@article {742, title = {Establishment of Expression in the SHORTROOT-SCARECROW Transcriptional Cascade through Opposing Activities of Both Activators and Repressors}, journal = {Dev Cell}, volume = {39}, year = {2016}, month = {12/2016}, pages = {585-596}, abstract = {

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.

}, keywords = {Arabidopsis Proteins/ genetics/ metabolism, Arabidopsis/ genetics/growth \& development/ metabolism, Computer Simulation, Gene Expression Regulation, Plant, Gene Regulatory Networks, Genes, Plant, Genes, Reporter, Genes, Synthetic, Models, Genetic, Plant Roots/cytology/metabolism, Plants, Genetically Modified, Promoter Regions, Genetic, Repressor Proteins/genetics/metabolism, Trans-Activators/genetics/metabolism, Transcription Factors/ genetics/ metabolism, Two-Hybrid System Techniques}, isbn = {1878-1551 (Electronic)1534-5807 (Linking)}, url = {https://doi.org/10.1016/j.devcel.2016.09.031}, author = {Sparks, E. E. and Drapek, C. and Gaudinier, A. and Li, S. and Ansariola, M. and Shen, N. and Hennacy, J. H. and Zhang, J. and Turco, G. and Petricka, J. J. and Foret, J. and Hartemink, A. J. and Gordan, R. and Megraw, M. and Brady, S. M. and Benfey, P. N.} } @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 {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 {319, title = {Paired-end analysis of transcription start sites in Arabidopsis reveals plant-specific promoter signatures.}, journal = {Plant Cell}, volume = {26}, year = {2014}, month = {2014 Jul}, pages = {2746-60}, abstract = {

Understanding plant gene promoter architecture has long been a challenge due to the lack of relevant large-scale data sets and analysis methods. Here, we present a publicly available, large-scale transcription start site (TSS) data set in plants using a high-resolution method for analysis of 5\&$\#$39; ends of mRNA transcripts. Our data set is produced using the paired-end analysis of transcription start sites (PEAT) protocol, providing millions of TSS locations from wild-type Columbia-0 Arabidopsis thaliana whole root samples. Using this data set, we grouped TSS reads into \"TSS tag clusters\" and categorized clusters into three spatial initiation patterns: narrow peak, broad with peak, and weak peak. We then designed a machine learning model that predicts the presence of TSS tag clusters with outstanding sensitivity and specificity for all three initiation patterns. We used this model to analyze the transcription factor binding site content of promoters exhibiting these initiation patterns. In contrast to the canonical notions of TATA-containing and more broad \"TATA-less\" promoters, the model shows that, in plants, the vast majority of transcription start sites are TATA free and are defined by a large compendium of known DNA sequence binding elements. We present results on the usage of these elements and provide our Plant PEAT Peaks (3PEAT) model that predicts the presence of TSSs directly from sequence.

[Link to Additional Data and Supplementary Materials]

}, keywords = {Arabidopsis, Arabidopsis Proteins, Binding Sites, Cluster Analysis, DNA, Plant, Gene Expression Regulation, Plant, Genome, Plant, Models, Genetic, Nucleotide Motifs, Plant Roots, Promoter Regions, Genetic, RNA, Messenger, RNA, Plant, Sequence Analysis, DNA, Species Specificity, TATA Box, Transcription Factors, Transcription Initiation Site}, issn = {1532-298X}, doi = {10.1105/tpc.114.125617}, author = {Morton, Taj and Petricka, Jalean and Corcoran, David L and Li, Song and Winter, Cara M and Carda, Alexa and Benfey, Philip N and Ohler, Uwe and Megraw, Molly} }