Exploring genome wide bisulfite sequencing for DNA methylation analysis in livestock: a technical assessment

Doherty, Rachael; Couldrey, Christine

doi:10.3389/fgene.2014.00126

Cited by 75 publications

(73 citation statements)

References 25 publications

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“…This discrepancy is likely due to the requirement of unique mapping to the sheep genome when next generation sequencing methods are used to interrogate DNA methylation, and/or the predominance of MspI sites in promoter regions that often display low levels of DNA methylation [9], [16].…”

Section: Discussionmentioning

confidence: 99%

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Genome-Wide DNA Methylation Patterns and Transcription Analysis in Sheep Muscle

et al. 2014

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DNA methylation plays a central role in regulating many aspects of growth and development in mammals through regulating gene expression. The development of next generation sequencing technologies have paved the way for genome-wide, high resolution analysis of DNA methylation landscapes using methodology known as reduced representation bisulfite sequencing (RRBS). While RRBS has proven to be effective in understanding DNA methylation landscapes in humans, mice, and rats, to date, few studies have utilised this powerful method for investigating DNA methylation in agricultural animals. Here we describe the utilisation of RRBS to investigate DNA methylation in sheep Longissimus dorsi muscles. RRBS analysis of ∼1% of the genome from Longissimus dorsi muscles provided data of suitably high precision and accuracy for DNA methylation analysis, at all levels of resolution from genome-wide to individual nucleotides. Combining RRBS data with mRNAseq data allowed the sheep Longissimus dorsi muscle methylome to be compared with methylomes from other species. While some species differences were identified, many similarities were observed between DNA methylation patterns in sheep and other more commonly studied species. The RRBS data presented here highlights the complexity of epigenetic regulation of genes. However, the similarities observed across species are promising, in that knowledge gained from epigenetic studies in human and mice may be applied, with caution, to agricultural species. The ability to accurately measure DNA methylation in agricultural animals will contribute an additional layer of information to the genetic analyses currently being used to maximise production gains in these species.

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Section: Discussionmentioning

confidence: 99%

“…Efficiency of adaptor ligation and size selection was determined by qualitative PCR as previously described [9].…”

Section: Methodsmentioning

confidence: 99%

Genome-Wide DNA Methylation Patterns and Transcription Analysis in Sheep Muscle

et al. 2014

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“…The sequencing depth was defined by Stein et al [98] as "the average number of times that a particular nucleotide is represented in a collection of random raw sequences". For WGBS, the Epigenomics Roadmap recommends from 5X to 30X of coverage [99] and about 10X of coverage for RRBS as 1-2% of the genome is sequenced using this technique [99]. To our knowledge, no specific chicken RRBS study has been published yet, therefore the pattern of MspI restriction enzyme in chicken should be carefully examined to estimate the fraction of the genome that will be included in such studies.…”

Section: Sequencing Considerationsmentioning

confidence: 99%

Genome-Wide Epigenetic Studies in Chicken: A Review

David¹,

Mersch

Foissac

et al. 2017

Epigenomes

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Over the years, farmed birds have been selected on various performance traits mainly through genetic selection. However, many studies have shown that genetics may not be the sole contributor to phenotypic plasticity. Gene expression programs can be influenced by environmentally induced epigenetic changes that may alter the phenotypes of the developing animals. Recently, high-throughput sequencing techniques became sufficiently affordable thanks to technological advances to study whole epigenetic landscapes in model plants and animals. In birds, a growing number of studies recently took advantage of these techniques to gain insights into the epigenetic mechanisms of gene regulation in processes such as immunity or environmental adaptation. Here, we review the current gain of knowledge on the chicken epigenome made possible by recent advances in high-throughput sequencing techniques by focusing on the two most studied epigenetic modifications, DNA methylation and histone post-translational modifications. We discuss and provide insights about designing and performing analyses to further explore avian epigenomes. A better understanding of the molecular mechanisms underlying the epigenetic regulation of gene expression in relation to bird phenotypes may provide new knowledge and markers that should undoubtedly contribute to a sustainable poultry production.

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“…20,28 The resulting methylation profiles per sample covered on average 1,764,402 CpG sites, of which 676,543 were assayed in all individuals. The overall methylation status changed very little within an individual (~98%) and between individuals (~97.5%) (Supplemental figure II), suggesting that methylation is a stable phenomenon and only a small number of sites are actively responding to environmental factors.…”

Section: Resultsmentioning

confidence: 99%

Remote Ischemic Conditioning Alters Methylation and Expression of Cell Cycle Genes in Aneurysmal Subarachnoid Hemorrhage

Nikkola

Laiwalla

et al. 2015

Stroke

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Background and purpose Remote ischemic conditioning (RIC) is a phenomenon in which short periods of non-fatal ischemia in one tissue confers protection to distant tissues. Here we performed a longitudinal human pilot study in patients with aneurysmal subarachnoid hemorrhage (aSAH) undergoing RIC by limb ischemia to compare changes in DNA methylation and transcriptome profiles before and after RIC. Methods Thirteen patients underwent 4 RIC sessions over 2–12 days after rupture of an intracranial aneurysm. We analyzed whole blood transcriptomes using RNA sequencing and genome-wide DNA methylomes using reduced representation bisulfite sequencing, both before and after RIC. We tested differential expression (DE) and differential methylation (DM) using an intra-individual paired study design, and then overlapped the DE and DM results for analyses of functional categories and protein-protein interactions. Results We observed 164 DE genes and 3,493 DM CpG sites after RIC, of which 204 CpG sites overlapped with 103 genes, enriched for pathways of cell cycle (P<3.8×10−4) and inflammatory responses (P<1.4×10−4). The cell cycle pathway genes form a significant protein-protein interaction network of tightly co-expressed genes (P<0.00001). Conclusions Gene expression and DNA methylation changes in aSAH patients undergoing RIC are involved in coordinated cell cycle and inflammatory responses.

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Exploring genome wide bisulfite sequencing for DNA methylation analysis in livestock: a technical assessment

Cited by 75 publications

References 25 publications

Genome-Wide DNA Methylation Patterns and Transcription Analysis in Sheep Muscle

Genome-Wide DNA Methylation Patterns and Transcription Analysis in Sheep Muscle

Genome-Wide Epigenetic Studies in Chicken: A Review

Remote Ischemic Conditioning Alters Methylation and Expression of Cell Cycle Genes in Aneurysmal Subarachnoid Hemorrhage

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