Comparative analysis on genome-wide DNA methylation in longissimus dorsi muscle between Small Tailed Han and Dorper×Small Tailed Han crossbred sheep
Objective The objective of this study was to compare the DNA methylation profile in the longissimus dorsi muscle between Small Tailed Han and Dorper×Small Tailed Han crossbred sheep which were known to exhibit significant difference in meat-production. Methods Six samples (three in each group) were...
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Asian-Australasian Association of Animal Production Societies
2017-11-01
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| Series: | Asian-Australasian Journal of Animal Sciences |
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| Online Access: | http://www.ajas.info/upload/pdf/ajas-30-11-1529.pdf |
| _version_ | 1828761121229635584 |
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| author | Yang Cao Hai-Guo Jin Hui-Hai Ma Zhi-Hui Zhao |
| author_facet | Yang Cao Hai-Guo Jin Hui-Hai Ma Zhi-Hui Zhao |
| author_sort | Yang Cao |
| collection | DOAJ |
| description | Objective The objective of this study was to compare the DNA methylation profile in the longissimus dorsi muscle between Small Tailed Han and Dorper×Small Tailed Han crossbred sheep which were known to exhibit significant difference in meat-production. Methods Six samples (three in each group) were subjected to the methylated DNA immunoprecipitation sequencing (MeDIP-seq) and subsequent bioinformatics analyses to detect differentially methylated regions (DMRs) between the two groups. Results 23.08 Gb clean data from six samples were generated and 808 DMRs were identified in gene body or their neighboring up/downstream regions. Compared with Small Tailed Han sheep, we observed a tendency toward a global loss of DNA methylation in these DMRs in the crossbred group. Gene ontology enrichment analysis found several gene sets which were hypo-methylated in gene-body region, including nucleoside binding, motor activity, phospholipid binding and cell junction. Numerous genes were found to be differentially methylated between the two groups with several genes significantly differentially methylated, including transforming growth factor beta 3 (TGFB3), acyl-CoA synthetase long chain family member 1 (ACSL1), ryanodine receptor 1 (RYR1), acyl-CoA oxidase 2 (ACOX2), peroxisome proliferator activated receptor-gamma2 (PPARG2), netrin 1 (NTN1), ras and rab interactor 2 (RIN2), microtubule associated protein RP/EB family member 1 (MAPRE1), ADAM metallopeptidase with thrombospondin type 1 motif 2 (ADAMTS2), myomesin 1 (MYOM1), zinc finger, DHHC type containing 13 (ZDHHC13), and SH3 and PX domains 2B (SH3PXD2B). The real-time quantitative polymerase chain reaction validation showed that the 12 genes are differentially expressed between the two groups. Conclusion In the current study, a tendency to a global loss of DNA methylation in these DMRs in the crossbred group was found. Twelve genes, TGFB3, ACSL1, RYR1, ACOX2, PPARG2, NTN1, RIN2, MAPRE1, ADAMTS2, MYOM1, ZDHHC13, and SH3PXD2B, were found to be differentially methylated between the two groups by gene ontology enrichment analysis. There are differences in the expression of 12 genes, of which ACSL1, RIN2, and ADAMTS2 have a negative correlation with methylation levels and the data suggest that DNA methylation levels in DMRs of the 3 genes may have an influence on the expression. These results will serve as a valuable resource for DNA methylation investigations on screening candidate genes which might be related to meat production in sheep. |
| first_indexed | 2024-12-11T01:24:51Z |
| format | Article |
| id | doaj.art-7996701acb4f42ea8c4d3ab22b99bb30 |
| institution | Directory Open Access Journal |
| issn | 1011-2367 1976-5517 |
| language | English |
| last_indexed | 2024-12-11T01:24:51Z |
| publishDate | 2017-11-01 |
| publisher | Asian-Australasian Association of Animal Production Societies |
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| series | Asian-Australasian Journal of Animal Sciences |
| spelling | doaj.art-7996701acb4f42ea8c4d3ab22b99bb302022-12-22T01:25:35ZengAsian-Australasian Association of Animal Production SocietiesAsian-Australasian Journal of Animal Sciences1011-23671976-55172017-11-0130111529153910.5713/ajas.17.015423792Comparative analysis on genome-wide DNA methylation in longissimus dorsi muscle between Small Tailed Han and Dorper×Small Tailed Han crossbred sheepYang Cao0Hai-Guo Jin1Hui-Hai Ma2Zhi-Hui Zhao3 College of Animal Science, Jilin University, Changchun 130012, China Branch of Animal Husbandry, Jilin Academy of Agricultural Sciences, Changchun 130033, China Branch of Animal Husbandry, Jilin Academy of Agricultural Sciences, Changchun 130033, China College of Animal Science, Jilin University, Changchun 130012, ChinaObjective The objective of this study was to compare the DNA methylation profile in the longissimus dorsi muscle between Small Tailed Han and Dorper×Small Tailed Han crossbred sheep which were known to exhibit significant difference in meat-production. Methods Six samples (three in each group) were subjected to the methylated DNA immunoprecipitation sequencing (MeDIP-seq) and subsequent bioinformatics analyses to detect differentially methylated regions (DMRs) between the two groups. Results 23.08 Gb clean data from six samples were generated and 808 DMRs were identified in gene body or their neighboring up/downstream regions. Compared with Small Tailed Han sheep, we observed a tendency toward a global loss of DNA methylation in these DMRs in the crossbred group. Gene ontology enrichment analysis found several gene sets which were hypo-methylated in gene-body region, including nucleoside binding, motor activity, phospholipid binding and cell junction. Numerous genes were found to be differentially methylated between the two groups with several genes significantly differentially methylated, including transforming growth factor beta 3 (TGFB3), acyl-CoA synthetase long chain family member 1 (ACSL1), ryanodine receptor 1 (RYR1), acyl-CoA oxidase 2 (ACOX2), peroxisome proliferator activated receptor-gamma2 (PPARG2), netrin 1 (NTN1), ras and rab interactor 2 (RIN2), microtubule associated protein RP/EB family member 1 (MAPRE1), ADAM metallopeptidase with thrombospondin type 1 motif 2 (ADAMTS2), myomesin 1 (MYOM1), zinc finger, DHHC type containing 13 (ZDHHC13), and SH3 and PX domains 2B (SH3PXD2B). The real-time quantitative polymerase chain reaction validation showed that the 12 genes are differentially expressed between the two groups. Conclusion In the current study, a tendency to a global loss of DNA methylation in these DMRs in the crossbred group was found. Twelve genes, TGFB3, ACSL1, RYR1, ACOX2, PPARG2, NTN1, RIN2, MAPRE1, ADAMTS2, MYOM1, ZDHHC13, and SH3PXD2B, were found to be differentially methylated between the two groups by gene ontology enrichment analysis. There are differences in the expression of 12 genes, of which ACSL1, RIN2, and ADAMTS2 have a negative correlation with methylation levels and the data suggest that DNA methylation levels in DMRs of the 3 genes may have an influence on the expression. These results will serve as a valuable resource for DNA methylation investigations on screening candidate genes which might be related to meat production in sheep.http://www.ajas.info/upload/pdf/ajas-30-11-1529.pdfDNA MethylationSmall Tailed Han SheepDorper×Small Tailed Han Crossbred SheepMethylated DNA Immunoprecipitation Sequencing (MeDIP-seq)Longissimus Dorsi Muscle |
| spellingShingle | Yang Cao Hai-Guo Jin Hui-Hai Ma Zhi-Hui Zhao Comparative analysis on genome-wide DNA methylation in longissimus dorsi muscle between Small Tailed Han and Dorper×Small Tailed Han crossbred sheep Asian-Australasian Journal of Animal Sciences DNA Methylation Small Tailed Han Sheep Dorper×Small Tailed Han Crossbred Sheep Methylated DNA Immunoprecipitation Sequencing (MeDIP-seq) Longissimus Dorsi Muscle |
| title | Comparative analysis on genome-wide DNA methylation in longissimus dorsi muscle between Small Tailed Han and Dorper×Small Tailed Han crossbred sheep |
| title_full | Comparative analysis on genome-wide DNA methylation in longissimus dorsi muscle between Small Tailed Han and Dorper×Small Tailed Han crossbred sheep |
| title_fullStr | Comparative analysis on genome-wide DNA methylation in longissimus dorsi muscle between Small Tailed Han and Dorper×Small Tailed Han crossbred sheep |
| title_full_unstemmed | Comparative analysis on genome-wide DNA methylation in longissimus dorsi muscle between Small Tailed Han and Dorper×Small Tailed Han crossbred sheep |
| title_short | Comparative analysis on genome-wide DNA methylation in longissimus dorsi muscle between Small Tailed Han and Dorper×Small Tailed Han crossbred sheep |
| title_sort | comparative analysis on genome wide dna methylation in longissimus dorsi muscle between small tailed han and dorper small tailed han crossbred sheep |
| topic | DNA Methylation Small Tailed Han Sheep Dorper×Small Tailed Han Crossbred Sheep Methylated DNA Immunoprecipitation Sequencing (MeDIP-seq) Longissimus Dorsi Muscle |
| url | http://www.ajas.info/upload/pdf/ajas-30-11-1529.pdf |
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