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Genome-Wide HDA18-Binding Sites in Arabidopsis Root Tips

ABSTRACT: We found that histone acetylation relays positional information and that a mutant altered in the histone deacetylase (HDAC) gene family member HDA18 exhibits altered H and N epidermal cell patterning. We then performed genome-wide location (ChIP-chip) analyses by using antibody against HDA18 in transgenic HDA18 overexpression Arabidopsis plants. These analyses identified statistically significant enriched DNA associated with HDA18. A total of 286 DNA fragments were enriched as putative HDA18 protein-binding sites. Root tips of P35S:HDA18 Arabidopsis plants (Col-0) ChIPed with HDA18 antibody vs. pre-immune mouse serum.

ORGANISM(S): Arabidopsis thaliana

SUBMITTER: Linchen Li

PROVIDER: E-GEOD-41991 | biostudies-arrayexpress |

REPOSITORIES: biostudies-arrayexpress

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Genome-Wide HDA18-Binding Sites in Arabidopsis Root Tips

Project description:We found that histone acetylation relays positional information and that a mutant altered in the histone deacetylase (HDAC) gene family member HDA18 exhibits altered H and N epidermal cell patterning. We then performed genome-wide location (ChIP-chip) analyses by using antibody against HDA18 in transgenic HDA18 overexpression Arabidopsis plants. These analyses identified statistically significant enriched DNA associated with HDA18. A total of 286 DNA fragments were enriched as putative HDA18 protein-binding sites.

2012-11-02 | GSE41991 | GEO

Genes regulated by GRF1 and GRF3 in Arabidopsis roots

Project description:Arabidopsis Affymetrix ATH1 GeneChips were used to compare the mRNA profiles of root tissues of the grf1/grf2/grf3 triple mutant and transgenic plants overexpressing miR396-resistant variants of GRF1 (P35S:rGRF1) or GRF3 (P35S:rGRF3) with those of the corresponding wild-type (Col-0 or WS). Wild-type (Arabidopsis thaliana ecotypes Col-0 and Ws), the triple mutant grf1/grf2/grf3, and transgenic plants overexpressing rGRF1 or rGRF3 were grown in vertical culture dishes on modified KnopM-bM-^@M-^Ys medium for 2 weeks and then root tissues were collected for RNA extraction. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Tarek Hewezi. The equivalent experiment is AT109 at PLEXdb.] genotype: Arabidopsis thaliana ecotypes Col-0(3-replications); genotype: Arabidopsis thaliana ecotypes WS(3-replications); genotype: Triple mutant grf1/grf2/grf3(3-replications); genotype: P35S:rGRF1 overexpression(3-replications); genotype: P35S:rGRF3 overexpression(3-replications)

2012-03-13 | E-GEOD-31593 | biostudies-arrayexpress

Transcript profiling of plants ectopically expressing DOF5.4 / OBF BINDING PROTEIN 4 (OBP4).

Project description:Transcription profiling of seven-day-old seedlings of p35S:OBP4-GR treated with DEX or EtOH for 12 and 24 h. Purpose: find transcriptionally regulated genes downstream of the dof transcription factors OBP4 in the root tip of Arabidopsis thaliana Method: compare transcript levels after ectopic induction of OBP4 for 12 h and 24 h. Ectopic expressing was induced by introducing the coding sequence of OBP4 fused to the glucocorticoid receptor under the control of the Cauliflower Mosaic Virus p35S promoter (p35S:OBP4-GR) in wild type Arabidopsis Col-0 plants. Seven day old plants expressing the construct were treated with Dexamethason (DEX) or ethanol (EtOH) as a mock for 12 and 24 h. After root tips of 300 seedlings per rep were collected.

2017-02-23 | E-MTAB-4838 | biostudies-arrayexpress

Genes regulated by GRF1 and GRF3 in Arabidopsis roots

Project description:Arabidopsis Affymetrix ATH1 GeneChips were used to compare the mRNA profiles of root tissues of the grf1/grf2/grf3 triple mutant and transgenic plants overexpressing miR396-resistant variants of GRF1 (P35S:rGRF1) or GRF3 (P35S:rGRF3) with those of the corresponding wild-type (Col-0 or WS). Wild-type (Arabidopsis thaliana ecotypes Col-0 and Ws), the triple mutant grf1/grf2/grf3, and transgenic plants overexpressing rGRF1 or rGRF3 were grown in vertical culture dishes on modified Knop’s medium for 2 weeks and then root tissues were collected for RNA extraction. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Tarek Hewezi. The equivalent experiment is AT109 at PLEXdb.]

2012-03-13 | GSE31593 | GEO

Identification of Peopod2 (PPD2) target genes through GSyellow-based ChIP-seq in Arabidopsis thaliana PSB-D cell cultures.

Project description:Genome-wide target genes of PPD2 were identified through ChIP-seq on Arabidopsis cell cultures. For ChIP-seq, PPD2 was fused to the GSyellow TAP tag and expressed from the 35S promoter. The p35S:PPD2-GSyellow construct was transformed into Arabidopsis thaliana PSB-D cell culture. ChIP was performed using anti-GFP antibody (abcam290).

2018-08-07 | E-MTAB-6513 | biostudies-arrayexpress

Genome-wide EML1 binding sites in Arabidopsis thaliana seedlings

Project description:To identify genomic targets involved in the EML-dependent control of seed development, we performed ChIP-chip using whole genome Arabidopsis tiling arrays from p35S::EML1-GFP seedlings using GFP antibodies. The analysis showed that EML1 displayed preferential binding to transposable elements (TEs), while showing no preference for protein coding genes.

2021-04-23 | GSE98977 | GEO

Transcription profiling of Arabidopsis root tips in response to hypoxia using immunopurified mRNA-ribosome complexes

Project description:Plant organs are comprised of distinct cell types with unique assemblages of mRNAs. This is a collection of CEL files of mRNA profiles of the total steady-state mRNAs and polysomal mRNAs of distinct cell types of the root tip of 7-d-old Arabidopsis thaliana seedlings. The cell type specific mRNA populations are those present in ribosome-mRNA complexes. This sub-population of mRNAs was obtained by first establishing a collection of Arabidopsis lines that express a FLAG-epitope tagged ribosomal protein L18 (RPL18) directed by promoters expressed in specific cell types and regions. Four different promoter:FLAG-RPL18 lines were used. The targeted cell types and promoters included root endodermis (pSCR) and root stelar xylem and pericycle (pWOL, pSHR). A CaMV 35S promoter:FLAG-RPL18 line was used to obtain the polysomal mRNA of multiple cell types. The immunopurification of ribosome-mRNA complexes of specific cell types was accomplished by the method described in Zanetti et al. (Plant Physiology, 138, 624-635; 2005). Hybridization of the immunopurified mRNAs to the Affymetrix ATH1 DNA microarray platform and subsequent data analysis permitted the identification of transcripts that are enriched or depleted in specific cell types of root tips. The dataset includes samples from cell types from seedlings grown under control conditions and cell types of seedlings exposed to low oxygen stress (hypoxia) for 2 h. Experiment Overall Design: 20 samples, 2 conditions (2 h hypoxia stress, 2 h non-stress), 2 RNA pools (Total mRNA and polysomal mRNA), 4 promoter lines, 2 replicates

2009-10-20 | E-GEOD-14493 | biostudies-arrayexpress

Expression data from poplar apices

Project description:We studied differences in gene expression between Populus P35S::EBB1 lines and control, affecting plant growth and differentiation, and dormancy. We used microarrays to detail the global program of gene expression underlying morphological and developmental changes driven by overexpression of the EBB1 gene. By screening activation tagging population, we identified the EARLY BUD-BREAK1 (EBB1) mutant. We positioned the tag, localized a putative candidate gene and verified transcription activation. The activated gene encodes an AP2/ERF transcription factor similar to a small B1 gene-subfamily in Arabidopsis encoding strong regulators of meristem function and lateral organ outgrowth. We fully recapitulated the phenotype by overexpression of the gene into the same genotype under a strong constitutive promoter (P35S::EBB1). We also found that EBB1 transcript abundance in wild type plants increases during the period prior to bud-break, and in response to the hormone cytokinin. Our data indicates that EBB1 plays an important role in the process of bud-break. Poplar apex was selected for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain homogeneous native expression of affected genes in P35S::EBB1 lines and control, in order to increase the resolution of expression profiles inducing the developmental changes in P35S::EBB1. To do that, we selected apex tissue from greenhouse healthy plants.

2010-05-27 | E-GEOD-16495 | biostudies-arrayexpress

Expression data from BIG LEAF

Project description:We study differences in gene expression between Populus P35S::BL (BL-oe) lines and control, affecting plant growth and differentiation, and dormancy. We used microarrays to detail the global program of gene expression underlying morphological and developmental changes droved by overexpression of BL gene. We identified an activation tagging mutant with increased leaf size and correspondingly name it BIG LEAF (BL). We positioned the tag, localized a putative candidate gene and verified transcription activation. The activated gene encodes a WD40 putative transcription regulator similar to the Arabidopsis thaliana STERILE APETALA (SAP). We recapitulated the phenotype by overexpression of the gene into the same genotype under strong constitutive promoter (P35S::BL, BL-oe). Transgenic up-regulation of the BL gene caused enhanced leaf size, early bud-break, and suppression of secondary growth. BL transcript abundance in wild type plants is in apical tissues, mostly in shoot meristem, leaf primordia and axillary meristem. Our data indicates that BL plays an important role in the process of tree growth. Poplar apex, secondary stem (30th internode), and leaves (at 30 node) was selected for RNA extraction and hybridization on Affymetrix microarrays. We sought to obtain expression of affected genes in P35S::BL lines and control wild type (WT-717), in order to increase the resolution of expression profiles inducing the developmental changes in P35S::BL. To do that, we selected apex, stem and leaf tissue from greenhouse healthy plants.

2017-05-11 | E-GEOD-68859 | biostudies-arrayexpress

Proteomic analysis of the role of RALF34 small signaling peptides in the regulation of cucumber (Cucumis sativus) root development

Project description:To elucidate the functional role of the small signaling peptide RALF34 in the parental root meristem and its role in lateral root initiation, we studied changes in Cucumis sativus proteome during CsRALF34 gene overexpression. Composite plants with transgenic root systems carrying the construct for CsRALF34 overexpression (p35S::CsRALF34-TermAct) and control roots carrying p35S-GUS-TermAct were obtained and their proteome profiles were compared.

2023-05-10 | PXD037725 | Pride

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