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Genome-wide transcriptional analysis of submerged lotus reveals cooperative regulation and gene responses.

ABSTRACT: Flooding severely limits plant growth even for some aquatic plants. Although much work has been done on submergence response of some important crop plants, little is known about the response mechanism of aquatic plants, i.e. lotus (Nelumbo nucifera). In this study, we investigated the genome-wide regulation lotus genes in response to submergence stress by high-throughput mRNA sequencing. A total of 4002 differentially expressed genes (DEGs) in lotus upon submergence stress. Among them, 1976 genes were up-regulated and 2026 down-regulated. Functional annotation of these genes by Gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) enrichment analysis revealed that they were mainly involved in processes of oxidation-reduction, abiotic stimuli, cellular metabolism and small molecule metabolism. Based on these data, previous work and quantitative RT-PCR (RT-qPCR) validation, we constructed a cooperative regulation network involved in several important DEGs in regards to the antioxidant system, disease resistance, hypoxia resistance and morphological adaptation. Further work confirmed that several innate immunity genes were induced during submergence and might confer higher resistance to lotus rot disease. In conclusion, these results provide useful information on molecular mechanisms underlying lotus responses to submergence stress.

SUBMITTER: Wang B

PROVIDER: S-EPMC6003939 | biostudies-literature | 2018 Jun

REPOSITORIES: biostudies-literature

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Genome-wide transcriptional analysis of submerged lotus reveals cooperative regulation and gene responses.

Wang Bei B Jin Qijiang Q Zhang Xiao X Mattson Neil S NS Ren Huihui H Cao Jing J Wang Yanjie Y Yao Dongrui D Xu Yingchun Y

Scientific reports 20180615 1

Flooding severely limits plant growth even for some aquatic plants. Although much work has been done on submergence response of some important crop plants, little is known about the response mechanism of aquatic plants, i.e. lotus (Nelumbo nucifera). In this study, we investigated the genome-wide regulation lotus genes in response to submergence stress by high-throughput mRNA sequencing. A total of 4002 differentially expressed genes (DEGs) in lotus upon submergence stress. Among them, 1976 gene ...[more]

PMID: 29907819

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Project description:BackgroundParkinson's disease (PD) is a complex, age-related neurodegenerative disorder of largely unknown etiology. PD is strongly associated with mitochondrial respiratory dysfunction, which can lead to epigenetic dysregulation and specifically altered histone acetylation. Nevertheless, and despite the emerging role of epigenetics in age-related brain disorders, the question of whether aberrant histone acetylation is involved in PD remains unresolved.MethodsWe studied fresh-frozen brain tissue from two independent cohorts of individuals with idiopathic PD (n = 28) and neurologically healthy controls (n = 21). We performed comprehensive immunoblotting to identify histone sites with altered acetylation levels in PD, followed by chromatin immunoprecipitation sequencing (ChIP-seq). RNA sequencing data from the same individuals was used to assess the impact of altered histone acetylation on gene expression.ResultsImmunoblotting analyses revealed increased acetylation at several histone sites in PD, with the most prominent change observed for H3K27, a marker of active promoters and enhancers. ChIP-seq analysis further indicated that H3K27 hyperacetylation in the PD brain is a genome-wide phenomenon with a strong predilection for genes implicated in the disease, including SNCA, PARK7, PRKN and MAPT. Integration of the ChIP-seq with transcriptomic data from the same individuals revealed that the correlation between promoter H3K27 acetylation and gene expression is attenuated in PD patients, suggesting that H3K27 acetylation may be decoupled from transcription in the PD brain. Strikingly, this decoupling was most pronounced among nuclear-encoded mitochondrial genes, corroborating the notion that impaired crosstalk between the nucleus and mitochondria is involved in the pathogenesis of PD. Our findings independently replicated in the two cohorts.ConclusionsOur findings strongly suggest that aberrant histone acetylation and altered transcriptional regulation are involved in the pathophysiology of PD. We demonstrate that PD-associated genes are particularly prone to epigenetic dysregulation and identify novel epigenetic signatures associated with the disease.

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Genome-wide transcriptional analysis of submerged lotus reveals cooperative regulation and gene responses.

Publications

Genome-wide transcriptional analysis of submerged lotus reveals cooperative regulation and gene responses.

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