Project description:Compared with non-cancerous lung tissues, lung cancer in Xuanwei tissues expressed a total of 6,899 differentially methylated regions, including 5,788 hypermethylated regions and 1,111 hypomethylated regions. Many differentially methylated regions have been found in lung cancer in Xuanwei.
Project description:As a non-invasive blood testing, the detection of cell-free DNA (cfDNA) methylation in plasma is raising increasing interest due to its diagnostic and biology applications. Although extensively used in cfDNA methylation analysis, bisulfite sequencing is less cost-effective. Through enriching methylated cfDNA fragments with MeDIP followed by deep sequencing, we aimed to characterize cfDNA methylome in cancer patients. In this study, we investigated the cfDNA methylation patterns in lung cancer patients by MeDIP-seq. MEDIPS package was used for the identification of differentially methylated regions (DMRs) between patients and normal ones. Overall, we identified 330 differentially methylated regions (DMRs) in gene promoter regions, 33 hypermethylation and 297 hypomethylation respectively, by comparing lung cancer patients and healthy individuals as controls. The 33 hypermethylation regions represent 32 genes. Some of the genes had been previously reported to be associated with lung cancers, such as GAS7, AQP10, HLF, CHRNA9 and HOPX. Taken together, our study provided an alternative method of cfDNA methylation analysis in lung cancer patients with potential clinical applications.
Project description:H2A.B is a unique histone H2A variant that shares only 40 ~ 50 % sequence identity with canonical H2A. It has only been identified in mammals and has quickly evolved with remarkable sequence diversity among different species. H2A.B is ubiquitously expressed in most cells and tissues. It is mainly deposited in gene body region. The localization of H2A.B is associated with methylated CpG islands in mouse ES cells. H2A.B facilitates transcription elongation to go through methylated CpG islands in the gene bodies. One typical example is that H2A.B regulates transcription elongation at imprinted loci. We found H2A.B enriched in some methylated loci. Using ChIP-seq and MeDIP-seq, we test the correlation of H2A.B and DNA methylation.
Project description:we used methylated DNA immunoprecipitation sequencing (MeDIP-Seq) to detect DNA methylation levels and lncRNA-seq to detect lncRNA expression levels in 3 lung cancer samples and 3 matched normal samples. Then 255 differentially methylated genes (DMGs) and 246 differentially expressed lncRNAs (DELs) were identified. Finally, LINC01354 was founded to be differentially methylated and predictive of transcription. Besides, the prognostic value of differential methylation related DELs was analyzed.
Project description:Using meDIP-chip to provide methylation profile in zdp mutant and identify hypermethylated regions comparing to wild type Arabidopsis plants.
Project description:Using meDIP-chip to provide methylation profile in zdp mutant and identify hypermethylated regions comparing to wild type Arabidopsis plants. Examination of zdp mutant's methylome. 4 samples(1 mutant, 1 WT, each has two biological replicates)
Project description:Malignant melanoma is the most fatal skin cancer with a high degree of genetic and epigenetic aberrations. To investigate the role of DNA methylation on melanoma heterogeneity, we performed methylated DNA immunoprecipitation (MeDIP) microarray analysis of 10 primary melanoma cell cultures.