ChIP-seq of LHP1 and H3K27me3 distribution in Arabidopsis thaliana
Ontology highlight
ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
SUBMITTER: Franziska Turck
PROVIDER: E-MTAB-1043 | biostudies-arrayexpress |
REPOSITORIES: biostudies-arrayexpress
Similar Datasets
Project description:Accumulation of unfolded/misfolded proteins in endoplasmic reticulum (ER) elicits a well conserved response called the Unfolded Protein Response (UPR), which triggers the up-regulation of downstream genes involved in protein folding, vesicle trafficking, and ER-Associated Degradation (ERAD). Although the dynamic transcriptomic responses and underlying major transcriptional regulators in ER stress response in plants have been well established, the proteome changes induced by ER stress have not been reported in plants. In the current study, we found that the Arabidopsis Ler ecotype is more sensitive to ER stress than the Col ecotype. Quantitative mass spectrometry analysis with Tandem Mass Tag (TMT) isobaric labeling showed that totally 7439 and 7035 proteins were identified from Col and Ler seedlings, with 88 and 113 differentially regulated (FC>1.3 or <0.7, P<0.05) proteins by ER stress in Col and Ler, respectively. Among them, 40 proteins were commonly up-regulated in Col and Ler, of which 10 were not up-regulated in bzip28 bzip60 double mutant (Col background) plants. Of the 19 specifically up-regulated proteins in Col comparing to that in Ler, components in ERAD, N-glycosylation, vesicle trafficking and molecular chaperones were represented. Quantitative RT-PCR showed that genes encoding 7 out of 19 proteins were not up-regulated (FC>1.3 or <0.7, P<0.05) by ER stress in both ecotypes while genes encoding 12 out of 19 proteins were up-regulated by ER stress with no obvious differences in fold change between Col and Ler. Our results experimentally demonstrated the robust ER stress response at proteome level in plants and revealed differentially regulated proteins that may contribute to differed ER stress sensitivity between Col and Ler ecotypes in Arabidopsis.
2021-09-09 | PXD022630 | Pride
Project description:Some flowering plant and vertebrate genes are expressed primarily or exclusively from either the maternal or paternal allele, a phenomenon called genomic imprinting. Flowering plant imprinted gene expression has been described primarily in endosperm, a terminal nutritive tissue consumed by the embryo during seed development or after germination. Imprinted expression in Arabidopsis thaliana endosperm is orchestrated by differences in cytosine DNA methylation between the paternal and maternal genomes, as well as by Polycomb group (PcG) proteins. Currently only eleven imprinted Arabidopsis genes are known. Here we use extensive sequencing of cDNA libraries to identify many new paternally and maternally imprinted genes in A. thaliana endosperm, including transcription factors, proteins involved in hormone signaling, and epigenetic regulators. The imprinted status of many maternally-expressed genes is not altered by mutations in the DNA-demethylating glycosylase DEMETER, the DNA methyltransferase MET1 or the core PcG protein FIE, indicating that these genes are regulated by novel mechanisms or deposited from maternal tissues. We did not find any imprinted genes in the embryo. Our results demonstrate that imprinted gene expression, particularly from the maternal genome, is an extensive, mechanistically complex phenomenon that likely affects multiple aspects of seed development. Epigenetics Examination of genomic imprinting in Arabidopsis endosperm
2011-03-10 | E-GEOD-24644 | biostudies-arrayexpress
Project description:Detection of genome-wide distribution of LHP1 and H3K27me3 in the two accessions Col and Ler of A. thaliana
2012-03-15 | E-MTAB-749 | biostudies-arrayexpress
Project description:The Arabidopsis thaliana central cell, the companion cell of the egg, undergoes DNA demethylation prior to fertilization, but the targeting preferences and biological significance of this process remain unclear. Here, we show that active DNA demethylation mediated by the DEMETER DNA glycosylase accounts for all of the demethylation in the central cell, and preferentially targets small, AT-rich and nucleosome-depleted transposable elements. The vegetative cell, the companion cell of sperm, also undergoes DEMETER-dependent demethylation of similar sequences, and lack of DEMETER in vegetative cells causes reduced small RNA-directed DNA methylation of transposons in sperm. Our results demonstrate that demethylation in companion cells reinforces transposon methylation in plant gametes, thereby assuring stable silencing of transposable elements across generations Examination of DNA methylation in Arabidopsis endosperm, embryo, and pollen
2012-09-21 | E-GEOD-38935 | biostudies-arrayexpress
Project description:adt05-04_drn - mutant vs wildtype - DRN targets - Ovules containing heart-stage/torpedo-stage embryos were dissected from siliques and imidiately shock frozen in liquid nitrogen. RNA was extracted and sent to Evry for comparison between mutant and wildtype transcriptome. Keywords: gene knock out 2 dye-swap - CATMA arrays
2010-04-30 | E-GEOD-19800 | biostudies-arrayexpress
Project description:The molecular mechanisms by which floral homeotic genes act as major developmental switches to specify the identity of floral organs, are still largely unknown. Floral homeotic genes encode transcription factors of the MADS-box family, which are supposed to assemble in a combinatorial fashion into organ-specific multimeric protein complexes. Major mediators of protein interactions are MADS-domain proteins of the SEPALLATA subfamily, which play a crucial role in the development of all types of floral organs. In order to characterize the roles of the SEPALLATA3 transcription factor complexes at the molecular level, we analyzed genome-wide the direct targets of SEPALLATA3. We used chromatin immunoprecipitation followed by ultrahigh-throughput sequencing or hybridization to whole-genome tiling arrays to obtain genome-wide DNA-binding patterns of SEPALLATA3. The results demonstrate that SEPALLATA3 binds to thousands of sites in the genome. Most potential target sites that were strongly bound in wild-type inflorescences, are also bound in the floral homeotic agamous mutant, which displays only the perianth organs, sepals and petals. Characterization of the target genes shows that SEPALLATA3 integrates and modulates different growth-related and hormonal pathways in a combinatorial fashion with other MADS-box proteins and possibly with non-MADS transcription factors. In particular, the results suggest multiple links between SEPALLATA3 and auxin signaling pathways. Our gene expression analyses link the genomic binding site data with the phenotype of plants expressing a dominant repressor version of SEPALLATA3, suggesting that it modulates auxin response to facilitate floral organ outgrowth and morphogenesis. Furthermore, the binding of the SEPALLATA3 protein to cis-regulatory elements of other MADS-box genes and expression analyses reveal that this protein is a key component in the regulatory transcriptional network underlying the formation of floral organs. ChIP experiments were performed on Arabidopsis wildtype and agamous mutant inflorescences using an antibody raised against a C-terminal peptide of SEP3. As control, ChIP experiments were performed on the sep3 mutant.
2009-04-20 | E-GEOD-14600 | biostudies-arrayexpress
Project description:miRNA levels depend on both biogenesis and turnover. The methyltransferase HEN1 stabilizes plant miRNAs, animal piRNAs, and siRNAs in both kingdoms via 3' terminal methylation. Loss of HEN1 in plants results in non-templated oligo-uridylation and accelerated degradation of miRNAs. In hen1 mutants from Arabidopsis and rice, we found that the patterns of miRNA truncation and uridylation differ substantially among miRNA families, but such patterns for the same miRNA are conserved between species. miR166 and miR163 are truncated predominantly to ~17 and ~16 nt, and subsequently recover via uridylation to approximately their original sizes, 21 and 24 nt, suggesting that in these cases miRNA truncation triggers uridylation. miR171 is untruncated but uridylated to 22 nt in hen1 mutants, gaining the ability to trigger production of phased, secondary siRNAs. Truncated and tailed variants were bound by ARGONAUTE1 (AGO1) in hen1, implying that these events occur while miRNAs are still bound by AGO1. Unexpectedly, a portion of miR158 in wildtype remains unmethylated and thus subject to uridylation and destabilization, suggesting that plants naturally utilize miRNA methylation to modulate miRNA accumulation. Our results suggest that the AGO1-containing RISC complex may undergo programming to reflect each bound miRNA, determining a defined, distinct decay destiny. In this analysis, we sequenced sRNAs from two hen1 mutant alleles in Arabidopsis and three hen1 alleles in rice. In Arabidopsis, the strong hen1-1 allele in the Landsberg erecta (Ler) ecotype is the first hen1 mutant and emerged from an enhancer screen in the hua1-1/hua2-1 background, and hen1-8 in the Columbia (Col) background is a weak allele. In rice, WAVY LEAF1 (WAF1) is the ortholog of Arabidopsis HEN1, and two mutant alleles waf1-1 and waf1-2 each bear a single-base substitution leading to a premature stop codon in the second exon and a non-functional splicing site of the fourth intron, respectively. We identified a third mutant allele of the rice HEN1 gene (Oshen1-3 from the Korean (POSTEC) rice T-DNA mutant population).
2013-07-22 | E-GEOD-35562 | biostudies-arrayexpress
Project description:We carried out a five-generation selection experiment in which two Arabidopsis accessions (Ler and Cvi) and 17 Recombinant Inbred Lines (RILs) derived from them were subjected in 24 replicated populations to four levels of micro-landscape fragmentation and two levels of disturbance, factorially crossed with each other to yield 8 experimental selection regimes. We used 19 lines (including the two parental Ler and Cvi) in generation 1 of our experiment, nine of which contained the erecta mutation and ten of which did not. Lines expressing the erecta mutation are short and compact and are likely to disperse seeds over shorter distances. Both the non-erecta and the erecta lines spanned the full available range of seed sizes from the original 162 RILs in the collection. We set up 24 experimental landscapes consisting of 2, 4, 8, or 16 patches where the total area was constrained to be equal. Plants that germinated outside the designated suitable patches were removed. In half of the landscapes which we termed static the top 2-3 mm of seeds and soil were removed from the surface of the suitable patches after 8 weeks of growth and reproduction. In the other half of the landscapes which we termed dynamic a number of Petri dishes, equivalent in size and number to the existing suitable patches, were distributed around the landscape at random, to catch dispersing seeds. The seeds collected by these two methods were cold-treated for one week while all patches were replenished with fresh substrate. Seeds were then returned to the surface of the new patches at the beginning of the next generation. Thus, in dynamic landscapes, seeds must disperse to have any chance of entering the next generation, while in static landscapes, only seeds that do not disperse have any chance of further propagation. After five generations of such selection, a single pod from approximately 70 individuals from each landscape was removed. Single individuals derived from such pods were reared under standardized conditions to measure several phenotypic characters, such as seed mass, height, presence of the erecta mutation, flowering time etc. Clear phenotypic differences are apparent between the different landscapes. However, we have no information as to the underlying genes, which might have been selected or the epigenetic modifications that might have occurred. Material for DNA extraction from each population (? 50 plants/population) was collected for subsequent genetic analyses. The allele frequencies of Ler and Cvi alleles was determined at the genome-wide level using ATH1 Affymetrix GeneChips® (each in quadruplicate = 8 parental microarrays). 26638 single feature polymorphisms (SFPs) between these two accessions could be detected. The relative contribution of Ler and Cvi alleles in a population at each locus, for which a single feature polymorphism can be detected, was assessed. We then analyzed the DNA isolated from the experimental populations (24 landscapes of generation 5 = 24 microarrays & original populations in triplicate = 3 microarrays) and determine the relative contributions of Ler and Cvi alleles for the 26638 identified SFPs (i.e. allele frequency shifts).
2010-05-12 | E-MTAB-107 | biostudies-arrayexpress
Project description:In this study, we analyzed the Arabidopsis homologue of PRMT5, AtPRMT5M-bM-^@M-^Ys function in RNA processing. RNA-seq analyses revealed that AtPRMT5 is involved in a subset of pre-mRNA splicing. Several RNA processing factors involved in regulating flowering time were validated that the corresponding intron retention surely exists in atprmt5 mutants. AtSm proteins can also be methylated by AtPRMT5 in vitro and in vivo, which may be the reasons for the pre-mRNA splicing defects in atprmt5. Contributed by The Institute of Genetics and Developmental Biology (IGDB) of the Chinese Academy of Sciences Investigate the role of AtPRMT5 in pre-mRNA splicing
2010-10-07 | E-GEOD-21323 | biostudies-arrayexpress
Project description:The H3K27me3 ChIP-seq data for the human bladder transitional cell carcinoma cell line CL1207 were generated in order to detect regions of regional epigenetic silencing in this cell line and test the performance of several peak calling tools: CCAT (Xu et al., 2010) and HMCan (Ashoor et al., "HMCan M-bM-^@M-^S a tool to detect chromatin modifications in cancer samples using ChIP-seq data", submitted). The human bladder cancer cell line CL1207 was derived from a muscle-invasive bladder cancer (De Boer et al., 1997). 5x105 cells were immunoprecipitated per ChIP assay with 4 M-NM-<g of rabbit polyclonal antibodies against trimethyl histone H3 lysine 27 (Upstate Biotechnology, Santa Cruz, CA) and DynabeadsM-BM-. Protein A (Invitrogen, Cergy Pontoise, France) in dilution buffer containing 1% Triton X-100, 150 mM NaCl, 2 mM EDTA, 20 mM TrisM-bM-^@M-^SHCl at pH 8.0, and protease inhibitors. Six ChIP assays in the same experimental conditions were necessary to perform one ChIP-Seq experiment, so the total of 3x106 cells for each of the duplicates.
2014-01-07 | E-GEOD-44438 | biostudies-arrayexpress