Bisulphite-sequencing of chromatin immunoprecipitated DNA (BisChiP-seq) directly informs methylation status
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ABSTRACT: Bisulphite sequencing enables DNA methylation analysis of every cytosine residue. We have optimized conditions for combining chromatin immunoprecipation (ChIP) with high throughput bisulphite sequencing to study the relationship between histone modifications and DNA methylation.
Project description:Bisulphite sequencing enables DNA methylation analysis of every cytosine residue. We have optimized conditions for combining chromatin immunoprecipation (ChIP) with high throughput bisulphite sequencing to study the relationship between histone modifications and DNA methylation. Paired-end bisulphite sequencing of H3K27me3-ChIP DNA for LNCaP and PrEC cell lines
Project description:This SuperSeries is composed of the following subset Series: GSE30558: Bisulphite-sequencing of chromatin immunoprecipitated DNA (BisChiP-seq) directly informs methylation status GSE34340: Bisulphite sequencing of native LNCaP and PrEC DNA [methylation array] Refer to individual Series
Project description:The complex relationship between DNA methylation, chromatin modification, and underlying DNA sequence is often difficult to unravel with existing technologies. Here, we describe a novel technique based on high-throughput sequencing of bisulfite-treated chromatin immunoprecipitated DNA (BisChIP-seq), which can directly interrogate genetic and epigenetic processes that occur in normal and diseased cells. Unlike most previous reports based on correlative techniques, we found using direct bisulfite sequencing of Polycomb H3K27me3-enriched DNA from normal and prostate cancer cells that DNA methylation and H3K27me3-marked histones are not always mutually exclusive, but can co-occur in a genomic region-dependent manner. Notably, in cancer, the co-dependency of marks is largely redistributed with an increase of the dual repressive marks at CpG islands and transcription start sites of silent genes. In contrast, there is a loss of DNA methylation in intergenic H3K27me3-marked regions. Allele-specific methylation status derived from the BisChIP-seq data clearly showed that both methylated and unmethylated alleles can simultaneously be associated with H3K27me3 histones, highlighting that DNA methylation status in these regions is not dependent on Polycomb chromatin status. BisChIP-seq is a novel approach that can be widely applied to directly interrogate the genomic relationship between allele-specific DNA methylation, histone modification, or other important epigenetic regulators.
Project description:In this study, we performed bisulphite of two stages of seed development in a small-seeded chickpea cultivar (Himchana 1) using Illumina platform. Paired-end reads were generated from 5 libraries. Data obtained in FASTQ files were pre-processed to remove adapters and low-quality reads. We identified methylation level at each cytosine residue covered in sequencing and differentially methylated regions (DMRs) between stages of seed development.
Project description:In this study, we performed bisulphite of five stages of seed development in a large-seeded chickpea cultivar (JGK 3) using Illumina platform. Paired-end reads were generated from 11 libraries. Data obtained in FASTQ files were pre-processed to remove adapters and low-quality reads. We identified methylation level at each cytosine residue covered in sequencing and differentially methylated regions (DMRs) between stages of seed development.
Project description:Library preparation for whole genome bisulphite sequencing (WGBS) is challenging due to side effects of the bisulphite treatment, which leads to extensive DNA damage. Recently, a new generation of methods for bisulphite sequencing library preparation have been devised. They are based on initial bisulphite treatment of the DNA, followed by adaptor tagging of single stranded DNA fragments, and enable WGBS using low quantities of input DNA. In this study, we present a novel approach for quick and cost effective WGBS library preparation that is based on splinted adaptor tagging (SPLAT) of bisulphite-converted single-stranded DNA. Moreover, we validate SPLAT against three commercially available WGBS library preparation techniques, two of which are based on bisulphite treatment prior to adaptor tagging and one is a conventional WGBS method.
Project description:While Illumina X technology has helped to reduce the cost of whole genome sequencing substantially, its application for bisulphite sequencing is not straightforward. We describe the optimization of a library preparation and sequencing approach that maximizes the yield and quality of sequencing, and how to eliminate a previously unrecognized artefact affecting several percent of bisulphite sequencing reads.
Project description:While Illumina X technology has helped to reduce the cost of whole genome sequencing substantially, its application for bisulphite sequencing is not straightforward. We describe the optimization of a library preparation and sequencing approach that maximizes the yield and quality of sequencing, and how to eliminate a previously unrecognized artefact affecting several percent of bisulphite sequencing reads.