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Reduced representation bisulphite sequencing of ten bovine somatic tissues reveals DNA methylation patterns and their impacts on gene expression

ABSTRACT: This SuperSeries is composed of the SubSeries listed below.

ORGANISM(S): Bos taurus

PROVIDER: GSE86324 | GEO | 2017/02/14

REPOSITORIES: GEO

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Reduced representation bisulphite sequencing of ten bovine somatic tissues reveals DNA methylation patterns and their impacts on gene expression.

Project description:BackgroundAs a major epigenetic component, DNA methylation plays important functions in individual development and various diseases. DNA methylation has been well studied in human and model organisms, but only limited data exist in economically important animals like cattle.ResultsUsing reduced representation bisulphite sequencing (RRBS), we obtained single-base-resolution maps of bovine DNA methylation from ten somatic tissues. In total, we evaluated 1,868,049 cytosines in CG-enriched regions. While we found slightly low methylation levels (29.87 to 38.06 %) in cattle, the methylation contexts (CGs and non-CGs) of cattle showed similar methylation patterns to other species. Non-CG methylation was detected but methylation levels in somatic tissues were significantly lower than in pluripotent cells. To study the potential function of the methylation, we detected 10,794 differentially methylated cytosines (DMCs) and 836 differentially methylated CG islands (DMIs). Further analyses in the same tissues revealed many DMCs (including non-CGs) and DMIs, which were highly correlated with the expression of genes involved in tissue development.ConclusionsIn summary, our study provides a baseline dataset and essential information for DNA methylation profiles of cattle.

| S-EPMC5053184 | biostudies-literature

Reduced representation bisulphite sequencing of ten bovine somatic tissues reveals DNA methylation patterns and their impacts on gene expression [RRBS-Seq]

Project description:As a key epigenetic modification, DNA methylation is essential for normal development by regulating processes like gene expression, genomic imprinting, and suppression of repetitive elements. However, DNA methylation in the cattle genome is not well understood. Here we presented the first single-base-resolution maps of DNA methylation in 10 diversely somatic tissues harvested from the sequenced Hereford cow L1 Dominette 01449 and her relatives using reduced representation bisulphite sequencing (RRBS). In total, we observed 1,868,049 high accuracy cytosines that located in the CG enriched regions. Similar to the methylation patterning in other species, the CG context was predominant methylated. Widespread differences were identified between the methylation patterns of CG and non-CG contexts. They were distributed differentially among the genomic features, including the genic regions, CpG islands, and repetitive sequences. Autocorrelation analysis among adjacent residues illustrated that methylation level of CGs were highly correlated in a region. In contrast, weak or no correlation was found among non-CGs or between CGs and non-CGs. The distinct distribution and low correlation of CG and non-CG methylation suggested that non-CG methylation may be independent from CG methylation and may be mediated by different mechanisms. We also detected 798 tissue-specific differentially methylated cytosines (tDMC) and 131 tissue-specific differentially methylated CpG islands. Combined analysis with the RNA-seq data, we discovered several non-CGs in tDMCs also highly correlated with gene expression, which implied the potential function of non-CG methylation in somatic cells in addition to pluripotent cells. In summary, we showed that non-CGs exist in bovine tissues and some of them were correlated with tissue-specific functions. This study provided essential information for the cytosine methylation patterning in bovine somatic tissues.

2017-02-14 | GSE76346 | GEO

Reduced representation bisulphite sequencing of ten bovine somatic tissues reveals DNA methylation patterns and their impacts on gene expression [RNA-Seq]

2017-02-14 | GSE86323 | GEO

Reduced representation bisulphite sequencing of ten bovine somatic tissues reveals DNA methylation patterns and their impacts on gene expression

Project description:Reduced representation bisulphite sequencing of ten bovine somatic tissues reveals DNA methylation patterns and their impacts on gene expression

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Reduced representation bisulphite sequencing of two chickpea genotypes to identify differential DNA methylation patterns associated with drought tolerance and sensitivity

Project description:In this study, to obtain a clear picture of drought mechanism involved in two distinctive chickpea genotype, the aim was to identify the DNA methylation patterns which potentially regulate drought tolerance/sensitivity of these selected genotypes. The leaf tissues from the shoot apical meristem from drought sensitive and drought tolerant genotypes were used for RRBS (Reduced representation bisulphite sequencing) under drought stress. The sequencing data was analysed using Bismark and methylkit to recall the methylation levels in control and samples for both genotypes and identify differentially methylated regions.

2021-12-01 | GSE129110 | GEO

Reduced Representation Bisulphite Sequencing on FACS purified cell subpopulations of human prostate cancers and normal tissues.

Project description:Prostate adenocarcinomas contain a predominance of cells with luminal features that display aberrant DNA methylation patterns with useful diagnostic and prognostic potential. However, the DNA methylation features of basal and luminal cells in both normal and cancer tissues remain largely unknown. We have generated genome-wide DNA methylation profiles for FACS purified basal and luminal prostate tumour cells, obtained from radical prostatectomy samples and their paired normal counterparts isolated from unaffected regions in the same patient’s gland.

2018-10-22 | GSE107596 | GEO

DNA methylation data from Reduced Representation Bisulphite sequencing in the Dutch Hunger Winter Families Study

2014-07-01 | GSE54983 | GEO

DNA methylation data from Reduced Representation Bisulphite sequencing in the Dutch Hunger Winter Families Study

Project description:We report on genome-wide DNA methylation differences associated with early gestational famine exposure. We find that open chromatin regions and enhancers are especially sensitive to prenatal famine exposure. We compared 24 individuals conceived during the Dutch Famine, a brief 6 month famine at the end of WWII, with a same sex sibling.

2014-07-01 | E-GEOD-54983 | biostudies-arrayexpress

Reduced Representation Bisulphite Sequencing of WT and AICDA KO iPCS clones

Project description:We report AICDA facilitates naïve pluripotency of mouse iPSCs by suppressing FGF/ERK signaling. In the absence of AICDA iPSCs fail to achive naïve pluripotent state and display chracteristics of EpiSCs and are primed for differentiation.

2019-04-03 | GSE129187 | GEO

PyMT 4 stages tumor progression ERRBS (Enhanced Reduced Representation Bisulphite Sequencing )

Project description:We sequenced mammary tissues of PyMT mice from 4 stages (hyperplasia at week 6, adenoma/MIN at week 8, early carcinoma at week 10, and late carcinoma at week 12) during tumor progression. We also sequenced mammary tissues of age-matched FVB controls.

2018-04-18 | GSE83623 | GEO

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