@article {746, title = {The Next Generation of Training for Arabidopsis Researchers: Bioinformatics and Quantitative Biology}, journal = {Plant Physiology}, volume = {175}, year = {2017}, month = {12/2017}, pages = {1499-1509}, abstract = {
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.
}, url = {http://www.plantphysiol.org/content/175/4/1499}, author = {Joanna Friesner and Sarah M. Assmann and Ruth Bastow and Julia Bailey-Serres and Jim Beynon and Volker Brendel and C. Robin Buell and Alexander Bucksch and Wolfgang Busch and Taku Demura and Jose R. Dinneny and Colleen J. Doherty and Andrea L. Eveland and Pascal Falter-Braun and Malia A. Gehan and Michael Gonzales and Erich Grotewold and Rodrigo Gutierrez and Ute Kramer and Gabriel Krouk and Shisong Ma and R.J. Cody Markelz and Molly Megraw and Blake C. Meyers and James A.H. Murray and Nicholas J. Provart and Sue Rhee and Roger Smith and Edgar P. Spalding and Crispin Taylor and Tracy K. Teal and Keiko U. Torii and Chris Town and Matthew Vaughn and Richard Vierstra and Doreen Ware and Olivia Wilkins and Cranos Williams and Siobhan M. Brady} } @article {315, title = {Environmental stresses modulate abundance and timing of alternatively spliced circadian transcripts in Arabidopsis.}, journal = {Mol Plant}, volume = {8}, year = {2015}, month = {2015 Feb}, pages = {207-27}, abstract = {

Environmental stresses profoundly altered accumulation of nonsense mRNAs including intron-retaining (IR) transcripts in Arabidopsis. Temporal patterns of stress-induced IR mRNAs were dissected using both oscillating and non-oscillating transcripts. Broad-range thermal cycles triggered a sharp increase in the long IR CCA1 isoforms and altered their phasing to different times of day. Both abiotic and biotic stresses such as drought or Pseudomonas syringae infection induced a similar increase. Thermal stress induced a time delay in accumulation of CCA1 I4Rb transcripts, whereas functional mRNA showed steady oscillations. Our data favor a hypothesis that stress-induced instabilities of the central oscillator can be in part compensated through fluctuations in abundance and out-of-phase oscillations of CCA1 IR transcripts. Taken together, our results support a concept that mRNA abundance can be modulated through altering ratios between functional and nonsense/IR transcripts. SR45 protein specifically bound to the retained CCA1 intron in\ vitro, suggesting that this splicing factor could be involved in regulation of intron retention. Transcriptomes of nonsense-mediated mRNA decay (NMD)-impaired and heat-stressed plants shared a set of retained introns associated with stress- and defense-inducible transcripts. Constitutive activation of certain stress response networks in an NMD mutant could be linked to disequilibrium between functional and nonsense mRNAs.

}, keywords = {Alternative Splicing, Arabidopsis, Arabidopsis Proteins, Circadian Clocks, Gene Expression Regulation, Plant, Introns, Nonsense Mediated mRNA Decay}, issn = {1752-9867}, doi = {10.1016/j.molp.2014.10.011}, author = {Filichkin, Sergei A and Cumbie, Jason S and Dharmawardhana, Palitha and Jaiswal, Pankaj and Chang, Jeff H and Palusa, Saiprasad G and Reddy, A S N and Megraw, Molly and Mockler, Todd C} } @article {317, title = {Environmental Stresses Modulate Abundance and Timing of Alternatively Spliced Circadian Transcripts in Arabidopsis.}, journal = {Mol Plant}, year = {2014}, month = {2014 Nov 3}, abstract = {

Environmental stresses profoundly altered accumulation of nonsense mRNAs including intron retaining (IR) transcripts in Arabidopsis. Temporal patterns of stress-induced IR mRNAs were dissected using both oscillating and non-oscillating transcripts. Broad range thermal cycles triggered a sharp increase in the long intron retaining CCA1 isoforms and altered their phasing to different times of day. Both abiotic and biotic stresses such as drought or P. syringae infection induced similar increase. Thermal stress induced a time delay in accumulation of CCA1 I4Rb transcripts whereas functional mRNA showed steady oscillations. Our data favor a hypothesis that stress-induced instabilities of the central oscillator can be in part compensated through fluctuations in abundance and out of phase oscillations of CCA1 IR transcripts. Altogether, our results support a concept that mRNA abundance can be modulated through altering ratios between functional and nonsense/IR transcripts. SR45 protein specifically bound to the retained CCA1 intron in vitro, suggesting that this splicing factor could be involved in regulation of intron retention. Transcriptomes of NMD-impaired and heat-stressed plants shared a set of retained introns associated with stress- and defense-inducible transcripts. Constitutive activation of certain stress response networks in an NMD mutant could be linked to disequilibrium between functional and nonsense mRNAs.

}, issn = {1752-9867}, doi = {10.1093/mp/ssu130}, author = {Filichkin, Sergei A and Cumbie, Jason S and Dharmawadhana, J Palitha and Jaiswal, Pankaj and Chang, Jeff H and Palusa, Saiprasad G and Reddy, A S N and Megraw, Molly and Mockler, Todd C} } @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 {331, title = {MicroRNA promoter element discovery in Arabidopsis.}, journal = {RNA}, volume = {12}, year = {2006}, month = {2006 Sep}, pages = {1612-9}, abstract = {

In this study we present a method of identifying Arabidopsis miRNA promoter elements using known transcription factor binding motifs. We provide a comparative analysis of the representation of these elements in miRNA promoters, protein-coding gene promoters, and random genomic sequences. We report five transcription factor (TF) binding motifs that show evidence of overrepresentation in miRNA promoter regions relative to the promoter regions of protein-coding genes. This investigation is based on the analysis of 800-nucleotide regions upstream of 63 experimentally verified Transcription Start Sites (TSS) for miRNA primary transcripts in Arabidopsis. While the TATA-box binding motif was also previously reported by Xie and colleagues, the transcription factors AtMYC2, ARF, SORLREP3, and LFY are identified for the first time as overrepresented binding motifs in miRNA promoters.

}, keywords = {Arabidopsis, Base Sequence, Binding Sites, Databases, Genetic, Feedback, Physiological, Genes, Plant, MicroRNAs, Promoter Regions, Genetic, TATA Box, Transcription Factors, Transcription Initiation Site}, issn = {1355-8382}, doi = {10.1261/rna.130506}, author = {Megraw, Molly and Baev, Vesselin and Rusinov, Ventsislav and Jensen, Shane T and Kalantidis, Kriton and Hatzigeorgiou, Artemis G} }