka, Jalean J A1 - Schauer, Monica A A1 - Megraw, Molly A1 - Breakfield, Natalie W A1 - Thompson, J Will A1 - Georgiev, Stoyan A1 - Soderblom, Erik J A1 - Ohler, Uwe A1 - Moseley, Martin Arthur A1 - Grossniklaus, Ueli A1 - Benfey, Philip N KW - Arabidopsis KW - Arabidopsis Proteins KW - Base Sequence KW - Chromatography, Liquid KW - DNA Primers KW - Gene Expression Profiling KW - Plant Roots KW - Plants, Genetically Modified KW - Protein Array Analysis KW - Protein Interaction Mapping KW - Proteome KW - Proteomics KW - RNA, Plant KW - Tandem Mass Spectrometry AB -

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.

VL - 109 IS - 18 ER - TY - JOUR T1 - A stele-enriched gene regulatory network in the Arabidopsis root. JF - Mol Syst Biol Y1 - 2011 A1 - Brady, Siobhan M A1 - Zhang, Lifang A1 - Megraw, Molly A1 - Martinez, Natalia J A1 - Jiang, Eric A1 - Yi, Charles S A1 - Liu, Weilin A1 - Zeng, Anna A1 - Taylor-Teeples, Mallorie A1 - Kim, Dahae A1 - Ahnert, Sebastian A1 - Ohler, Uwe A1 - Ware, Doreen A1 - Walhout, Albertha J M A1 - Benfey, Philip N KW - Arabidopsis KW - Arabidopsis Proteins KW - Gene Expression Profiling KW - Gene Regulatory Networks KW - MicroRNAs KW - Plant Roots KW - Reproducibility of Results KW - Systems Biology KW - Transcription Factors KW - Two-Hybrid System Techniques AB -

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.

VL - 7 ER - TY - JOUR T1 - Genomic and epigenetic alterations deregulate microRNA expression in human epithelial ovarian cancer. JF - Proc Natl Acad Sci U S A Y1 - 2008 A1 - Zhang, Lin A1 - Volinia, Stefano A1 - Bonome, Tomas A1 - Calin, George Adrian A1 - Greshock, Joel A1 - Yang, Nuo A1 - Liu, Chang-Gong A1 - Giannakakis, Antonis A1 - Alexiou, Pangiotis A1 - Hasegawa, Kosei A1 - Johnstone, Cameron N A1 - Megraw, Molly S A1 - Adams, Sarah A1 - Lassus, Heini A1 - Huang, Jia A1 - Kaur, Sippy A1 - Liang, Shun A1 - Sethupathy, Praveen A1 - Leminen, Arto A1 - Simossis, Victor A A1 - Sandaltzopoulos, Raphael A1 - Naomoto, Yoshio A1 - Katsaros, Dionyssios A1 - Gimotty, Phyllis A A1 - DeMichele, Angela A1 - Huang, Qihong A1 - Bützow, Ralf A1 - Rustgi, Anil K A1 - Weber, Barbara L A1 - Birrer, Michael J A1 - Hatzigeorgiou, Artemis G A1 - Croce, Carlo M A1 - Coukos, George KW - DNA, Neoplasm KW - Down-Regulation KW - Epigenesis, Genetic KW - Epithelial Cells KW - Female KW - Gene Expression Profiling KW - Gene Expression Regulation, Neoplastic KW - Genome, Human KW - Humans KW - MicroRNAs KW - Neoplasm Staging KW - Ovarian Neoplasms KW - Ribonuclease III KW - RNA, Messenger KW - Survival Analysis AB -

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.

VL - 105 IS - 19 ER - TY - JOUR T1 - microRNAs exhibit high frequency genomic alterations in human cancer. JF - Proc Natl Acad Sci U S A Y1 - 2006 A1 - Zhang, Lin A1 - Huang, Jia A1 - Yang, Nuo A1 - Greshock, Joel A1 - Megraw, Molly S A1 - Giannakakis, Antonis A1 - Liang, Shun A1 - Naylor, Tara L A1 - Barchetti, Andrea A1 - Ward, Michelle R A1 - Yao, George A1 - Medina, Angelica A1 - O'brien-Jenkins, Ann A1 - Katsaros, Dionyssios A1 - Hatzigeorgiou, Artemis A1 - Gimotty, Phyllis A A1 - Weber, Barbara L A1 - Coukos, George KW - Breast Neoplasms KW - Female KW - Gene Dosage KW - Gene Expression Profiling KW - Humans KW - MicroRNAs KW - Neoplasms KW - Nucleic Acid Hybridization KW - Oligonucleotide Array Sequence Analysis KW - Ovarian Neoplasms KW - Statistics as Topic AB -

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.

VL - 103 IS - 24 ER -