Exploring TSA-Induced Haploid Embryogenesis in Brassica napus
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA1159199 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR30620700.fastq.gz | Fastqsanger.gz | |||
| SRR30620701.fastq.gz | Fastqsanger.gz | |||
| SRR30620702.fastq.gz | Fastqsanger.gz | |||
| SRR30620703.fastq.gz | Fastqsanger.gz | |||
| SRR30620704.fastq.gz | Fastqsanger.gz |
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Project description:Haploid embryos can be induced from cultured immature pollen following stress treatment. In Brassica napus, the application of the histone/lysine deacetylase (HDAC/KDAC) inhibitor trichostatin A (TSA) to pollen cultures enhances the production of differentiated embryos and embryogenic callus when applied together with heat stress (Li et al., 2014). To identify genes associated with the induction of haploid embryogenesis and to investigate which genes may be responsible for TSA-induced lipid and starch accumulation in the embryogenic structures, we compared the transcriptomes of pollen cultures treated with heat stress and 0.05 µM TSA to those of untreated pollen cultures, both at two days.
2024-09-25 | GSE276833 | GEO
Project description:Haploid embryos can be induced from cultured immature pollen following a stress treatment. In Brassica napus, application of the histone/lysine deacetylase (HDAC/KDAC) inhibitor trichostatin A (TSA) to pollen cultures enhances the production of differentiated embryos and embryogenic callus when applied together with heat stress (Li et al., 2014). To identify genes associated with the induction of B. napus haploid embryogenesis, we compared the transcriptomes of untreated pollen cultures and pollen cultures treated with either heat-stress or heat-stress plus TSA.
2020-08-03 | GSE140969 | GEO
Project description:Effect of HDAC inhibitor TSA on haploid embryogenesis [dataset 1]
| PRJNA591595 | ENA
Project description:The haploid multicellular male gametophyte of plants, the pollen grain, is a terminally differentiated structure whose function ends at fertilization. Unlike pollen grains, the immature gametophyte retains its capacity for totipotent growth when cultured in vitro. Haploid embryo production from cultured immature male gametophytes is a widely used plant breeding and propagation technique that was described nearly 50 years ago, but one that is poorly understood at the mechanistic level. Using a chemical approach, we show that the switch to haploid embryogenesis is controlled by the activity of histone deacetylases (HDACs). Blocking HDAC activity with trichostatin A (TSA) in cultured immature male gametophytes of Brassica napus leads to a large increase in the proportion of cells that switch from pollen to embryogenic growth. Embryogenic growth is enhanced by, but not dependent on, the high temperature stress that is normally used to induce haploid embryogenesis in B. napus. The immature male gametophyte of Arabidopsis thaliana, which is recalcitrant for haploid embryo development in culture, also forms embryogenic cell clusters after TSA treatment. TSA treatment of immature male gametophytes for as little as eight hours was accompanied by hyperacetylation of histones H3 and H4, and by the upregulation of genes involved in cell-cycle progression, the auxin pathway and cell wall catabolism pathways. We propose that the totipotency of the immature male gametophyte in planta is kept in check by an HDAC-dependent mechanism, and that high temperature or other stresses used to induce haploid embryo development in culture impinge on this HDAC-dependent pathway. 8 samples were analyzed. We generated the following pairwise comparisons between treatment and the corresponding mock treatment: TSA+CHX (2 replicates) vs CHX (2 replicates); TSA (2 replicates) vs DMSO (2 replicates).
2016-07-03 | E-GEOD-49070 | biostudies-arrayexpress
Project description:The haploid multicellular male gametophyte of plants, the pollen grain, is a terminally differentiated structure whose function ends at fertilization. Unlike pollen grains, the immature gametophyte retains its capacity for totipotent growth when cultured in vitro. Haploid embryo production from cultured immature male gametophytes is a widely used plant breeding and propagation technique that was described nearly 50 years ago, but one that is poorly understood at the mechanistic level. Using a chemical approach, we show that the switch to haploid embryogenesis is controlled by the activity of histone deacetylases (HDACs). Blocking HDAC activity with trichostatin A (TSA) in cultured immature male gametophytes of Brassica napus leads to a large increase in the proportion of cells that switch from pollen to embryogenic growth. Embryogenic growth is enhanced by, but not dependent on, the high temperature stress that is normally used to induce haploid embryogenesis in B. napus. The immature male gametophyte of Arabidopsis thaliana, which is recalcitrant for haploid embryo development in culture, also forms embryogenic cell clusters after TSA treatment. TSA treatment of immature male gametophytes for as little as eight hours was accompanied by hyperacetylation of histones H3 and H4, and by the upregulation of genes involved in cell-cycle progression, the auxin pathway and cell wall catabolism pathways. We propose that the totipotency of the immature male gametophyte in planta is kept in check by an HDAC-dependent mechanism, and that high temperature or other stresses used to induce haploid embryo development in culture impinge on this HDAC-dependent pathway.
2016-01-01 | GSE49070 | GEO
Project description:Somatic embryogenesis closely resembles zygotic embryogenesis and hence, it is considered as a model system to explore dynamic events of embryogenesis, at a molecular level. We sequenced three district developmental time points of somatic embryo development in Arabidopsis thaliana with the aim of exploring transcriptomes at a global scale.
2016-01-31 | E-MTAB-2403 | biostudies-arrayexpress
Project description:MicroRNAs (miRNAs) are important post-transcriptional regulators of plant development and seed formation. In Brassica napus, an important edible oil crop, valuable lipids are synthesized and stored in specific seed tissues during embryogenesis. The miRNA transcriptome of B. napus is currently poorly characterized, especially at different seed developmental stages. This work aims to describe the miRNAome of developing seeds of B. napus by identifying plant-conserved and novel miRNAs and comparing miRNA abundance in mature versus developing seeds. A total of 62 miRNA families were detected through a computational analysis of a large number of reads obtained from deep sequencing two small RNA and two RNA-seq libraries of (i) pooled immature developing stages and (ii) mature B. napus seeds. Among these miRNA families, 17 families are currently known to exist in B. napus; additionally, 32 families not reported in B. napus but conserved in other plant species were identified by alignment with known plant mature miRNAs. The contigs from the assembled mRNA-seq data allowed for a search for putative new precursors and led to the identification of 13 novel miRNA families. Differential expression between the libraries was determined through a statistical analysis of normalized miRNA reads and revealed several miRNAs and isomiRNAs that were more abundant during the developing stages. The predicted miRNA target genes encode a broad range of proteins related to seed development and energy storage. This work presents a comprehensive study of the miRNA transcriptome of B. napus seeds and will provide a basis for future research on more targeted studies of individual miRNAs and their functions in embryogenesis, seed maturation and lipid accumulation in B. napus. RNA profiles in 2 different seed libraries (mature seeds and a pool of developing seed stages) of Brassica napus by deep sequencing (Illumina HiSeq2000).
2014-08-01 | E-GEOD-38018 | biostudies-arrayexpress
Project description:MicroRNAs (miRNAs) are important post-transcriptional regulators of plant development and seed formation. In Brassica napus, an important edible oil crop, valuable lipids are synthesized and stored in specific seed tissues during embryogenesis. The miRNA transcriptome of B. napus is currently poorly characterized, especially at different seed developmental stages. This work aims to describe the miRNAome of developing seeds of B. napus by identifying plant-conserved and novel miRNAs and comparing miRNA abundance in mature versus developing seeds. A total of 62 miRNA families were detected through a computational analysis of a large number of reads obtained from deep sequencing two small RNA and two RNA-seq libraries of (i) pooled immature developing stages and (ii) mature B. napus seeds. Among these miRNA families, 17 families are currently known to exist in B. napus; additionally, 32 families not reported in B. napus but conserved in other plant species were identified by alignment with known plant mature miRNAs. The contigs from the assembled mRNA-seq data allowed for a search for putative new precursors and led to the identification of 13 novel miRNA families. Differential expression between the libraries was determined through a statistical analysis of normalized miRNA reads and revealed several miRNAs and isomiRNAs that were more abundant during the developing stages. The predicted miRNA target genes encode a broad range of proteins related to seed development and energy storage. This work presents a comprehensive study of the miRNA transcriptome of B. napus seeds and will provide a basis for future research on more targeted studies of individual miRNAs and their functions in embryogenesis, seed maturation and lipid accumulation in B. napus. microRNA profiles in 2 different seed libraries (mature seeds and a pool of developing seed stages) of Brassica napus by deep sequencing (Illumina HiSeq2000).
2014-08-01 | E-GEOD-38019 | biostudies-arrayexpress
Project description:MicroRNAs (miRNAs) are important post-transcriptional regulators of plant development and seed formation. In Brassica napus, an important edible oil crop, valuable lipids are synthesized and stored in specific seed tissues during embryogenesis. The miRNA transcriptome of B. napus is currently poorly characterized, especially at different seed developmental stages. This work aims to describe the miRNAome of developing seeds of B. napus by identifying plant-conserved and novel miRNAs and comparing miRNA abundance in mature versus developing seeds. A total of 62 miRNA families were detected through a computational analysis of a large number of reads obtained from deep sequencing two small RNA and two RNA-seq libraries of (i) pooled immature developing stages and (ii) mature B. napus seeds. Among these miRNA families, 17 families are currently known to exist in B. napus; additionally, 32 families not reported in B. napus but conserved in other plant species were identified by alignment with known plant mature miRNAs. The contigs from the assembled mRNA-seq data allowed for a search for putative new precursors and led to the identification of 13 novel miRNA families. Differential expression between the libraries was determined through a statistical analysis of normalized miRNA reads and revealed several miRNAs and isomiRNAs that were more abundant during the developing stages. The predicted miRNA target genes encode a broad range of proteins related to seed development and energy storage. This work presents a comprehensive study of the miRNA transcriptome of B. napus seeds and will provide a basis for future research on more targeted studies of individual miRNAs and their functions in embryogenesis, seed maturation and lipid accumulation in B. napus.
2014-08-01 | GSE38018 | GEO
Project description:In order to identify the TSA responsive genes, we performed a gene expression microarray analysis for the RNAs isolated from TSA-untreated and TSA-treated human keratinocytes
2018-12-31 | GSE121902 | GEO