Similar Datasets
Project description:The scarcity of accessible sites that are dynamic or cell type-specific in plants may be due in part to tissue heterogeneity in bulk studies. To assess the effects of tissue heterogeneity, we apply single-cell ATAC-seq to Arabidopsis thaliana roots and identify thousands of differentially accessible sites, sufficient to resolve all major cell types of the root. We find that the entirety of a cell's regulatory landscape and its transcriptome independently capture cell type identity. We leverage this shared information on cell identity to integrate accessibility and transcriptome data to characterize developmental progression, endoreduplication and cell division. We further use the combined data to characterize cell type-specific motif enrichments of transcription factor families and link the expression of family members to changing accessibility at specific loci, resolving direct and indirect effects that shape expression. Our approach provides an analytical framework to infer the gene regulatory networks that execute plant development.
| S-EPMC8184767 | biostudies-literature
Project description:Comparison of gene expression between shoots of root-wounded seedlings and shoots of control seedlings in Arabidopsis. We identified wounding-induced early (30 min) and late (360 min) root to shoot responsive genes (RtS).
2010-12-31 | GSE26374 | GEO
Project description:Plant roots located in the upper soil layers are prone to experience high temperatures. To gain insight into the effect of high temperature on root development and functioning, we exposed five-day-old Arabidopsis thaliana seedlings grown on agar plates to 30 °C for 48 hours, and compared the gene expression profile in the root tip with that from seedlings that remained at 22 °C.
2024-02-07 | GSE254973 | GEO
Project description:Waters Raw data can be downloaded for shoot- and root parts of Arabidopsis thaliana accessions.
2018-11-14 | ST001096 | MetabolomicsWorkbench
Project description:Lateral root organogenesis plays an essential role in defining plant root system architecture. In Arabidopsis, the AP2-family transcription factor PUCHI controls cell proliferation in lateral root primordia. To identify downstream targets of PUCHI, we engineered a transgenic line with inducible PUCHI activity by expressing a fusion protein of PUCHI and rat glucocorticoid receptor (GR) under the control of its own regulatory region (gPUCHI-GR) in the puchi-1 mutant.
2019-06-12 | GSE128721 | GEO
Project description:Background: There is a growing interest in the role of chromatin in acquiring and maintaining cell identity. Despite the ever growing availability of genome-wide gene expression data, understanding how transcription programs are established and regulated to define cell identity remains a puzzle. An important mechanism of gene regulation is the binding of transcription factors to specific DNA sequence motifs across the genome. However, these sequences are hindered by the packaging of DNA to chromatin. Thus the accessibility of these loci for TF binding is highly regulated and determines where and when TF bind. We present a workflow for measuring chromatin accessibility in Arabidopsis thaliana, and define organ-specific regulatory sites and binding motifs of transcription factors at these sites. Results: We coupled the recently described INTACT (Isolation of Nuclei TAgged in specific Cell Types) and ATAC-seq (Assay for Transposase-Accessible Chromatin with highthroughput sequencing) as a genome-wide strategy to uncover accessible regulatory sites in Arabidopsis, based on their accessibility to nuclease digestion. By applying this pipeline in Arabidopsis roots, we revealed 41,419 accessible sites, of which approximately half are found in gene promoters and contain the H3K4me3 active histone mark. The root-unique accessible sites from this group are enriched for root processes. Interestingly, most of the root-unique accessible sites are found in nongenic regions, but are correlated with root-specific expression of distant genes. Importantly these gene-distant sites are enriched for binding motifs of TFs important for root development, as well as motifs for TFs that may play a role as novel transcriptional regulators in roots, suggesting that these accessible loci are functional novel genedistant regulatory elements. Conclusion: By coupling the INTACT with ATAC-seq methods, we present a feasible pipeline to profile accessible chromatin in plants. We also introduce a rapid measure of the experiment quality. We find that chromatin accessibility at promoter regions is strongly associated with transcription and active histone marks. However, root specific chromatin accessibility is primarily found at intergenic regions, suggesting their predominance in defining organ identity, possibly via long-range chromatin interactions. This workflow can be rapidly applied to study the regulatory landscape in other cell types, plant species and conditions.
2018-12-23 | GSE122771 | GEO
Project description:Background: There is a growing interest in the role of chromatin in acquiring and maintaining cell identity. Despite the ever growing availability of genome-wide gene expression data, understanding how transcription programs are established and regulated to define cell identity remains a puzzle. An important mechanism of gene regulation is the binding of transcription factors to specific DNA sequence motifs across the genome. However, these sequences are hindered by the packaging of DNA to chromatin. Thus the accessibility of these loci for TF binding is highly regulated and determines where and when TF bind. We present a workflow for measuring chromatin accessibility in Arabidopsis thaliana, and define organ-specific regulatory sites and binding motifs of transcription factors at these sites. Results: We coupled the recently described INTACT (Isolation of Nuclei TAgged in specific Cell Types) and ATAC-seq (Assay for Transposase-Accessible Chromatin with highthroughput sequencing) as a genome-wide strategy to uncover accessible regulatory sites in Arabidopsis, based on their accessibility to nuclease digestion. By applying this pipeline in Arabidopsis roots, we revealed 41,419 accessible sites, of which approximately half are found in gene promoters and contain the H3K4me3 active histone mark. The root-unique accessible sites from this group are enriched for root processes. Interestingly, most of the root-unique accessible sites are found in nongenic regions, but are correlated with root-specific expression of distant genes. Importantly these gene-distant sites are enriched for binding motifs of TFs important for root development, as well as motifs for TFs that may play a role as novel transcriptional regulators in roots, suggesting that these accessible loci are functional novel genedistant regulatory elements. Conclusion: By coupling the INTACT with ATAC-seq methods, we present a feasible pipeline to profile accessible chromatin in plants. We also introduce a rapid measure of the experiment quality. We find that chromatin accessibility at promoter regions is strongly associated with transcription and active histone marks. However, root specific chromatin accessibility is primarily found at intergenic regions, suggesting their predominance in defining organ identity, possibly via long-range chromatin interactions. This workflow can be rapidly applied to study the regulatory landscape in other cell types, plant species and conditions.
2018-12-23 | GSE122770 | GEO
Project description:Long oligonucleotide microarrays were used for the study of expression profile changes during seedling photomorphogenesis in rice and in Arabidopsis. Different light quality treatments were applied to seedlings. To dissect organ-specific light effects, we further profiled shoot and root organs in both species. Keywords = rice Keywords = Arabidopsis Keywords = photomorphogenesis Keywords: ordered
2005-05-02 | GSE2360 | GEO
Project description:WOX5 maintains columella stem cells in the Arabidopsis root and prevents their differentiation. In order to understand the molecular mode of WOX5 action the genes differentially expressed by WOX5 inducible over-expression were determined by analysis of microarray hybridizations. Seedlings transformed with a dexamethasone inducible WOX5 construct were induced for one or four hours with dexamethasone or a mock solution. Other seedlings were treated one hour with cycloheximide ( a protein synthesis inhibitor to reduce secondary transcriptional effects after WOX5 activation) and either dexamethasone or a mock solution. Root tips were harvested, RNA extracted, and the RNA samples prepared for hybridization to Affymetrix microarrays. Potential target genes of WOX5 were further analyzed by transcriptional markers, qPCR and EMSA (electrophoretic mobility shift assay).
2016-10-16 | E-MTAB-2853 | biostudies-arrayexpress
Project description:Post-transcriptional gene regulation plays a significant role in the response to Pi starvation. Here, we utilized advances in next-generation sequencing technology to examine changes in transcriptional control, RNA association with translating ribosomes in 14-day-old Arabidopsis seedlings subjected to 7 days of Pi starvation.
2017-05-06 | GSE98610 | GEO