Chromatin attachment to the nuclear matrix represses hypocotyl elongation in Arabidopsis thaliana
Ontology highlight
ABSTRACT:
ORGANISM(S): Arabidopsis thaliana
PROVIDER: GSE215135 | GEO | 2024/02/23
REPOSITORIES: GEO
Similar Datasets
Project description:Identification of novel proteins attaching chromatin regions at the nuclear matrix in Arabidopsis thaliana.
| MSV000090406 | MassIVE
Project description:FAR-RED ELONGATED HYPOCOTYL 3 (FHY3) and its homolog FAR-RED IMPAIRED RESPONSE 1 (FAR1) are two transposase-derived transcription factors initially identified as the key components in phytochrome A signaling and recently shown to function in the circadian clock. However, whether FHY3 and FAR1 are involved in other processes of plant development remains largely unknown. Here, we explored chromatin immunoprecipitation-based sequencing (ChIP-seq) analysis to identify 1745 and 1171 FHY3 direct binding target genes in darkness and far-red light conditions, respectively in the Arabidopsis thaliana genome. This analysis revealed that FHY3 preferentially binds to the gene promoters through the previously identified typical FHY3/FAR1 binding motif. Interestingly, FHY3 also binds to two novel motifs in the 178-bp repeats of the Arabidopsis centromere regions in vivo. Comparison between the ChIP-seq and microarray data indicates that FHY3 regulates the expression of 196 and 85 genes in dark and far-red respectively by directly binding to their promoters. FHY3 also co-regulates a number of common target genes with PHYTOCHROME INTERACTING FACTOR 3-LIKE 5 (PIL5) and ELONGATED HYPOCOTYL 5 (HY5). Moreover, our genome-wide identification of FHY3 direct target genes ultimately led to the discovery and validation of a new role of FHY3 in controlling chloroplast development, by directly activating the expression of ACCUMULATION AND REPLICATION OF CHLOROPLASTS5 (ARC5), a key gene regulating chloroplast constriction and division. Taken together, our data suggest that FHY3 is involved in regulating multiple facets of plant development, thus providing new insights into the functions of this type of transposase-derived transcription factors.
2011-08-02 | GSE30712 | GEO
Project description:FAR-RED ELONGATED HYPOCOTYL 3 (FHY3) and its homolog FAR-RED IMPAIRED RESPONSE 1 (FAR1) are two transposase-derived transcription factors initially identified as the key components in phytochrome A signaling and recently shown to function in the circadian clock. However, whether FHY3 and FAR1 are involved in other processes of plant development remains largely unknown. Here, we explored chromatin immunoprecipitation-based sequencing (ChIP-seq) analysis to identify 1745 and 1171 FHY3 direct binding target genes in darkness and far-red light conditions, respectively in the Arabidopsis thaliana genome. This analysis revealed that FHY3 preferentially binds to the gene promoters through the previously identified typical FHY3/FAR1 binding motif. Interestingly, FHY3 also binds to two novel motifs in the 178-bp repeats of the Arabidopsis centromere regions in vivo. Comparison between the ChIP-seq and microarray data indicates that FHY3 regulates the expression of 196 and 85 genes in dark and far-red respectively by directly binding to their promoters. FHY3 also co-regulates a number of common target genes with PHYTOCHROME INTERACTING FACTOR 3-LIKE 5 (PIL5) and ELONGATED HYPOCOTYL 5 (HY5). Moreover, our genome-wide identification of FHY3 direct target genes ultimately led to the discovery and validation of a new role of FHY3 in controlling chloroplast development, by directly activating the expression of ACCUMULATION AND REPLICATION OF CHLOROPLASTS5 (ARC5), a key gene regulating chloroplast constriction and division. Taken together, our data suggest that FHY3 is involved in regulating multiple facets of plant development, thus providing new insights into the functions of this type of transposase-derived transcription factors.
2011-08-02 | GSE30711 | GEO
Project description:We used in vivo biotin labeling of a nuclear envelope protein in individual cell types followed by affinity isolation of labeled nuclei to measure gene expression and chromatin features of the hair and non-hair cell types of the Arabidopsis root epidermis. Keywords: Chromatin affinity-purification on microarray All experiments were done using two channels per chip. Two types of experiments were performed. Expression profiling was performed by comparing cDNAs synthesized from nuclear RNA isolated from INTACT-prepared Arabidopsis nuclei to total sonicated genomic DNA isolated from Arabidopsis plants. Chromatin profiling was performed using INTACT-prepared Arabidopsis nuclei. DNA isolated by Chromatin immunoprecipitation (ChIP) using antibodies to modified histones was compared to histone H3 ChIP DNA from the same sample.
2010-06-13 | E-GEOD-19654 | biostudies-arrayexpress
Project description:FAR-RED ELONGATED HYPOCOTYL 3 (FHY3) and its homolog FAR-RED IMPAIRED RESPONSE 1 (FAR1) are two transposase-derived transcription factors initially identified as the key components in phytochrome A signaling and recently shown to function in the circadian clock. However, whether FHY3 and FAR1 are involved in other processes of plant development remains largely unknown. Here, we explored chromatin immunoprecipitation-based sequencing (ChIP-seq) analysis to identify 1745 and 1171 FHY3 direct binding target genes in darkness and far-red light conditions, respectively in the Arabidopsis thaliana genome. This analysis revealed that FHY3 preferentially binds to the gene promoters through the previously identified typical FHY3/FAR1 binding motif. Interestingly, FHY3 also binds to two novel motifs in the 178-bp repeats of the Arabidopsis centromere regions in vivo. Comparison between the ChIP-seq and microarray data indicates that FHY3 regulates the expression of 196 and 85 genes in dark and far-red respectively by directly binding to their promoters. FHY3 also co-regulates a number of common target genes with PHYTOCHROME INTERACTING FACTOR 3-LIKE 5 (PIL5) and ELONGATED HYPOCOTYL 5 (HY5). Moreover, our genome-wide identification of FHY3 direct target genes ultimately led to the discovery and validation of a new role of FHY3 in controlling chloroplast development, by directly activating the expression of ACCUMULATION AND REPLICATION OF CHLOROPLASTS5 (ARC5), a key gene regulating chloroplast constriction and division. Taken together, our data suggest that FHY3 is involved in regulating multiple facets of plant development, thus providing new insights into the functions of this type of transposase-derived transcription factors. To determine the global in vivo binding sites of FHY3, we performed ChIP-seq analysis using 35S:3FLAG-FHY3-3HA fhy3-4 transgenic lines in which the 3FLAG-FHY3-3HA fusion proteins could largely rescue the long hypocotyl phenotype of the fhy3-4 mutants The seedlings were grown in D or continuous FR light conditions for 4 days, and then chromatin fragments were prepared using the commercially monoclonal anti-FLAG antibodies. We then generated two DNA libraries, one for D and one for FR -grown samples, which were then subjected to ultra-high throughput Solexa (Illumina) sequencing
2011-08-02 | E-GEOD-30711 | biostudies-arrayexpress
Project description:Efficient storing and readout of genetic information is not only dependent on tight epigenetic regulation but also on the spatial organization and folding of chromosomes. Although the epigenome of the model plant Arabidopsis has been extensively studied, its interplay with chromosomal architecture is less well understood. We show that chromosomal architecture is tightly linked to the epigenetic state and furthermore how physical constraints such as nuclear size influence folding principles of chromatin. In addition to global principles of chromatin organisation, we describe a novel nuclear structure, termed KNOT, in which genomic regions of all five Arabidopsis chromosomes highly interact. These regions are characterized as heterochromatic islands within the euchromatin and likely represent preferred landing sites for transposons, suggesting a novel transposon defence mechanism in the Arabidopsis nucleus. HiC experiments were performed on Arabidopsis thaliana Col-0 wildtype, homozygous crwn1-1, and homozygous crwn4-1 14-day-old seedlings
2014-08-18 | E-GEOD-55960 | biostudies-arrayexpress
Project description:Efficient storing and readout of genetic information is not only dependent on tight epigenetic regulation but also on the spatial organization and folding of chromosomes. Although the epigenome of the model plant Arabidopsis has been extensively studied, its interplay with chromosomal architecture is less well understood. We show that chromosomal architecture is tightly linked to the epigenetic state and furthermore how physical constraints such as nuclear size influence folding principles of chromatin. In addition to global principles of chromatin organisation, we describe a novel nuclear structure, termed KNOT, in which genomic regions of all five Arabidopsis chromosomes highly interact. These regions are characterized as heterochromatic islands within the euchromatin and likely represent preferred landing sites for transposons, suggesting a novel transposon defence mechanism in the Arabidopsis nucleus.
2014-08-18 | GSE55960 | GEO
Project description:FAR-RED ELONGATED HYPOCOTYL 3 (FHY3) and its homolog FAR-RED IMPAIRED RESPONSE 1 (FAR1) are two transposase-derived transcription factors initially identified as the key components in phytochrome A signaling and recently shown to function in the circadian clock. However, whether FHY3 and FAR1 are involved in other processes of plant development remains largely unknown. Here, we explored chromatin immunoprecipitation-based sequencing (ChIP-seq) analysis to identify 1745 and 1171 FHY3 direct binding target genes in darkness and far-red light conditions, respectively in the Arabidopsis thaliana genome. This analysis revealed that FHY3 preferentially binds to the gene promoters through the previously identified typical FHY3/FAR1 binding motif. Interestingly, FHY3 also binds to two novel motifs in the 178-bp repeats of the Arabidopsis centromere regions in vivo. Comparison between the ChIP-seq and microarray data indicates that FHY3 regulates the expression of 196 and 85 genes in dark and far-red respectively by directly binding to their promoters. FHY3 also co-regulates a number of common target genes with PHYTOCHROME INTERACTING FACTOR 3-LIKE 5 (PIL5) and ELONGATED HYPOCOTYL 5 (HY5). Moreover, our genome-wide identification of FHY3 direct target genes ultimately led to the discovery and validation of a new role of FHY3 in controlling chloroplast development, by directly activating the expression of ACCUMULATION AND REPLICATION OF CHLOROPLASTS5 (ARC5), a key gene regulating chloroplast constriction and division. Taken together, our data suggest that FHY3 is involved in regulating multiple facets of plant development, thus providing new insights into the functions of this type of transposase-derived transcription factors. We used the FHY3p:FHY3-GR fhy3-4 transgenic lines expressing FHY3-glucocorticoid receptor (GR) fusion proteins under the control of the FHY3 native promoter, in which, without dexamethasone (DEX), the GR-fusion proteins localize in the cytoplasm, whereas, when treated with DEX, the fusion proteins translocate into the nucleus. The seedlings were grown in D or continuous FR light for 4 days, then treated with DEX or mock (equal volume of ethanol), and grown in the same conditions for a further 2 hours before the samples were harvested. RNA samples were extracted from these samples, and then hybridized with Affymetrix Arabidopsis ATH1 genome arrays. Four independent biological replicates for each treatment were used for the microarray analysis.
2011-08-01 | E-GEOD-30712 | biostudies-arrayexpress
Project description:Guanylate Binding Proteins (GBPs) are prominent regulators of immunity unknown to be required for nuclear envelope formation and function. The Arabidopsis GBP orthologue AtGBPL3 was identified as a novel component of the plant lamina, with essential functions in mitotic nuclear envelope reformation. AtGBPL3 is preferentially expressed in mitotically active root tips and accumulates at the nuclear envelope. Furthermore, fluorescent lifetime imaging experiments in the presence or absence of the chromatin-labelling dye Sytox-Orange suggested that GBPL3 might be able to interact with chromatin. Chromatin-immunoprecipitation followed by sequencing (ChIP-Seq) revealed only few GBPL3-associated chromatin domains, which were concentrated particularly within or near centromeric regions.
2022-12-23 | GSE221668 | GEO