TY - JOUR T1 - Arabidopsis bioinformatics resources: The current state, challenges, and priorities for the future JF - Plant Direct Y1 - 2019 A1 - Colleen Doherty A1 - Joanna Friesner A1 - Brian Gregory A1 - Ann Loraine A1 - Molly Megraw A1 - Nicholas Provart A1 - R Keith Slotkin A1 - Chris Town A1 - Sarah M Assmann A1 - Michael Axtell A1 - Tanya Berardini A1 - Sixue Chen A1 - Malia Gehan A1 - Eva Huala A1 - Pankaj Jaiswal A1 - Stephen Larson A1 - Song Li A1 - Sean May A1 - Todd Michael A1 - Chris Pires A1 - Chris Topp A1 - Justin Walley A1 - Eve Wurtele VL - 3 UR - https://onlinelibrary.wiley.com/doi/full/10.1002/pld3.109 IS - 1 ER - TY - JOUR T1 - PlantSimLab-a modeling and simulation web tool for plant biologists JF - BMC Bioinformatics Y1 - 2019 A1 - S Ha A1 - E Dimitrova A1 - Stefan Hoops A1 - D Altarawy A1 - M Ansariola A1 - D Deb A1 - J Glazebrook A1 - R Hillmer A1 - H Shahin A1 - F Katagiri A1 - J McDowell A1 - M Megraw A1 - J Setubal A1 - BM Tyler A1 - Reinhard Laubenbacher VL - 20 UR - https://bmcbioinformatics.biomedcentral.com/articles/10.1186/s12859-019-3094-9 IS - 1 ER - TY - JOUR T1 - The Next Generation of Training for Arabidopsis Researchers: Bioinformatics and Quantitative Biology JF - Plant Physiology Y1 - 2017 A1 - Joanna Friesner A1 - Sarah M. Assmann A1 - Ruth Bastow A1 - Julia Bailey-Serres A1 - Jim Beynon A1 - Volker Brendel A1 - C. Robin Buell A1 - Alexander Bucksch A1 - Wolfgang Busch A1 - Taku Demura A1 - Jose R. Dinneny A1 - Colleen J. Doherty A1 - Andrea L. Eveland A1 - Pascal Falter-Braun A1 - Malia A. Gehan A1 - Michael Gonzales A1 - Erich Grotewold A1 - Rodrigo Gutierrez A1 - Ute Kramer A1 - Gabriel Krouk A1 - Shisong Ma A1 - R.J. Cody Markelz A1 - Molly Megraw A1 - Blake C. Meyers A1 - James A.H. Murray A1 - Nicholas J. Provart A1 - Sue Rhee A1 - Roger Smith A1 - Edgar P. Spalding A1 - Crispin Taylor A1 - Tracy K. Teal A1 - Keiko U. Torii A1 - Chris Town A1 - Matthew Vaughn A1 - Richard Vierstra A1 - Doreen Ware A1 - Olivia Wilkins A1 - Cranos Williams A1 - Siobhan M. Brady AB -
It has been more than 50 years since Arabidopsis (Arabidopsis thaliana) was first introduced as a model organism to understand basic processes in plant biology. A well-organized scientific community has used this small reference plant species to make numerous fundamental plant biology discoveries (Provart et al., 2016). Due to an extremely well-annotated genome and advances in high-throughput sequencing, our understanding of this organism and other plant species has become even more intricate and complex. Computational resources, including CyVerse,3 Araport,4 The Arabidopsis Information Resource (TAIR),5 and BAR,6 have further facilitated novel findings with just the click of a mouse. As we move toward understanding biological systems, Arabidopsis researchers will need to use more quantitative and computational approaches to extract novel biological findings from these data. Here, we discuss guidelines, skill sets, and core competencies that should be considered when developing curricula or training undergraduate or graduate students, postdoctoral researchers, and faculty. A selected case study provides more specificity as to the concrete issues plant biologists face and how best to address such challenges.
VL - 175 UR - http://www.plantphysiol.org/content/175/4/1499 ER - TY - JOUR T1 - Establishment of Expression in the SHORTROOT-SCARECROW Transcriptional Cascade through Opposing Activities of Both Activators and Repressors JF - Dev Cell Y1 - 2016 A1 - Sparks, E. E. A1 - Drapek, C. A1 - Gaudinier, A. A1 - Li, S. A1 - Ansariola, M. A1 - Shen, N. A1 - Hennacy, J. H. A1 - Zhang, J. A1 - Turco, G. A1 - Petricka, J. J. A1 - Foret, J. A1 - Hartemink, A. J. A1 - Gordan, R. A1 - Megraw, M. A1 - Brady, S. M. A1 - Benfey, P. N. KW - Arabidopsis Proteins/ genetics/ metabolism KW - Arabidopsis/ genetics/growth & development/ metabolism KW - Computer Simulation KW - Gene Expression Regulation, Plant KW - Gene Regulatory Networks KW - Genes, Plant KW - Genes, Reporter KW - Genes, Synthetic KW - Models, Genetic KW - Plant Roots/cytology/metabolism KW - Plants, Genetically Modified KW - Promoter Regions, Genetic KW - Repressor Proteins/genetics/metabolism KW - Trans-Activators/genetics/metabolism KW - Transcription Factors/ genetics/ metabolism KW - Two-Hybrid System Techniques AB -

Tissue-specific gene expression is often thought to arise from spatially restricted transcriptional cascades. However, it is unclear how expression is established at the top of these cascades in the absence of pre-existing specificity. We generated a transcriptional network to explore how transcription factor expression is established in the Arabidopsis thaliana root ground tissue. Regulators of the SHORTROOT-SCARECROW transcriptional cascade were validated in planta. At the top of this cascade, we identified both activators and repressors of SHORTROOT. The aggregate spatial expression of these regulators is not sufficient to predict transcriptional specificity. Instead, modeling, transcriptional reporters, and synthetic promoters support a mechanism whereby expression at the top of the SHORTROOT-SCARECROW cascade is established through opposing activities of activators and repressors.

VL - 39 SN - 1878-1551 (Electronic)1534-5807 (Linking) UR - https://doi.org/10.1016/j.devcel.2016.09.031 JO - Developmental cell 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 - Editing of Epstein-Barr virus-encoded BART6 microRNAs controls their dicer targeting and consequently affects viral latency. JF - J Biol Chem Y1 - 2010 A1 - Iizasa, Hisashi A1 - Wulff, Bjorn-Erik A1 - Alla, Nageswara R A1 - Maragkakis, Manolis A1 - Megraw, Molly A1 - Hatzigeorgiou, Artemis A1 - Iwakiri, Dai A1 - Takada, Kenzo A1 - Wiedmer, Andreas A1 - Showe, Louise A1 - Lieberman, Paul A1 - Nishikura, Kazuko KW - Cell Line, Tumor KW - Epstein-Barr Virus Infections KW - Epstein-Barr Virus Nuclear Antigens KW - Gene Silencing KW - Herpesvirus 4, Human KW - Humans KW - Immediate-Early Proteins KW - MicroRNAs KW - Ribonuclease III KW - RNA Editing KW - RNA, Viral KW - Trans-Activators KW - Viral Proteins KW - Virus Latency AB -

Certain primary transcripts of miRNA (pri-microRNAs) undergo RNA editing that converts adenosine to inosine. The Epstein-Barr virus (EBV) genome encodes multiple microRNA genes of its own. Here we report that primary transcripts of ebv-miR-BART6 (pri-miR-BART6) are edited in latently EBV-infected cells. Editing of wild-type pri-miR-BART6 RNAs dramatically reduced loading of miR-BART6-5p RNAs onto the microRNA-induced silencing complex. Editing of a mutation-containing pri-miR-BART6 found in Daudi Burkitt lymphoma and nasopharyngeal carcinoma C666-1 cell lines suppressed processing of miR-BART6 RNAs. Most importantly, miR-BART6-5p RNAs silence Dicer through multiple target sites located in the 3'-UTR of Dicer mRNA. The significance of miR-BART6 was further investigated in cells in various stages of latency. We found that miR-BART6-5p RNAs suppress the EBNA2 viral oncogene required for transition from immunologically less responsive type I and type II latency to the more immunoreactive type III latency as well as Zta and Rta viral proteins essential for lytic replication, revealing the regulatory function of miR-BART6 in EBV infection and latency. Mutation and A-to-I editing appear to be adaptive mechanisms that antagonize miR-BART6 activities.

VL - 285 IS - 43 ER -