Oryza sativa
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ABSTRACT:
PROVIDER: PRJNA1058151 | ENA |
REPOSITORIES: ENA
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Project description:Rice is one of the most important global food crops, and is also a model organism for cereal research 31 . Complete genome sequencing of rice, together with advances in transcriptomics and proteomics, has had a dramatic impact on plant growth and 5 breeding programs 32 . Genomic analysis of DNA methylation in rice has revealed methylation patterns associated with gene bodies and promoters, and the occurrence of high levels of DNA methylation in the centromeric domain 33 . A genome-wide investigation of acetylation in rice revealed that H3K9ac and H3K27ac are mainly enriched at transcription start sites associated with active transcription 34 . Furthermore, global proteome analysis has shown that phosphorylation and succinylation are involved in diverse cellular and metabolic processes 35, 36 . However, despite these considerable advances in our knowledge, additional large-scale analysis of the lysine acetylome in rice is expected to identify many more Kac sites and acetylated proteins in this improtant crop plant. In this study, affinity enrichment and high-resolution LC-MS/MS were used for large-scale analysis of the lysine acetylome in rice variety Nipponbare. In total, 1353 lysine acetylation sites were detected in 866 protein groups in rice seedlings. Proteomic analysis showed that Kac occurs in proteins involved in diverse biological processes with varied cellular functions and subcellular localization.
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Project description:IDS1 is a rice AP2-type transcription factor with transcritpional repression activity. To understand how IDS1 regulate rice salt tolerance, the ChIP-seq experiments were performed to identify IDS1 binding site in globle genomic level. The two-weeks-old rice seedlings were lysated and sonificated and IDS1-DNA complexes were immune precipated with myc-antibody and protein A beads. The purified DNA samples were used to construct sequencing libraries and sequenced with Illumina. The data were then analyzed with bio-informatic tools.
2018-04-30 | E-MTAB-6504 | biostudies-arrayexpress
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