RNAseq analysis of Arabis alpina buds in the dormant zone (V2) and buds in the growing zone (V3) at the end of vernalization (+0) and 5 days later (+5d)
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PROVIDER: PRJNA523826 | ENA |
REPOSITORIES: ENA
Similar Datasets
Project description:Arabis alpina, similar to woody perennials, has a complex architecture with a zone of axillary vegetative branches and a zone of dormant buds that serve as perennating organs. We show that floral development during vernalization is the key for shaping the dormant bud zone by facilitating a synchronized and rapid growth after vernalization and thereby causing an increase in auxin transport, response and endogenous indole-3-acetic acid (IAA) levels in the stem. Floral development during vernalization is associated with the development of axillary buds in subapical nodes. Our transcriptome analysis indicated that these buds are not dormant during vernalization but only reach sustained growth after the return to warm temperatures. Floral and subapical vegetative branches grow after vernalization and inhibit the development of the buds below. Dormancy in these buds is regulated across the A. alpina life cycle by low temperatures and by apical dominance in a BRANCHED 1 dependent mechanism.
2020-03-01 | GSE126944 | GEO
Project description:Falster is a Danish perennial ryegrass ecotype with strong vernalization requirement, while Veyo is an Italian variety with no requirement for vernalization in order to flower. The transcriptome of these two perennial ryegrass genotypes with contrasting vernalization requirements was studied during primary (vernalization and short day conditions), and secondary induction (higher temperature and long day conditions) using an RNA-Seq approach, in order to reveal transcripts with expression profiles indicative of a role in floral induction, both in the promotion and repression of flowering.
2014-09-17 | E-MTAB-2623 | biostudies-arrayexpress
Project description:In this work, we present the first comprehensive analyses of transcriptomic and epigenomic dynamics during the vernalization process in Arabidopsis thaliana. Six major clusters of genes exhibiting distinctive features were identified. Temporary changes in histone H3K4me3 levels were observed that likely coordinate photosynthesis and prevent oxidative damage during cold. In addition, vernalization induced a stable accumulation of H3K27me3 over genes encoding many development-related transcription factors, resulting in either inhibition of transcription or a bivalent status of the genes. Lastly, FLC-like and VIN3-like genes were identified that appear to be novel components of the vernalization pathway.
2020-08-01 | GSE130291 | GEO
Project description:Vernalization, the requirement of long-term exposure to low environmental temperature for flowering, is a typical epigenetic phenomenon in plants. Histone modifications have been analyzed for key vernalization genes, but genome-wide regulation remains unclear. Here, we performed global analysis of histone 3 lysine 4 (H3K4me3) and 27 (H3K27me3) trimethylation with Chromatin Immunoprecipitation-Sequencing (ChIP-Seq) during and after vernalization to obtain complete view of histone modification fluctuation both on whole genome scale and for single genes, even different regions of genes. The critical role of H3K27me3 was revealed. During vernalization H3K27me3 regulation concentrated on a few biological processes, with two essential environmental responses, transcription regulation and anti-stress reactions, being main targets, as indicated by change pattern and GO analysis. The regulation of H3K4me3, however, showed no obvious focus. For gene expression, H3K27me3 is involved in multiple trends of control. H3K4me3, however, mainly focuses on unidirectional regulation. After vernalization most of H3K27me3 changes were kept, but relatively small proportion of H3K4me3 changes could be maintained, as shown by multiple-level analysis, suggesting the active role of H3K27me3 in epigenetic memory. Vernalization-induced histone modification changes were uncovered for VRN3, a gene integrating vernalization/photoperiod signals, suggesting its regulation role at epigenetic level. Memory-related genes were genome-widely identified and a high proportion of them showed quantitative response to vernalization-treatment, suggesting broad existence of this mechanism. Our studies shed new light on epigenetic role of H3K27me3 and VRN3 in vernalization, revealed mechanism underlying epigenetic memory, which helps us to further understand vernalization, a mechanism with great potential in agriculture.
2018-05-22 | GSE93140 | GEO
Project description:We used Illumina RNA-Seq technology to carry out digital gene expression profiling of Dormant and non dormant buds of Shine Muscat Cultivar.127 pathways were annotated by Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis, and metabolic, biosynthesis of secondry metabolite and. Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis demonstrated that DEGs were involved in various metabolic processes, including phytohormone metabolism. The newly generated transcriptome and gene expression profiling data provide valuable genetic information for revealing transcriptomic variation during dormant and non dormant period in Grapevine and ultimately helpful in uplifting of table grape industry.
2017-03-08 | GSE77119 | GEO
Project description:Persistence of the invasive perennial weed leafy spurge is mainly attributed to seasonal production of underground adventitious buds (UABs), which undergo well-defined phases of dormancy (para-, endo- and eco-dormancy). These well-defined phases of dormancy also allow UABs of leafy spurge to survive extreme seasonal variations, including dehydration-stress. Consequently, objectives of this study include understanding the effects of dehydration-stress on vegetative reproduction, flowering competence, and transcript profiles at different phases of bud dormancy. The vegetative growth potential of UABs was monitored by removing the aerial portion of dehydration-stressed plants and re-watering the root system. Further, microarray analysis was used to follow transcriptome profiles to identify critical defense- and signaling-pathways at different phases of dormancy in UABs. Surprisingly, only 3 days of dehydration-stress is required to break the endodormant phase in UABs. In leafy spurge, vernalization of endodormant UABs has previously been shown to induce flower competence, while breaking of endodormancy via dehydration-stress did not induce floral induction. Thus, these two environmental treatments open a unique approach to independently dissect molecular mechanisms involved in endodormancy maintenance and floral competence. Bioinformatics analysis of transcriptome data helped to identify models and overlapping pathways. During endodormancy break, LEC1, PHOTOSYSTEM I RC, and brassinosteroids were identified as ooverlapping hubs of up-regulated genes, and DREB1A, CBF2, GPA1, MYC2, BHLH, BZIP, and flavonoids were identified as overlapping hubs of down-regulated genes. Additionally, key genes involved in metabolic activity, chromatin modification, and cross-talk between growth regulators were identified as playing a role during endodormancy maintenance.
2011-04-05 | GSE28047 | GEO
Project description:We conducted genome-wide transcriptome analysis using the inbred Chinese cabbage line, ‘4004’, which displayed early flowering in response to vernalization. A total of 1,677 differentially-expressed genes (DEGs) were identified with and without vernalization. Transcriptome analysis identified 223 homologs of Arabidopsis Ft genes in Chinese cabbage, and 50 of these genes responded to vernalization. RT-qPCR analysis of major Ft genes showed that the majority of flowering enhancers were up-regulated in response to vernalization, whereas most flowering repressors were down-regulated in response to vernalization. Among the major Ft genes, the expression of BrCOL1-2, BrFT1/2, BrSOC1/2/3, BrFLC1/2/3/5, and BrMAF was strongly affected by vernalization.
2018-11-02 | GSE106444 | GEO
Project description:Protein post-translational modification (PTM) increases the functional diversity of the proteome and regulates numerous biological processes in eukaryotes. Two types of PTMs, O-linked-acetyl glucosamine modification (O-GlcNAc) and phosphorylation have been identified on the same amino acid, are considered as Yin-Yang modification for their antagonistic function recently. Vernalization, a prolonged cold exposure promoted flowering, is important for grain yield in temperate cereals, such as winter wheat. O-GlcNAcylation on TaGRP2 and phosphorylation on VER2 are involved in regulation of vernalization response (VRN) genes. However, less is known about how plant senses vernalization with general Yin-Yang modifications. Here we report that altering O-GlcNAc signaling by chemical inhibitors could change the vernalization response and affect flowering transition. Furthermore, we enriched O-GlcNAcylated and phosphorylated peptides from winter wheat plumules at different processing time points during vernalization by Lectin weak affinity chromatography (LWAC) and iTRAQ-TiO2, respectively. In total, about 200 O-GlcNAcylated proteins and 124 differential expressed phosphorylated proteins were identified by Mass Spectrum (MS). Based on GO enrichment, the identified O-GlcNAcylated proteins are mainly involved in response to abiotic stimulus and hormone, metabolic processing and gene expression. While dynamic phosphorylated proteins during vernalization participate in translation, transcription and metabolic processing. Of note, 31 proteins with both phosphorylation and O-GlcNAcylation modification were identified. Among them, TaGRP2 was further confirmed to participate in regulation of vernalization promoted flowering. The global modification profiles and genetic data at specific regulator suggested that the dynamic network of O-GlcNAcylation and phosphorylation on the key nodes regulate vernalization response and mediate flowering in wheat.
2020-12-18 | PXD008285 | Pride
Project description:We report here NGS RNA-seqencing datasets for htree different vernalization time course of radish cultivar, "Taebaek".
2021-08-31 | GSE182885 | GEO
Project description:Sugarcane is the raw material for the production of ethanol and sugar, and its by-products are used in cogeneration of energy in addition to various industrial processes. The cane field establishment is dependent of the axillary buds sprouting. The present study aimed to catalog the total proteome of germinative axillary bud and dormant axillary buds, and to identify important budding proteins, which are differentially expressed in these types of axillary buds. The proteome was obtained by extraction of total proteins using the TCA acetone method adapted for axillary buds. The experiment was carried out in biological triplicate. Protein samples were submitted to denaturing polyacrylamide gel electrophoresis (SDS-PAGE) and stained with comassie blue. Each lane of the polyacrylamide gel was fractionated (11 slice) and treated for purification and isolation of the polypeptides. Tryptic digestion was performed on each fragment with subsequent UPLC separation (Nano Acquity). The polypeptides were analyzed on Waters® Micromass® ESI-Q-Tof micro ™ mass spectrometer. Protein samples from the germinative and dormant axillary buds showed distinct bands patterns in the SDS-PAGE gel. Mass spectrometry data were analyzed by MASCOT tool (http://www.matrixscience.com).
2019-08-04 | PXD008008 | JPOST Repository