Similar Datasets
Project description:DNA methylation is considered a stable epigenetic mark due to its presumed long-term inheritance through cell divisions. Here, we perform high-throughput bisulfite sequencing on clonally derived cell lines to quantitatively measure mitotic methylation inheritance at the nucleotide level. We find that although DNA methylation is generally faithfully maintained at hypo- and hypermethylated sites, this is not the case at intermediately methylated CpGs. Low fidelity intermediate methylation is interspersed throughout the genome and within genes with no or low transcriptional activity. Moreover, we determine that the probabilistic changes that occur at intermediately methylated sites are due to DNMT1 rather than DNMT3A/3B activity. The observed lack of clonal inheritance at intermediately methylated sites challenges the concept of DNA methylation as a consistently stable epigenetic mark.
2023-06-30 | GSE234028 | GEO
Project description:DNA methylation is considered a stable epigenetic mark due to its presumed long-term inheritance through cell divisions. Here, we perform high-throughput bisulfite sequencing on clonally derived cell lines to quantitatively measure mitotic methylation inheritance at the nucleotide level. We find that although DNA methylation is generally faithfully maintained at hypo- and hypermethylated sites, this is not the case at intermediately methylated CpGs. Low fidelity intermediate methylation is interspersed throughout the genome and within genes with no or low transcriptional activity. Moreover, we determine that the probabilistic changes that occur at intermediately methylated sites are due to DNMT1 rather than DNMT3A/3B activity. The observed lack of clonal inheritance at intermediately methylated sites challenges the concept of DNA methylation as a consistently stable epigenetic mark.
2023-06-30 | GSE234029 | GEO
Project description:DNA methylation is considered a stable epigenetic mark due to its presumed long-term inheritance through cell divisions. Here, we perform high-throughput bisulfite sequencing on clonally derived cell lines to quantitatively measure mitotic methylation inheritance at the nucleotide level. We find that although DNA methylation is generally faithfully maintained at hypo- and hypermethylated sites, this is not the case at intermediately methylated CpGs. Low fidelity intermediate methylation is interspersed throughout the genome and within genes with no or low transcriptional activity. Moreover, we determine that the probabilistic changes that occur at intermediately methylated sites are due to DNMT1 rather than DNMT3A/3B activity. The observed lack of clonal inheritance at intermediately methylated sites challenges the concept of DNA methylation as a consistently stable epigenetic mark.
2023-06-30 | GSE234024 | GEO
Project description:Target capture bisulfite sequencing (tcBS-seq) to evaluate clonal methylation inheritance
| PRJNA982764 | ENA
Project description:Target capture bisulfite sequencing (tcBS-seq) to evaluate clonal methylation inheritance [BiSulfite-seq]
| PRJNA979209 | ENA
Project description:Target capture bisulfite sequencing (tcBS-seq) to evaluate clonal methylation inheritance [BiSulfite-seq 2]
| PRJNA979217 | ENA
Project description:Target capture bisulfite sequencing (tcBS-seq) to evaluate clonal methylation inheritance [RNA-seq]
| PRJNA979208 | ENA
Project description:BackgroundDNA methylation plays important roles in gene regulation during both normal developmental and disease states. In the past decade, a number of methods have been developed and applied to characterize the genome-wide distribution of DNA methylation. Most of these methods endeavored to screen whole genome and turned to be enormously costly and time consuming for studies of the complex mammalian genome. Thus, they are not practical for researchers to study multiple clinical samples in biomarker research.ResultsHere, we display a novel strategy that relies on the selective capture of target regions by liquid hybridization followed by bisulfite conversion and deep sequencing, which is referred to as liquid hybridization capture-based bisulfite sequencing (LHC-BS). To estimate this method, we utilized about 2 μg of native genomic DNA from YanHuang (YH) whole blood samples and a mature dendritic cell (mDC) line, respectively, to evaluate their methylation statuses of target regions of exome. The results indicated that the LHC-BS system was able to cover more than 97% of the exome regions and detect their methylation statuses with acceptable allele dropouts. Most of the regions that couldn't provide accurate methylation information were distributed in chromosomes 6 and Y because of multiple mapping to those regions. The accuracy of this strategy was evaluated by pair-wise comparisons using the results from whole genome bisulfite sequencing and validated by bisulfite specific PCR sequencing.ConclusionsIn the present study, we employed a liquid hybridisation capture system to enrich for exon regions and then combined with bisulfite sequencing to examine the methylation statuses for the first time. This technique is highly sensitive and flexible and can be applied to identify differentially methylated regions (DMRs) at specific genomic locations of interest, such as regulatory elements or promoters.
| S-EPMC3295804 | biostudies-literature
Project description:DNA methylation stabilizes developmentally programmed gene expression states. Aberrant methylation is associated with disease progression and is a common feature of cancer genomes. Presently, few methods enable quantitative, large-scale, single-base resolution mapping of DNA methylation states in desired regions of a complex mammalian genome. Here, we present an approach that combines array-based hybrid selection and massively parallel bisulfite sequencing to profile DNA methylation in genomic regions spanning hundreds of thousands of bases. This single molecule strategy enables methylation variable positions to be quantitatively examined with high sampling precision. Using bisulfite capture, we assessed methylation patterns across 324 randomly selected CpG islands (CGI) representing more than 25,000 CpG sites. A single lane of Illumina sequencing permitted methylation states to be definitively called for >90% of target sties. The accuracy of the hybrid-selection approach was verified using conventional bisulfite capillary sequencing of cloned PCR products amplified from a subset of the selected regions. This confirmed that even partially methylated states could be successfully called. A comparison of human primary and cancer cells revealed multiple differentially methylated regions. More than 25% of islands showed complex methylation patterns either with partial methylation states defining the entire CGI or with contrasting methylation states appearing in specific regional blocks within the island. We observed that transitions in methylation state often correlate with genomic landmarks, including transcriptional start sites and intron-exon junctions. Methylation, along with specific histone marks, was enriched in exonic regions, suggesting that chromatin states can foreshadow the content of mature mRNAs.
| S-EPMC2752124 | biostudies-literature
Project description:BackgroundEpigenetic alterations, such as aberrant DNA methylation of promoter and enhancer regions, which lead to atypical gene expression, have been associated with carcinogenesis. In hepatocellular carcinoma (HCC), genome-wide analysis of methylation has only recently been used. For a better understanding of hepatocarcinogenesis, we applied an even higher resolution analysis of the promoter methylome to identify previously unknown regions and genes differentially methylated in HCC.ResultsOptimized liquid hybridization capture-based bisulfite sequencing (LHC-BS) was developed to quantitatively analyze 1.86 million CpG sites in individual samples from eight pairs of HCC and adjacent tissues. By linking the differentially methylated regions (DMRs) in promoters to the differentially expressed genes (DEGs), we identified 12 DMR-associated genes. We further utilized Illumina MiSeq combining the bisulfite sequencing PCR approach to validate the 12 candidate genes. Analysis of an additional 78 HCC pairs on the Illumina MiSeq platform confirmed that 7 genes showed either promoter hyper-methylation (SMAD6, IFITM1, LRRC4, CHST4, and TBX15) or hypo-methylation (CCL20 and NQO1) in HCC.ConclusionsNovel methylome profiling provides a cost-efficient approach to identifying candidate genes in human HCC that may contribute to hepatocarcinogenesis. Our work provides further information critical for understanding the epigenetic processes underlying tumorigenesis and development of HCC.
| S-EPMC4546208 | biostudies-literature