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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)

ABSTRACT: 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)

PROVIDER: PRJNA523826 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR8609120.fastq.gz	Fastqsanger.gz
	SRR8609130.fastq.gz	Fastqsanger.gz
	SRR8609121.fastq.gz	Fastqsanger.gz
	SRR8609131.fastq.gz	Fastqsanger.gz
	SRR8609122.fastq.gz	Fastqsanger.gz

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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)

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

Cytokinin-promoted secondary growth and nutrient storage in the perennial stem zone of Arabis alpina

Project description:Perennial plants maintain their life span through several growth seasons. Arabis alpina serves as model Brassicaceae species to study perennial traits. A. alpina lateral stems have a proximal vegetative zone with a dormant bud zone, and a distal senescing seed-producing inflorescence zone. We addressed the questions of how this zonation is distinguished at the anatomical level, whether it is related to nutrient storage, and which signals affect the zonation. We found that the vegetative zone ehxibits secondary growth, which we termed the perennial growth zone (PZ). High-molecular weight carbon compounds accumulate there in cambium and cambium derivatives. Neither vernalization nor flowering were requirements for secondary growth and sequestration of storage compounds. The inflorescence zone with only primary growth, termed annual growth zone (AZ), or roots exhibited different storage characteristics. Following cytokinin application, cambium activity was enhanced and secondary phloem parenchyma was formed in the PZ and also in the AZ. In transcriptome analysis cytokinin-related genes represented enriched gene ontology terms and were expressed at higher level in PZ than AZ. Thus, A. alpina uses primarily the vegetative PZ for nutrient storage, coupled to cytokinin-promoted secondary growth. This finding lays a foundation for future studies addressing signals for perennial growth.

2020-06-14 | GSE152417 | GEO

The Arabis alpina APETALA2 orthologue delays flowering by repressing floral meristem identity genes during vernalization

Project description:PEP2 regulates flowering in response to vernalization in a PEP1 -dependent and PEP1-independent pathway

2019-02-27 | GSE117977 | GEO

Vernalization mediated changes in the Lolium perenne transcriptome

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

Identifications of vernalization regulatory elements by epigenomic approaches in winter wheat (ATAC-Seq)

Project description:Epigenetic modification plays a key role in the vernalization process and maintains gene expression states after low temperature. In this study, the Chinese main cultivar Aikang58 was used to construct the chromatin accessibility maps, expression profile and histone modification (including H3K27me3, H3K27ac, H3K36me3 and H3K4me3) maps of winter wheat before and after vernalization. We provided a crucial data resource for deep understanding of epigenome in vernalization. What’s more, important core regulatory elements and corresponding transcription factors were discovered, and the complex regulatory network of wheat vernalization was analyzed. ATAC-seq of leaf, axillary bud and shoot apex before and after vernalization

2024-07-22 | GSE232424 | GEO

Transcriptome and epigenome analyses of vernalization in Arabidopsis thaliana

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

Identifications of vernalization regulatory elements by epigenomic approaches in winter wheat (RNA-Seq)

2024-07-22 | GSE232428 | GEO

Identifications of vernalization regulatory elements by epigenomic approaches in winter wheat (ChIP-Seq)

2024-07-22 | GSE232426 | GEO

Genome-wide profiling of H3K4me3 and H3K27me3 modifications during and after vernalization in Brachypodium

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

Breaking endodormancy in leafy spurge crown buds by dehydration-stress and vernalization identifies overlapping molecular networks linked to growth regulators

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

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