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Reduced representation bisulfite sequencing (RRBS) of brown adipose tissue from postnatal day 12 mice perinatally exposed to vehicle or DDT

ABSTRACT: Reduced representation bisulfite sequencing (RRBS) of brown adipose tissue from postnatal day 12 mice perinatally exposed to vehicle or DDT

PROVIDER: PRJNA1074053 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR27896000.fastq.gz	Fastqsanger.gz
	SRR27896100.fastq.gz	Fastqsanger.gz
	SRR27896001.fastq.gz	Fastqsanger.gz
	SRR27896101.fastq.gz	Fastqsanger.gz
	SRR27896002.fastq.gz	Fastqsanger.gz

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Reduced representation bisulfite sequencing (RRBS) of brown adipose tissue from postnatal day 12 mice perinatally exposed to vehicle or DDT

Project description:The insecticide dichlorodiphenyltrichloroethane (DDT) and its persistent metabolite, dichlorodiphenyldichloroethylene (DDE), have been associated with increased adiposity and obesity in rodent and human studies. These lipophilic pollutants accumulate in adipose tissue and it is theorized that their exposure leads to decreased decrease energy expenditure through the impairment of thermogenesis in brown adipose tissue. We hypothesized that impaired thermogenesis is due to persistent epigenetic modifications of brown adipose tissue. To address this, we exposed C57BL/6J mice to DDT from gestational day 11.5 to postnatal day 5 and isolated brown adipose tissue for RRBS from one offspring per litter when mice reached postnatal day 12 (n=20 DDT litters and 22 vehicle litters). DNA methylation levels in brown adipose tissue of mice perinatally exposed to vehicle or DDT were determined using RRBS. Analyses of differential methylation and KEGG pathway enrichment were performed.

2024-10-05 | GSE255231 | GEO

High concordance between Illumina HiSeq2500 and NextSeq500 for Reduced Representation Bisulfite Sequencing (RRBS)

Project description:Reduced representation bisulfite sequencing (RRBS) provides an efficient method for measuring DNA methylation at single base resolution in regions of high CpG density. This technique has been extensively tested on the HiSeq2500, which uses a 4-colour detection method, however it is unclear if the method will also work on the NextSeq500 platform, which employs a 2-colour detection system. We created an RRBS library and sequenced it on both the HiSeq2500 and NextSeq500, and found no significant difference in the base composition of reads derived from either machine. Moreover, the methylation calls made from the data of each instrument were highly concordant, with methylation patterns across the genome appearing as expected. Therefore, RRBS can be sequenced on the Nextseq500 with comparable quality to that of the HiSeq2500.

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Project description:DNA methylation is an important regulatory mechanism that contributes to transcriptional repression. To examine whether DNA methylation affects the transcriptional changes of DNA repair genes under H2O2-induced oxidative stress, we performed reduced representation bisulfite sequencing (RRBS) in H2O2-treated and untreated HCT116 cells.

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Project description:DNA methylation is a mechanism for long-term transcriptional regulation and is required for normal cellular differentiation. Failure to properly establish or maintain DNA methylation patterns leads to cell dysfunction and diseases such as cancer. Identifying DNA methylation signatures in complex tissues can be challenging due to inaccurate cell enrichment methods and low DNA yields. We have developed a technique called Laser Capture Microdissection-Reduced Representation Bisulfite Sequencing (LCM-RRBS) for the multiplexed interrogation of the DNA methylation status of CpG Islands and promoters. LCM-RRBS accurately and reproducibly profiles genome-wide methylation of DNA extracted from microdissected fresh frozen or formalin-fixed paraffin-embedded tissue samples. To demonstrate the utility of LCM-RRBS, we characterized changes in DNA methylation associated with gonadectomy-induced adrenocortical neoplasia in the mouse. Compared to adjacent normal tissue, the adrenocortical tumors showed reproducible gains and losses of DNA methylation at genes involved in cell differentiation and organ development. LCM-RRBS is a rapid, cost-effective, and sensitive technique for analyzing DNA methylation in heterogeneous tissues and will facilitate the investigation of DNA methylation in cancer and organ development. Laser capture microdissection-reduced representation bisulfite sequencing and reduced representation bisulfite sequencing on human blood leukocyte, human endometrial tumor, mouse liver tissue, and mouse normal and neoplastic adrenal tissue

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Sperm Epimutation Biomarkers of Obesity and Pathologies following DDT Induced Epigenetic Transgenerational Inheritance of Disease

Project description:Gestating F0 generational female rats were transiently exposed to DDT during fetal gonadal sex determination and the incidence of adult onset pathologies was assessed in the subsequent F1, F2, and F3 generations. In addition, sperm differential DNA methylation regions (DMRs) that were associated with specific pathologies in the F3 generation males were investigated. No pathology was observed in the F1 generation DDT lineage males or females compared with F1 generation controls (vehicle exposure). There was an increase of testis disease and early onset puberty in the F2 generation DDT lineage males. The F3 generation DDT males had significant increases in testis disease, prostate disease, and late onset puberty. The F3 generation DDT females had significant increases in ovarian and kidney disease. Both the F3 generation males and females had significant increases in the frequency of obesity and multiple disease. The F3 generation sperm was collected to examine DMRs for the ancestrally exposed DDT male population. Unique sets of DMRs were associated with late onset puberty, kidney disease, and multiple disease pathologies.

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