OBJECTIVE: To assess Atractylodis Rhizoma Alba extract(ARE) neuroprotective function in 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine(MPTP)-treated mice and related genes. METHODS: Examined m RNA-DNA methylation change...OBJECTIVE: To assess Atractylodis Rhizoma Alba extract(ARE) neuroprotective function in 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine(MPTP)-treated mice and related genes. METHODS: Examined m RNA-DNA methylation changes induced by ARE in MPTP-induced Parkinson's disease(PD) model's substantia nigra. RESULTS: ARE mitigated MPTP-induced motor impairment in rotarod and open field tests and preserved tyrosine hydroxylase-positive neuronal cells in substantia nigra and striatum. Genome RNA-Sequencing and Methyl-Sequencing in substantia nigra of vehicle/ARE-treated MPTP-induced PD mice showed 84 differentially expressed genes(DEGs) and 1804 differentially methylated regions(DMRs). Upregulated genes involved zinc ion homeostasis, cilium protein localization, and transcription;downregulated genes linked to ephrin receptor signaling, somitogenesis, and gene expression regulation. Hyper/hypomethylated DMRs post-ARE treatment associated with Wnt signaling, mitochondrial organization, dopamine biosynthesis, and hindbrain development. No significant correlation between DEGs and methylated genes related to PD pathogenesis. CONCLUSION: This research has identified the epigenetic targets of ARE's therapeutic action and gives insight on how ARE protects neurons in Parkinson's disease.展开更多
Background: Tibetan pigs, which inhabit the Tibetan Plateau, exhibit distinct phenotypic and physiological characteristics from those of lowland pigs and have adapted well to the extreme conditions at high altitude.Ho...Background: Tibetan pigs, which inhabit the Tibetan Plateau, exhibit distinct phenotypic and physiological characteristics from those of lowland pigs and have adapted well to the extreme conditions at high altitude.However, the genetic and epigenetic mechanisms of hypoxic adaptation in animals remain unclear.Methods: Whole-genome DNA methylation data were generated for heart tissues of Tibetan pigs grown in the highland(TH, n = 4) and lowland(TL, n = 4), as well as Yorkshire pigs grown in the highland(YH, n = 4) and lowland(YL, n = 4), using methylated DNA immunoprecipitation sequencing.Results: We obtained 480 million reads and detected 280679, 287224, 259066, and 332078 methylation enrichment peaks in TH, YH, TL, and YL, respectively. Pairwise TH vs. YH, TL vs. YL, TH vs. TL, and YH vs. YL comparisons revealed6829, 11997, 2828, and 1286 differentially methylated regions(DMRs), respectively. These DMRs contained 384, 619,192, and 92 differentially methylated genes(DMGs), respectively. DMGs that were enriched in the hypoxia-inducible factor 1 signaling pathway and pathways involved in cancer and hypoxia-related processes were considered to be important candidate genes for high-altitude adaptation in Tibetan pigs.Conclusions: This study elucidates the molecular and epigenetic mechanisms involved in hypoxic adaptation in pigs and may help further understand human hypoxia-related diseases.展开更多
The analysis of cytosine methylation provides a new way to assess and describe epigenetic regulation at a whole-genome level in many eukaryotes.DNA methylation has a demonstrated role in the genome stability and prote...The analysis of cytosine methylation provides a new way to assess and describe epigenetic regulation at a whole-genome level in many eukaryotes.DNA methylation has a demonstrated role in the genome stability and protection,regulation of gene expression and many other aspects of genome function and maintenance.BS-seq is a relatively unbiased method for profiling the DNA methylation,with a resolution capable of measuring methylation at individual cytosines.Here we describe,as an example,a workflow to handle DNA methylation analysis,from BS-seq library preparation to the data visualization.We describe some applications for the analysis and interpretation of these data.Our laboratory provides public access to plant DNA methylation data via visualization tools available at our ＂Next-Gen Sequence＂ websites（http：//mpss.udel.edu）,along with small RNA,RNA-seq and other data types.展开更多
DNA methylation is an important epigenetic change affecting gene expression in plants in both normal and stress conditions. The organelles, mitochondria and chloroplast play a significant role in sensing and initiatin...DNA methylation is an important epigenetic change affecting gene expression in plants in both normal and stress conditions. The organelles, mitochondria and chloroplast play a significant role in sensing and initiating stress response. In this study, we report the methylation pattern in chloroplast and mitochondrial genomes in irrigated and water stressed conditions and its relationship with gene expression of a drought tolerant </span><i><span style="font-family:Verdana;">Zea</span></i> <i><span style="font-family:Verdana;">mays</span></i><span style="font-family:Verdana;"> cultivar, Z59. Whole genome bisulfite sequencing was done to analyze the pattern of methylation in both the conditions. Mapping of bisulfite reads to B73 reference of mitochondrial and chloroplast genomes showed hypomethylation in water stressed plants when compared to irrigated plants. Sliding window approach to the methylation count data showed highest peak at 419,800 to 420,800 bp region in mitochondria and at 36,900 to 37,900 bp region in chloroplast genomes in both samples. Annotation of the methylated genomes showed that, genes related to photosystem I & II in chloroplast and nad4 gene in mitochondria were hypo methylated in the water stressed sample. RNA-seq analysis of</span><span style="font-family:Verdana;"> transcriptomic</span></span><span></span><span></span><span style="font-family:Verdana;">s</span><span style="font-family:Verdana;"> reads mapped to the same reference showed regulation of rps3, rps2A, ccmFC, atp1 and many uncharacterized genes in mitochondria and psbA, psbD, psbc, psaA, and atpA, genes in chloroplast.展开更多
基金the Development of Sustainable Application for Standard Herbal Resource by the Korea Institute of Oriental Medicine (No. KSN2012320)。
文摘OBJECTIVE: To assess Atractylodis Rhizoma Alba extract(ARE) neuroprotective function in 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine(MPTP)-treated mice and related genes. METHODS: Examined m RNA-DNA methylation changes induced by ARE in MPTP-induced Parkinson's disease(PD) model's substantia nigra. RESULTS: ARE mitigated MPTP-induced motor impairment in rotarod and open field tests and preserved tyrosine hydroxylase-positive neuronal cells in substantia nigra and striatum. Genome RNA-Sequencing and Methyl-Sequencing in substantia nigra of vehicle/ARE-treated MPTP-induced PD mice showed 84 differentially expressed genes(DEGs) and 1804 differentially methylated regions(DMRs). Upregulated genes involved zinc ion homeostasis, cilium protein localization, and transcription;downregulated genes linked to ephrin receptor signaling, somitogenesis, and gene expression regulation. Hyper/hypomethylated DMRs post-ARE treatment associated with Wnt signaling, mitochondrial organization, dopamine biosynthesis, and hindbrain development. No significant correlation between DEGs and methylated genes related to PD pathogenesis. CONCLUSION: This research has identified the epigenetic targets of ARE's therapeutic action and gives insight on how ARE protects neurons in Parkinson's disease.
基金supported by the National Natural Science Foundation of China(No.31560615)the National Key Technology Research and Development Program(No.2015BAD03B02)+1 种基金the Program for Changjiang Scholars and Innovation Research Team in University(No.IRT_15R62)the Innovation Base Cultivation and Development Project(No.Z171100002217072)
文摘Background: Tibetan pigs, which inhabit the Tibetan Plateau, exhibit distinct phenotypic and physiological characteristics from those of lowland pigs and have adapted well to the extreme conditions at high altitude.However, the genetic and epigenetic mechanisms of hypoxic adaptation in animals remain unclear.Methods: Whole-genome DNA methylation data were generated for heart tissues of Tibetan pigs grown in the highland(TH, n = 4) and lowland(TL, n = 4), as well as Yorkshire pigs grown in the highland(YH, n = 4) and lowland(YL, n = 4), using methylated DNA immunoprecipitation sequencing.Results: We obtained 480 million reads and detected 280679, 287224, 259066, and 332078 methylation enrichment peaks in TH, YH, TL, and YL, respectively. Pairwise TH vs. YH, TL vs. YL, TH vs. TL, and YH vs. YL comparisons revealed6829, 11997, 2828, and 1286 differentially methylated regions(DMRs), respectively. These DMRs contained 384, 619,192, and 92 differentially methylated genes(DMGs), respectively. DMGs that were enriched in the hypoxia-inducible factor 1 signaling pathway and pathways involved in cancer and hypoxia-related processes were considered to be important candidate genes for high-altitude adaptation in Tibetan pigs.Conclusions: This study elucidates the molecular and epigenetic mechanisms involved in hypoxic adaptation in pigs and may help further understand human hypoxia-related diseases.
基金supported by the Grant from the National Institute of Food and Agriculture,U.S.Department of Agriculture, Competitive Grants Program(No.2011-67013- 30036)support from the U.S.National Science Foundation(Award 0701745)
文摘The analysis of cytosine methylation provides a new way to assess and describe epigenetic regulation at a whole-genome level in many eukaryotes.DNA methylation has a demonstrated role in the genome stability and protection,regulation of gene expression and many other aspects of genome function and maintenance.BS-seq is a relatively unbiased method for profiling the DNA methylation,with a resolution capable of measuring methylation at individual cytosines.Here we describe,as an example,a workflow to handle DNA methylation analysis,from BS-seq library preparation to the data visualization.We describe some applications for the analysis and interpretation of these data.Our laboratory provides public access to plant DNA methylation data via visualization tools available at our ＂Next-Gen Sequence＂ websites（http：//mpss.udel.edu）,along with small RNA,RNA-seq and other data types.
文摘DNA methylation is an important epigenetic change affecting gene expression in plants in both normal and stress conditions. The organelles, mitochondria and chloroplast play a significant role in sensing and initiating stress response. In this study, we report the methylation pattern in chloroplast and mitochondrial genomes in irrigated and water stressed conditions and its relationship with gene expression of a drought tolerant </span><i><span style="font-family:Verdana;">Zea</span></i> <i><span style="font-family:Verdana;">mays</span></i><span style="font-family:Verdana;"> cultivar, Z59. Whole genome bisulfite sequencing was done to analyze the pattern of methylation in both the conditions. Mapping of bisulfite reads to B73 reference of mitochondrial and chloroplast genomes showed hypomethylation in water stressed plants when compared to irrigated plants. Sliding window approach to the methylation count data showed highest peak at 419,800 to 420,800 bp region in mitochondria and at 36,900 to 37,900 bp region in chloroplast genomes in both samples. Annotation of the methylated genomes showed that, genes related to photosystem I & II in chloroplast and nad4 gene in mitochondria were hypo methylated in the water stressed sample. RNA-seq analysis of</span><span style="font-family:Verdana;"> transcriptomic</span></span><span></span><span></span><span style="font-family:Verdana;">s</span><span style="font-family:Verdana;"> reads mapped to the same reference showed regulation of rps3, rps2A, ccmFC, atp1 and many uncharacterized genes in mitochondria and psbA, psbD, psbc, psaA, and atpA, genes in chloroplast.
