Genome-wide analysis of DNA methylation in bovine placentas

Su, Jianmin; Wang, Yongsheng; Xing, Xupeng; Li, Jun; Zhang, Yong

doi:10.1186/1471-2164-15-12

Cited by 75 publications

(83 citation statements)

References 52 publications

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“…In the present study, CpG islands showed a higher methylation density compared with previous studies in other species. Recent works on horse, cattle and chicken epigenomes found 10 to 20% of methylated CGIs across the genomes [14, 16, 17]. The results in the present work indicate that almost 50% of the CGIs in goat are methylated in hypothalamus and ovary.…”

Section: Discussionsupporting

confidence: 65%

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Genome-wide analysis of DNA methylation in hypothalamus and ovary of Capra hircus

et al. 2017

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BackgroundDNA methylation is a frequently studied epigenetic modification due to its role in regulating gene expression and hence in biological processes and in determining phenotypic plasticity in organisms. Rudimentary DNA methylation patterns for some livestock species are publically available: among these, goat methylome deserves to be further explored.ResultsGenome-wide DNA methylation maps of the hypothalamus and ovary from Saanen goats were generated using Methyl-CpG binding domain protein sequencing (MBD-seq). Analysis of DNA methylation patterns indicate that the majority of methylation peaks found within genes are located gene body regions, for both organs. Analysis of the distribution of methylated sites per chromosome showed that chromosome X had the lowest number of methylation peaks. The X chromosome has one of the highest percentages of methylated CpG islands in both organs, and approximately 50% of the CpG islands in the goat epigenome are methylated in hypothalamus and ovary. Organ-specific Differentially Methylated Genes (DMGs) were correlated with the expression levels.ConclusionsThe comparison between transcriptome and methylome in hypothalamus and ovary showed that a higher level of methylation is not accompanied by a higher gene suppression. The genome-wide DNA methylation map for two goat organs produced here is a valuable starting point for studying the involvement of epigenetic modifications in regulating goat reproduction performance.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-017-3866-4) contains supplementary material, which is available to authorized users.

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Section: Discussionsupporting

confidence: 65%

“…comparing the DNA methylation distribution pattern in goat to that found in bovine placenta and horse [14, 17]. In bovine placenta, the DNA methylation level decreased before the TSS, noticeably increases in intragenic regions, and is constantly low downstream of genes.…”

Section: Discussionmentioning

confidence: 99%

Genome-wide analysis of DNA methylation in hypothalamus and ovary of Capra hircus

et al. 2017

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“…These results specified that most CGIs are unmethylated. In the study of Su et al (2014) in cattle, 20.12% of CGIs were methylated, which could be probably due to the different approaches used to detect CGIs. When comparing the status of methylated CGIs investigated in different regions of the genome, most of the methylated CGIs were present in the introns, intergenic and CDS regions and the lowest number of the methylated CGIs existed in the promoter regions (Figure 4).…”

Section: Resultsmentioning

confidence: 99%

“…To assess the methylation status of CpG islands, the MeDIP-seq methylation data of placental tissue downloaded from Su et al (2014) study was used. Here, highly methylated regions (HMRs), which are also called peaks, were used to evaluate the methylation status in CGIs.…”

Section: Methodsmentioning

confidence: 99%

Genome-wide analysis of CpG islands in some livestock genomes and their relationship with genomic features

Barazandeh¹,

Mohammadabadi²,

Ghaderi–Zefrehei³

et al. 2016

Czech J. Anim. Sci.

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CpG islands (CGIs) are an important group of CpG dinucleotides in the guanine-and cytosinerich regions as they harbour functionally relevant epigenetic loci for whole genome studies. As a matter of fact, since there has not been a formal comparative analysis of CGIs in domestic even-toed ungulate genomes, this study was performed to serve this comparison. The Hidden Markov Model was used to detect CGIs in the genomes. The results indicated that the CGIs number and CGI densities had scant variations across genomes. The goat genome had the highest number of CGIs (99 070), whereas the alpaca genome had the highest CGI density (43.39 CGIs/Mb). Significant positive correlations were observed among CGI densities with chromosome pair number, observed CpG/expected CpG, recombination rate, and gene density. When the size of chromosomes increased, the CGI densities decreased and a trend of higher CGI densities in the telomeric regions was observed. Only 10.96% of CGIs were methylated underscoring this postulation that the majority of CGIs remains to be unmethylated. The highest amount of the methylated CGIs was observed in the introns, intergenic, and coding (CDS) regions and the lowest amount of the methylated CGIs was observed in the promoter regions, implying that the DNA methylation of CGIs may control gene expression at the genome level. Detected differences between even-toed ungulate and other vertebrate genomes showed that CGI densities varied greatly among the genomes. These findings would contribute to better understanding the even-toed ungulate (epi) genomes, the role of CGIs in epigenomic functions and molecular evolution.

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“…The production of clones from an adult somatic cell is enabled by the capacity of the oocyte to reprogramme the epigenome of a differentiated nucleus to totipotency, and aberrant epigenetic reprogramming is recognized as one of the leading causes of the developmental abnormalities encountered in clones4. Accordingly, DNA methylation defects have been reported in bovine clones, at both the global level56 and at candidate loci789, but genome-wide views of the affected regions are still scarce10 and associations with phenotypic anomalies have not been clearly demonstrated.…”

mentioning

confidence: 99%

Altered DNA methylation associated with an abnormal liver phenotype in a cattle model with a high incidence of perinatal pathologies

Kiefer

Jouneau

Campion

et al. 2016

Sci Rep

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Cloning enables the generation of both clinically normal and pathological individuals from the same donor cells, and may therefore be a DNA sequence-independent driver of phenotypic variability. We took advantage of cattle clones with identical genotypes but different developmental abilities to investigate the role of epigenetic factors in perinatal mortality, a complex trait with increasing prevalence in dairy cattle. We studied livers from pathological clones dying during the perinatal period, clinically normal adult clones with the same genotypes as perinatal clones and conventional age-matched controls. The livers from deceased perinatal clones displayed histological lesions, modifications to quantitative histomorphometric and metabolic parameters such as glycogen storage and fatty acid composition, and an absence of birth-induced maturation. In a genome-wide epigenetic analysis, we identified DNA methylation patterns underlying these phenotypic alterations and targeting genes relevant to liver metabolism, including the type 2 diabetes gene TCF7L2. The adult clones were devoid of major phenotypic and epigenetic abnormalities in the liver, ruling out the effects of genotype on the phenotype observed. These results thus provide the first demonstration of a genome-wide association between DNA methylation and perinatal mortality in cattle, and highlight epigenetics as a driving force for phenotypic variability in farmed animals.

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Genome-wide analysis of DNA methylation in bovine placentas

Cited by 75 publications

References 52 publications

Genome-wide analysis of DNA methylation in hypothalamus and ovary of Capra hircus

Genome-wide analysis of DNA methylation in hypothalamus and ovary of Capra hircus

Genome-wide analysis of CpG islands in some livestock genomes and their relationship with genomic features

Altered DNA methylation associated with an abnormal liver phenotype in a cattle model with a high incidence of perinatal pathologies

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