898 research outputs found

    Architecture and dynamics of the jasmonic acid gene regulatory network

    Get PDF
    Jasmonic acid (JA) is a critical hormonal regulator of plant growth and defense. To advance our understanding of the architecture and dynamic regulation of the JA gene regulatory network, we performed a high-resolution RNA-seq time series of methyl JA-treated Arabidopsis thaliana at 15 time points over a 16-h period. Computational analysis showed that methyl JA (MeJA) induces a burst of transcriptional activity, generating diverse expression patterns over time that partition into distinct sectors of the JA response targeting specific biological processes. The presence of transcription factor (TF) DNA binding motifs correlated with specific TF activity during temporal MeJA-induced transcriptional reprogramming. Insight into the underlying dynamic transcriptional regulation mechanisms was captured in a chronological model of the JA gene regulatory network. Several TFs, including MYB59 and bHLH27, were uncovered as early network components with a role in pathogen and insect resistance. Analysis of subnetworks surrounding the TFs ORA47, RAP2.6L, MYB59, and ANAC055, using transcriptome profiling of overexpressors and mutants, provided insights into their regulatory role in defined modules of the JA network. Collectively, our work illuminates the complexity of the JA gene regulatory network, pinpoints and validates previously unknown regulators, and provides a valuable resource for functional studies on JA signaling components in plant defense and development

    組織特異的発現遺伝子におけるプロモーター構造の学習

    Get PDF
    学位の種別: 課程博士審査委員会委員 : (主査)東京大学教授 鈴木 穣, 東京大学教授 浅井 潔, 東京大学教授 中井 謙太, 東京大学准教授 木立 尚孝, 東京大学准教授 渋谷 哲朗University of Tokyo(東京大学

    Characterisation of Transcription Factor SPL15, an Integrator of Multiple Flowering Time Pathways

    Get PDF
    The transition from vegetative to reproductive development in plants is tightly controlled to ensure their reproductive success. Plants integrate many different environmental signals to flower at the appropriate time, and complex regulatory networks underlie this decision. In Arabidopsis thaliana, the model organism for plant molecular research, the timing of floral transition is influenced by environmental cues, which include temperature and day length, and by internal factors, including the age of the plant and the levels of the phytohormone gibberellin. During the transition, Arabidopsis switches from producing leaves to producing flowers, a process that includes morphological and identity changes in the shoot apical meristem (SAM). In favourable environmental conditions, such as floral inductive long-days, Arabidopsis accelerates the floral transition and quickly bolts and flowers. In the absence of floral inductive signals, these plants still undergo the floral transition, but do so later after producing many more leaves. The transcription factor SQUAMOSA PROMOTER BINDING PROTEIN LIKE 15 (SPL15) promotes flowering in non-inductive conditions. SPL15 integrates signals from multiple floral induction pathways at the shoot apical meristem and is proposed to directly activate transcription of two other genes with a prominent function in flowering: FRUITFULL (FUL), which encodes a MADS box transcription factor, and MICRORNA172b (MIR172B), which encodes a short non-coding RNA. However, the precise role of SPL15 in floral induction remains unknown. To gain understanding of the importance of SPL15 targets and other downstream components, I genetically assessed their contribution to floral induction. I found that FUL and MIR172B were important for SPL15 function during floral induction. However, in their absence, increased expression of SPL15 still induced early bolting of the inflorescence, but could not induce floral development. These analyses suggested that SPL15 regulates more target genes than FUL and MIR172B during the floral transition. Subsequently, I identified the binding sites of SPL15 in the FUL promoter, and studied the effect of mutating them. This revealed that SPL15 is not the only SPL protein that recognises these sites to regulate floral transition. I therefore propose that during vegetative growth, other SPLs bind there to repress the expression of FUL. Lastly, I set out to identify additional putative target genes of SPL15 by two complementary transcriptome analyses. The resulting high confidence list of putative target genes of SPL15 showed that SPL15 likely regulates several other genes with described functions in floral induction. In addition, SPL15 regulates a set of genes with functions in cell proliferation, which might be relevant for the morphological changes occurring in the SAM during the floral transition. Altogether this thesis has contributed to a better understanding of how SPL15 regulates different stages of the floral transition in A. thaliana under non-inductive conditions

    GENE REGULATORY NETWORKS OF AGL15 A PLANT MADS TRANSCRIPTION FACTOR

    Get PDF
    Plant embryogenesis is an intriguing developmental process that is controlled by many genes. AGAMOUS Like 15 (AGL15) is a MADS-domain transcriptional regulator that accumulates preferentially during this stage. However, at the onset of this work it was unknown which genes are regulated by AGL15 or how AGL15 is regulated. This dissertation is part of the ongoing effort to understand the biological roles of AGL15. To decipher how AGL15 functions during plant development, a chromatin immunoprecipitation (ChIP) approach was adapted to obtain DNA fragments that are directly bound by AGL15 in vivo. Putative AGL15 targets were isolated, and binding and regulation was confirmed for one such target gene, ABF3. In addition, microarray experiments were performed to globally assess genes that are differentially expressed between wild type and agl15 young seeds. Among them, a gene, At5g23405, encoding an HMGB domain protein was identified and its response to AGL15 was confirmed. Preliminary results suggest that the loss-of-function of At5g23405 might have an effect on somatic embryogenesis, consistent with AGL15 repression of the expression of this gene. Lastly, to address the question about how the regulator is regulated, the cis elements controlling the expression of AGL15 must be identified. Deletion analysis of the AGL15 promoter indicated the presence of putative positive and negative cis elements contributing to the expression of AGL15. Further analysis suggested that AGL15 regulates the expression of its own gene and this regulation may partially be explained by the direct binding of the protein to the AGL15 promoter. The data presented in this dissertation demonstrate that ChIP can be used to identify previously unsuspected targets of AGL15. Based on ChIP, a ChIP-chip technique is being developed in the lab to allow a more global analysis of in vivo binding sites. The identification of target genes and cis elements in AGL15 promoter is a step towards characterization of the biological roles of AGL15

    Functional analysis of rice bidirectional promoters

    Get PDF
    Bidirectional promoters regulate adjacent genes organized in a divergent fashion (head to head orientation). Several Reports pertaining to bidirectional promoters on a genomic scale exists in mammals. This work provides the essential background on theoretical and experimental work to carry out a genomic scale analysis of bidirectional promoters in plants. A computational study was performed to identify putative bidirectional promoters and the over-represented cis-regulatory motifs from three sequenced plant genomes: rice (Oryza sativa), Arabidopsis thaliana, and Populus trichocarpa using the Plant Cis-acting Regulatory DNA Elements (PLACE) and PLANT CARE databases. Over-represented motifs along with their possible function were described with the help of a few conserved representative putative bidirectional promoters from the three model plants. By doing so a foundation was laid for the experimental evaluation of bidirectional promoters in plants. A novel Agrobacterium tumefaciens mediated transient expression assay (AmTEA) was developed for young plants of different cereal species and the model dicot Arabidopsis thaliana. AmTEA was evaluated using five promoters (six constructs) and two reporter genes, gus and egfp. Efficacy and stability of AmTEA was compared with stable transgenics using the Arabidopsis DEAD-box RNA helicase family gene promoter. AmTEA was primarily developed to overcome the many problems associated with the development of transgenics and expression studies in plants. Finally a possible mechanism for the bidirectional activity of bidirectional promoters was highlighted. Deletion analysis using promoter-reporter gene constructs identified three rice promoters to be bidirectional. Regulatory elements located in the 5’- untranslated regions (UTR) of one of the genes of the divergent gene pair were found to be responsible for their bidirectional ctivit

    Characterization of Putative cis

    Get PDF

    Chromatin accessibility dynamics in the Arabidopsis root epidermis and endodermis during cold acclimation

    Get PDF
    Understanding cell-type specific transcriptional responses to environmental conditions is limited by a lack of knowledge of transcriptional control due to epigenetic dynamics. Additionally, cell-type analyses are limited by difficulties in applying current technologies to single cell-types. A novel DNase-seq protocol and analysis procedure, deemed DNase-DTS, was developed to identify DHSs in the Arabidopsis epidermis and endodermis under control and cold acclimation conditions. Results identified thousands of DHSs within each cell-type and experimental condition. DHSs showed strong association to gene expression, DNA methylation, and histone modifications. A priori mapping of existing DNA binding motifs within accessible genes and the cold C-repeat/dehydration responsive element-binding factor pathway resulted in unique motif mapping patterns. In summary, a collection of endodermal and epidermal cold acclimation induced chromatin accessibility sites may be used to understand mechanisms of gene expression and to best design synthetic promoters

    Genome-wide identification and transcriptional profiling of small heat shock protein gene family under diverse abiotic stress conditions in Sorghum bicolor (L.)

    Get PDF
    The small heat shock proteins (sHsps/Hsp20s) are the molecular chaperones that maintain proper folding, trafficking and disaggregation of proteins under diverse abiotic stress conditions. In the present investigation, a genome-wide scan revealed the presence of a total of 47 sHsps in Sorghum bicolor (SbsHsps), distributed across 10 subfamilies, the major subfamily being P (plastid) group with 17 genes. Chromosomes 1 and 3 appear as the hot spot regions for SbsHsps, and majority of them were found acidic, hydrophilic, unstable and intron less. Interestingly, promoter analysis indicated that they are associated with both biotic and abiotic stresses, as well as plant development. Sorghum sHsps exhibited 15 paralogous and 20 orthologous duplications. Expression analysis of 15 genes selected from different subfamilies showed high transcript levels in roots and leaves implying that they are likely to participate in the developmental processes. SbsHsp genes were highly induced by diverse abiotic stresses inferring their critical role in mediating the environmental stress responses. Gene expression data revealed that SbsHsp-02 is a candidate gene expressed in all the tissues under varied stress conditions tested. Our results contribute to the understanding of the complexity of SbsHsp genes and help to analyse them further for functional validation
    corecore