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

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 genes up-regulated by NAC1

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Lin XU

PROVIDER: E-GEOD-74584 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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

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 wound site of leaf explants and leaf residu

2015-12-31 | E-GEOD-74585 | biostudies-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 epigeneticÂ blueprintÂ 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.

2016-01-19 | E-GEOD-67322 | biostudies-arrayexpress

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

2015-12-31 | GSE74585 | GEO

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

2015-12-31 | GSE74584 | GEO

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).

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2023-10-24 | PXD035534 | Pride

LC-MSMS of primary AML class I immunopeptidome (ERE-derived MAPs identification approach)

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2021-03-19 | PXD018542 | Pride

REF6 recognizes specific DNA sequence to regulate H3K27me3 demethylation and organ boundary formation

Project description:RELATIVE OF EARLY FLOWERING 6 (REF6, also known as JMJ12) counteracts Polycomb mediated gene silencing through demethylating histone H3 lysine 27 trimethylation (H3K27me3) in Arabidopsis. Genome-wide analysis has demonstrated that REF6 dependent H3K37me3 demethylation occurs on hundreds of genes. However, how these genes are selectively subjected to H3K27me3 demethylation remains elusive. Here we show that a tandem array of four Cys2-His2 zinc finger domains (C2H2-ZF) at REF6 C-terminus are essential for REF6 function. Mechanistically, we find that C2H2-ZF cluster can directly recognize a specific DNA sequence motif, and is essential for binding of REF6 to its targets. In addition, we demonstrate that CUP-SHAPED COTYLEDON 1 (CUC1) and CUC3 harbor such sequence motif and are direct targets of REF6; while their close homolog, CUC2, without such binding motif is not bound by REF6. Furthermore, REF6 is essential for proper H3K27me3 level at CUC1 locus, CUC1 activation and cotyledon separation. Collectively, our study reveals not only a novel mechanism of H3K27me3 demethylase genome targeting to counteract Polycomb silencing, but also a new function of H3K27me3 demethylation in organ boundary formation. All seeds, except for H3K9me2 ChIP-seq, were grown on 1/2MS plate at 23Â°C under long day condition. 12 day after germination (12DAG), whole seedling were harvested for ChIP-seq. anti-HA ChIP-seq were performed with three samples: Col (WT,Negtive control), REF6-HA(REF6p::REF6-HA ref6-1),REF6-ZnF-HA(REF6p::REF6-ZnF-HA ref6-1). anti-H3K27me3 ChIP-seq were performed with four samples: Col (WT), ref6-1 (mutant), REF6-HA(REF6p::REF6-HA ref6-1),REF6-ZnF-HA(REF6p::REF6-ZnF-HA ref6-1).For H3K9me2 ChIP-seq, plants were grown in soil at 23Â°C under long day condition. Aerial part of plants were harvested for ChIP-seq 28d after germination.

2016-03-22 | E-GEOD-65329 | biostudies-arrayexpress

A genetics screen highlights emerging roles for CPL3, RST1 and URT1 in RNA metabolism and silencing (mRNA profiling part)

Project description:CPL3, RST1 and URT1 are three new genes involved in RNA metabolism and suppressing RNA silencing in Arabidopsis. To investigate how transcripts and small RNAs varies in the absence of them, RNA and small RNA sequencing were performed on the shoot tissues of 17-day-old EMS mutants of CPL3, URT1 or RST1 and control line.

2019-04-25 | E-MTAB-7873 | biostudies-arrayexpress

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