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

ABSTRACT: 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.

ORGANISM(S): Triticum aestivum

PROVIDER: GSE232428 | GEO | 2024/07/22

REPOSITORIES: GEO

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

2024-07-22 | GSE232426 | GEO

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

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Dynamic Yin-Yang regulation network of O-GlcNAcylation and phosphorylation mediates vernalization response for flowering in winter wheat

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

Dynamic Yin-Yang regulation network of O-GlcNAcylation and phosphorylation mediatesvernalization response for flowering in winter wheat, part 2

2021-05-18 | PXD008298 | Pride

Temporal expression study of microRNAs in crown tissues of winter wheat grown under natural growth condition

Project description:MicroRNAs (miRNAs) are single strand small non-coding RNAs that regulate target mRNAs at post-transcription level. Winter wheat (Triticum aestivum L.), is an important crop plant all over the world. Long term cold exposure (vernalization) is necessary for winter wheat transition from vegetative growth to reproductive growth, yet the involvement of miRNAs in these stages remains unknown. Therefore, we performed next generation sequencing of small RNAs profiles in crown tissues at three-leaf stage, winter dormancy stage, spring greenup stage and jointing stage.

2021-11-10 | GSE155963 | GEO

Identifications of vernalization regulatory elements by epigenomic approaches in winter wheat

Project description:This SuperSeries is composed of the SubSeries listed below.

2024-07-22 | GSE232430 | GEO

Winter wheat gene expression vs agricultural production systems

Project description:Comparative transcriptome profiling in winter wheat grown under different agricultural practices

2012-11-30 | E-MTAB-903 | biostudies-arrayexpress

Identification and Temporal Expression Analysis of Conserved and Novel MicroRNAs in the Leaves of Winter Wheat Grown in the Field

Project description:MicroRNAs (miRNAs) are small non-coding RNAs that regulate target mRNAs by inducing degradation or preventing translation of their target mRNAs. Winter wheat, Triticum aestivum., is an important crop plant, yet there are only a few studies on the association of miRNAs and growth and development of winter wheat grown in the field. Here we carried out experimental analysis of miRNAs in wheat leaves by analyzing small RNA profiles at different growth stages.

2019-10-01 | GSE125391 | 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

Comparison of isogenic lines differing in vernalization requirement

Project description:Gene expression was assyed in seedlings of isogenic barley lines differing in vernalization requirement. Seedlings were harvested after 5 days germination in darkness at 20 degrees. Seedlings were then subjected to 1 day at 4 degrees after 5 days germination in darkness at 20. Genotypes include the winter barley parent Dairokakku, and isogenic lines carrying a deletion of VRN2, active VRN1 allleles (VRN1-10, or VRN1-8) or an active allele of FT1/VRN3. ****[PLEXdb(http://www.plexdb.org) has submitted this series at GEO on behalf of the original contributor, Ben Trevaskis. The equivalent experiment is BB97 at PLEXdb.]

2016-01-23 | GSE43704 | GEO

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