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Omics score: 89

Auxin-independent NAC pathway regulates cell wall metabolism in response to explant-specific wounding during regeneration in Arabidopsis II

ABSTRACT: In this study, through a genome-wide transcriptome analysis of wounding in the leaf explant, we identified NAC1 (petunia NAM and Arabidopsis ATAF1, ATAF2, and CUC2) family transcription factor gene that acts in response to wounding and functions in regulation of cell wall metabolism. RNA-Seq analysis of the wound site of leaf explants and leaf residu

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Guifang Zhang Xiaodong Chen Lin XU Jingfei Cheng

PROVIDER: E-GEOD-74585 | ArrayExpress | 2016-01-18

SECONDARY ACCESSION(S): SRP065615GSE74585PRJNA300876

REPOSITORIES: GEO, ArrayExpress, ENA

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Auxin-independent NAC pathway regulates cell wall metabolism in response to explant-specific wounding during regeneration in Arabidopsis I

Project description:In this study, through a genome-wide transcriptome analysis of wounding in the leaf explant, we identified NAC1 (petunia NAM and Arabidopsis ATAF1, ATAF2, and CUC2) family transcription factor gene that acts in response to wounding and functions in regulation of cell wall metabolism. RNA-Seq analysis of the genes up-regulated by NAC1

2016-01-18 | E-GEOD-74584 | ArrayExpress

Arabidopsis Flower and Embryo Developmental Genes are Repressed in Seedlings by Different Combinations of Polycomb Group Proteins in Association with Distinct Sets of Cis-regulatory Elements

Project description:Polycomb Group Proteins (PcGs) is critical in defining the epigenetic blueprint for animal and plant development. In plants, loss of different PcGs display both common and unique phenotypic defects, yet little is known about how these are established. Here, based on quantitative comparison of epigenomics data from mutants of key PcG components in Arabidopsis seedlings, we found that the PcG partners of CURLY LEAF (CLF), one of the major plant H3K27 trimethyltransferases, determines its selectivity in repressing gene loci involved in distinct developmental programs. The non-redundant role of CLF in determining flower development is specifically associated with HETEROCHROMATIN PROTEIN1 (LHP1). This context dependent effect of CLF corresponds well with tissue-biased target gene expression, and importantly, to differential co-occupancy of transcription factors, such as MADS box and B3-domain transcription factors. These results provide valuable insight as to the dynamic interplay between different PcGs and their collaborative control of plant development. To compare the effect of different PcGs on epigenetic structure from the genome-wide scale, we used chromatin immunoprecipitation followed by high-throughtput sequencing (ChIP-seq) to characterize the genome-wide binding profile of H3K27me3 in Col, clf-29, tfl2-2, atbmi1a/b and atring1a/b ; To investigate the functional consequence of the distinct H3K27me3 profile controlled by different combinations of PcGs, we characterized the transcriptome change in PcG mutants, including Col, clf-29, tfl2-2, lhp1-6, atbmi1a/b, atring1a/b, and clf29swn21.

2016-01-23 | E-GEOD-67322 | ArrayExpress

Genome-wide ATAF1 binding sites in Arabidopsis thaliana

Project description:Using a transgenic line expressing HA-tagged ATAF1 uncovered >400 ChIP-seq peaks in ATAF1-HA plants compared to Col-0 wild-type plants. Only a small sub-set of the candidate peaks could be verified using ChIP-qpcr or EMSA. Among the verified peaks we uncovered the key ABA biosynthetic gene NCED3 as a target of ATAF1 ChIP was performed using anti-HA antibodies on wild-type Col-0 plants and plants expressing HA-tagged ATAF1

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Time course RNA-seq data from barley infested with Tetranychus urticae and Banks grass mite

Project description:Spider mites, including the two-spotted spider mite (Tetranychus urticae, TSSM) and the Banks grass mite (Oligonychus pratensis, BGM), are becoming increasingly important agricultural pests. The TSSM is an extreme generalist documented to feed on more than 1100 plant hosts. In contrast, the BGM is a grass specialist, with hosts including important cereal crops like maize, wheat, sorghum and barley. Historically, studies of plant-herbivore interactions have focused largely on insects. However, far less is known about plant responses to spider mite herbivores, especially in grasses, and whether responses differ between generalists and specialists. To identify plant defense pathways responding to spider mites, we collected time course RNA-seq data from barley (Hordeum vulgare L.) infested with TSSMs and BGMs. Additionally, and as a comparison to the physical damage caused by spider mite feeding, a wounding treatment was also included. The experiment was performed with four biological replicates across each of the following (28 samples in total): no infestation (C, control), 2hr after wounding (W2), 24hr after wounding (W24), 2hr after TSSM infestation (T2), 24hr after TSSM infestation (T24), 2hr after BGM infestation (B2), and 24hr after BGM infestation (B24).

2017-12-22 | E-GEOD-83676 | ArrayExpress

Transcription profiling by high throughput sequencing of Arabidopsis IBH1 and IBL1 gain-of-function mutants and ibh1 and ibl1 loss-of-function mutants

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2016-03-02 | E-GEOD-51119 | ArrayExpress

Transcriptome-wide high-throughput deep m6A-seq reveals unique m6A methylation differential patterns among three organs in Arabidopsis

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2015-12-08 | E-GEOD-72706 | ArrayExpress

Transcription profiling by array of Arabidopsis mutant for ataf1 after infection with Blumeria graminis f.sp. hordei

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2015-04-29 | E-GEOD-12856 | ArrayExpress

RNA-seq of Arabidopsis rosette leaves at four time points (29, 35, 42, and 57 day) during developmental senescence

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