Exploring genome wide bisulfite sequencing for DNA methylation analysis in livestock: A technical assessment
Recent advances made in omics technologies are contributing to a revolution in livestock selection and breeding practices. Epigenetic mechanisms, including DNA methylation are important determinants for the control of gene expression in mammals. DNA methylation research will help our understanding o...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2014-05-01
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| Series: | Frontiers in Genetics |
| Subjects: | |
| Online Access: | http://journal.frontiersin.org/Journal/10.3389/fgene.2014.00126/full |
| _version_ | 1829481473213726720 |
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| author | Rachael eDoherty Christine eCouldrey |
| author_facet | Rachael eDoherty Christine eCouldrey |
| author_sort | Rachael eDoherty |
| collection | DOAJ |
| description | Recent advances made in omics technologies are contributing to a revolution in livestock selection and breeding practices. Epigenetic mechanisms, including DNA methylation are important determinants for the control of gene expression in mammals. DNA methylation research will help our understanding of how environmental factors contribute to phenotypic variation of complex production and health traits. High-throughput sequencing is a vital tool for the comprehensive analysis of DNA methylation, and bisulfite-based strategies coupled with DNA sequencing allows for quantitative, site-specific methylation analysis at the genome level or genome wide. Reduced representation bisulfite sequencing (RRBS) and more recently whole genome bisulfite sequencing (WGBS) have proven to be effective techniques for studying DNA methylation in both humans and mice. Here we report the development of RRBS and WGBS for use in sheep, the first application of this technology in livestock species. Important technical issues associated with these methodologies including fragment size selection and sequence depth are examined and discussed. |
| first_indexed | 2024-12-14T21:28:17Z |
| format | Article |
| id | doaj.art-57210212d16647e9a1089aab1eb79fac |
| institution | Directory Open Access Journal |
| issn | 1664-8021 |
| language | English |
| last_indexed | 2024-12-14T21:28:17Z |
| publishDate | 2014-05-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Genetics |
| spelling | doaj.art-57210212d16647e9a1089aab1eb79fac2022-12-21T22:46:44ZengFrontiers Media S.A.Frontiers in Genetics1664-80212014-05-01510.3389/fgene.2014.0012687786Exploring genome wide bisulfite sequencing for DNA methylation analysis in livestock: A technical assessmentRachael eDoherty0Christine eCouldrey1TeagascAgResearchRecent advances made in omics technologies are contributing to a revolution in livestock selection and breeding practices. Epigenetic mechanisms, including DNA methylation are important determinants for the control of gene expression in mammals. DNA methylation research will help our understanding of how environmental factors contribute to phenotypic variation of complex production and health traits. High-throughput sequencing is a vital tool for the comprehensive analysis of DNA methylation, and bisulfite-based strategies coupled with DNA sequencing allows for quantitative, site-specific methylation analysis at the genome level or genome wide. Reduced representation bisulfite sequencing (RRBS) and more recently whole genome bisulfite sequencing (WGBS) have proven to be effective techniques for studying DNA methylation in both humans and mice. Here we report the development of RRBS and WGBS for use in sheep, the first application of this technology in livestock species. Important technical issues associated with these methodologies including fragment size selection and sequence depth are examined and discussed.http://journal.frontiersin.org/Journal/10.3389/fgene.2014.00126/fullDNA MethylationSheepepigeneticsquantificationRRBSWGBS |
| spellingShingle | Rachael eDoherty Christine eCouldrey Exploring genome wide bisulfite sequencing for DNA methylation analysis in livestock: A technical assessment Frontiers in Genetics DNA Methylation Sheep epigenetics quantification RRBS WGBS |
| title | Exploring genome wide bisulfite sequencing for DNA methylation analysis in livestock: A technical assessment |
| title_full | Exploring genome wide bisulfite sequencing for DNA methylation analysis in livestock: A technical assessment |
| title_fullStr | Exploring genome wide bisulfite sequencing for DNA methylation analysis in livestock: A technical assessment |
| title_full_unstemmed | Exploring genome wide bisulfite sequencing for DNA methylation analysis in livestock: A technical assessment |
| title_short | Exploring genome wide bisulfite sequencing for DNA methylation analysis in livestock: A technical assessment |
| title_sort | exploring genome wide bisulfite sequencing for dna methylation analysis in livestock a technical assessment |
| topic | DNA Methylation Sheep epigenetics quantification RRBS WGBS |
| url | http://journal.frontiersin.org/Journal/10.3389/fgene.2014.00126/full |
| work_keys_str_mv | AT rachaeledoherty exploringgenomewidebisulfitesequencingfordnamethylationanalysisinlivestockatechnicalassessment AT christineecouldrey exploringgenomewidebisulfitesequencingfordnamethylationanalysisinlivestockatechnicalassessment |