Similar Datasets
Project description:Cell-specific transcriptional regulatory networks (TRNs) play vital roles in plant development and response to environmental stresses. However, traditional single-cell mono-omics techniques are unable to directly capture the relationships and dynamics between different layers of molecular information within the same cells. While advanced algorithm facilitates merging scRNA-seq and scATAC-seq datasets, accurate data integration remains a challenge, particularly when investigating cell-type-specific TRNs. By examining gene expression and chromatin accessibility simultaneously in 16,670 Arabidopsis root tip nuclei, the TRNs are reconstructed that govern root tip development under osmotic stress. In contrast to commonly used computational integration at cell-type level, 12,968 peak-to-gene linkage is captured at the bona fide single-cell level and construct TRNs at an unprecedented resolution. Furthermore, the unprecedented datasets allow to more accurately reconstruct the coordinated changes of gene expression and chromatin states during cellular state transition. During root tip development, chromatin accessibility of initial cells precedes gene expression, suggesting that changes in chromatin accessibility may prime cells for subsequent differentiation steps. Pseudo-time trajectory analysis reveal that osmotic stress can shift the functional differentiation of trichoblast. Candidate stress-related gene-linked cis-regulatory elements (gl-cCREs) as well as potential target genes are also identified, and uncovered large cellular heterogeneity under osmotic stress.
| S-EPMC11199978 | biostudies-literature
Project description:Cell-specific transcriptional regulatory networks (TRNs) play vital roles in plant development and response to environmental stresses. However, traditional single-cell mono-omics techniques are unable to fully capture the relationships and dynamics of molecular information within cells. While data integration algorithm facilitates the merging of single-cell RNA-seq and single-cell ATAC-seq data, ensuring the accuracy of the integration process remains a challenge, particularly when investigating cell-type-specific TRNs. In this study, we aimed to elucidate the TRNs of Arabidopsis under osmotic stress at the single-cell level by employing single-cell multi-omics technology to simultaneously examine gene expression and chromatin accessibility of 16,670 Arabidopsis root tip nuclei. We performed 12,968 peak-to-gene linkage at bona fide single-cell level, instead of previous computational integration at cell type level, which enabled us to obtain an unprecedented resolution to reconstruct transcriptional regulation. Pseudotime developmental trajectories revealed that osmotic stress led to shift the developmental status of Suberin synthetic endodermis (Suberin-endo) and trichoblast cells. We identified candidate stress-related cell-specific enhancers and cis-regulatory elements as well as potential target genes, and uncovered large cellular heterogeneity. We also found that cis-regulatory elements became accessible prior to gene expression and these cis-regulatory elements could form a positive feedback loop with epigenetic modification H3K4me3 in response to osmotic stress in columella cells.
2024-04-25 | GSE235495 | GEO
Project description:Cell-specific transcriptional regulatory networks (TRNs) play vital roles in plant development and response to environmental stresses. However, traditional single-cell mono-omics techniques are unable to fully capture the relationships and dynamics of molecular information within cells. While data integration algorithm facilitates the merging of single-cell RNA-seq and single-cell ATAC-seq data, ensuring the accuracy of the integration process remains a challenge, particularly when investigating cell-type-specific TRNs. In this study, we aimed to elucidate the TRNs of Arabidopsis under osmotic stress at the single-cell level by employing single-cell multi-omics technology to simultaneously examine gene expression and chromatin accessibility of 16,670 Arabidopsis root tip nuclei. We performed 12,968 peak-to-gene linkage at bona fide single-cell level, instead of previous computational integration at cell type level, which enabled us to obtain an unprecedented resolution to reconstruct transcriptional regulation. Pseudotime developmental trajectories revealed that osmotic stress led to shift the developmental status of Suberin synthetic endodermis (Suberin-endo) and trichoblast cells. We identified candidate stress-related cell-specific enhancers and cis-regulatory elements as well as potential target genes, and uncovered large cellular heterogeneity. We also found that cis-regulatory elements became accessible prior to gene expression and these cis-regulatory elements could form a positive feedback loop with epigenetic modification H3K4me3 in response to osmotic stress in columella cells.
2024-04-25 | GSE235494 | GEO
Project description:Cell-specific transcriptional regulatory networks (TRNs) play vital roles in plant development and response to environmental stresses. However, traditional single-cell mono-omics techniques are unable to fully capture the relationships and dynamics of molecular information within cells. While data integration algorithm facilitates the merging of single-cell RNA-seq and single-cell ATAC-seq data, ensuring the accuracy of the integration process remains a challenge, particularly when investigating cell-type-specific TRNs. In this study, we aimed to elucidate the TRNs of Arabidopsis under osmotic stress at the single-cell level by employing single-cell multi-omics technology to simultaneously examine gene expression and chromatin accessibility of 16,670 Arabidopsis root tip nuclei. We performed 12,968 peak-to-gene linkage at bona fide single-cell level, instead of previous computational integration at cell type level, which enabled us to obtain an unprecedented resolution to reconstruct transcriptional regulation. Pseudotime developmental trajectories revealed that osmotic stress led to shift the developmental status of Suberin synthetic endodermis (Suberin-endo) and trichoblast cells. We identified candidate stress-related cell-specific enhancers and cis-regulatory elements as well as potential target genes, and uncovered large cellular heterogeneity. We also found that cis-regulatory elements became accessible prior to gene expression and these cis-regulatory elements could form a positive feedback loop with epigenetic modification H3K4me3 in response to osmotic stress in columella cells.
2024-04-25 | GSE235509 | GEO
Project description:Multiome in the same cell revealed the impact of osmotic stress on Arabidopsis root tip development at single-cell level
| PRJNA986159 | ENA
Project description:Single-cell transcriptome sequencing (scRNA-seq) is a powerful tool for describing the transcriptome dynamics of plant development but has not yet been utilized to analyze the tissue ontology of sweetpotato. This study established a stable method for isolating single protoplast cells for scRNA-seq to reveal the cell heterogeneity of sweetpotato root tip meristems at the single-cell level. The study analyzed 12,172 single cells and 27,355 genes in the root tips of the sweetpotato variety Guangshu 87, which were distributed into 15 cell clusters. Pseudo-time analysis showed that there were transitional cells in the apical development trajectory of mature cell types from stem cell niches. Furthermore, we identified novel development regulators of sweetpotato tubers via trajectory analysis. The transcription factor IbGATA4 was highly expressed in the adventitious roots during the development of sweetpotato root tips, where it may regulate the development of sweetpotato root tips. In addition, significant differences were observed in the transcriptional profiles of cell types between sweetpotato, Arabidopsis thaliana, and maize. This study mapped the single-cell transcriptome of sweetpotato root tips, laying a foundation for studying the types, functions, differentiation, and development of sweetpotato root tip cells.
| S-EPMC11475360 | biostudies-literature
Project description:The objective of this project is to identify genes that are expressed in the Arabidopsis thaliana root tip and that are early induced (or repressed) by phoshate deficiency. Seedlings were germinated and grown (for 6 days) on phosphate rich medium and transfered to either a phosphate poor medium (Pi- = 20uM Pi treatment) or a phosphate rich medium (Pi+ = 500uM, Pi = control). Fifteen and 60 minutes after transfer, the tip (~800um) of the primary root was cut under a dissecting microscope. About 100 root tips per condition were harvested and there mRNA was analysed with the use of microarrays.
2011-09-09 | GSE31135 | GEO
Project description:Compared with other organisms, plants have an extraordinary capacity for self-repair. Even if the entire tissues, including the stem cells, are resected, most plant species are able to completely regenerate whole tissues. However, the mechanism by which plants efficiently regenerate the stem cell niche during tissue reorganization is still largely unknown. Here, we found that the signaling mediated by plant steroid hormones brassinosteroids is activated during stem cell formation after root tip excision in Arabidopsis. Treatment with brassinazole, an inhibitor of brassinosteroid biosynthesis, delayed the recovery of stem cell niche after root tip excision. Regeneration of root tip after resection was also delayed in a brassinosteroid receptor mutant. Therefore, we propose that brassinosteroids participate in efficient root tip regeneration, thereby enabling efficient tissue regeneration to ensure continuous root growth after resection.
| S-EPMC9200090 | biostudies-literature
Project description:Nitrogen and phosphorus are among the most widely used fertilizers worldwide. Nitrate (NO3(-)) and phosphate (PO4(3-)) are also signalling molecules whose respective transduction pathways are being intensively studied. However, plants are continuously challenged with combined nutritional deficiencies, yet very little is known about how these signalling pathways are integrated. Here we report the identification of a highly NO3(-)-inducible NRT1.1-controlled GARP transcription factor, HRS1, document its genome-wide transcriptional targets, and validate its cis-regulatory elements. We demonstrate that this transcription factor and a close homologue repress the primary root growth in response to P deficiency conditions, but only when NO3(-) is present. This system defines a molecular logic gate integrating P and N signals. We propose that NO3(-) and P signalling converge via double transcriptional and post-transcriptional control of the same protein, HRS1.
| S-EPMC4373655 | biostudies-literature
Project description:The ability of plants to sense and orient their root growth towards gravity is studied in many laboratories. It is known that manual analysis of image data is subjected to human bias. Several semi-automated tools are available for analysing images from flatbed scanners, but there is no solution to automatically measure root bending angle over time for vertical-stage microscopy images. To address these problems, we developed ACORBA, which is an automated software that can measure root bending angle over time from vertical-stage microscope and flatbed scanner images. ACORBA also has a semi-automated mode for camera or stereomicroscope images. It represents a flexible approach based on both traditional image processing and deep machine learning segmentation to measure root angle progression over time. As the software is automated, it limits human interactions and is reproducible. ACORBA will support the plant biologist community by reducing labour and increasing reproducibility of image analysis of root gravitropism.
| S-EPMC10095971 | biostudies-literature