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Genome-wide analysis of DNA methylation patterns in horse.

Lee JR, Hong CP, Moon JW, Jung YD, Kim DS, Kim TH, Gim JA, Bae JH, Choi Y, Eo J, Kwon YJ, Song S, Ko J, Yang YM, Lee HK, Park KD, Ahn K, Do KT, Ha HS, Han K, Yi JM, Cha HJ, Cho BW, Bhak J, Kim HS - BMC Genomics (2014)

Bottom Line: The analysis of the DNA methylation patterns indicated that the average methylation density was the lowest in the promoter region, while the density in the coding DNA sequence region was the highest.Among repeat elements, a relatively high density of methylation was observed in long interspersed nuclear elements compared to short interspersed nuclear elements or long terminal repeat elements.We also successfully identified differential methylated regions through a comparative analysis of corresponding tissues from TH and JH, indicating that the gene body regions showed a high methylation density.

View Article: PubMed Central - PubMed

Affiliation: Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 609-735, Republic of Korea. jongbhak@genomics.org.

ABSTRACT

Background: DNA methylation is an epigenetic regulatory mechanism that plays an essential role in mediating biological processes and determining phenotypic plasticity in organisms. Although the horse reference genome and whole transcriptome data are publically available the global DNA methylation data are yet to be known.

Results: We report the first genome-wide DNA methylation characteristics data from skeletal muscle, heart, lung, and cerebrum tissues of thoroughbred (TH) and Jeju (JH) horses, an indigenous Korea breed, respectively by methyl-DNA immunoprecipitation sequencing. The analysis of the DNA methylation patterns indicated that the average methylation density was the lowest in the promoter region, while the density in the coding DNA sequence region was the highest. Among repeat elements, a relatively high density of methylation was observed in long interspersed nuclear elements compared to short interspersed nuclear elements or long terminal repeat elements. We also successfully identified differential methylated regions through a comparative analysis of corresponding tissues from TH and JH, indicating that the gene body regions showed a high methylation density.

Conclusions: We provide report the first DNA methylation landscape and differentially methylated genomic regions (DMRs) of thoroughbred and Jeju horses, providing comprehensive DMRs maps of the DNA methylome. These data are invaluable resource to better understanding of epigenetics in the horse providing information for the further biological function analyses.

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Genomic distribution of differentially methylated regions (DMRs) in the thoroughbred horse compared to the Jeju horse. (A) The number of hyper- and hypomethylated DMRs in 4 different tissues of thoroughbred horses. (B) Distribution of hyper- and hypomethylation density in different genomic regions such as intergenic, gene body, and promoter regions. (C) Hyper- and hypomethylation density in repeat regions, classified according to the family.
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Fig2: Genomic distribution of differentially methylated regions (DMRs) in the thoroughbred horse compared to the Jeju horse. (A) The number of hyper- and hypomethylated DMRs in 4 different tissues of thoroughbred horses. (B) Distribution of hyper- and hypomethylation density in different genomic regions such as intergenic, gene body, and promoter regions. (C) Hyper- and hypomethylation density in repeat regions, classified according to the family.

Mentions: We observed a total of 35,467 differentially methylated regions (DMRs) in the four different TH and JH tissues, indicating differences in their methylation profiles (Additional file 1: Table S2). The TH’s skeletal muscle was hypermethylated compared to that of JH, whereas the heart, lung, and cerebrum of TH showed a hypomethylated pattern compared to those of JH (Figure 2A). We also analyzed methylation events in the intergenic, gene body, and promoter regions in the four tissues of TH and JH. As shown in Figure 2B, the gene body region in the skeletal muscle of TH showed a relatively high level of methylation, whereas the gene body in the heart of TH showed a high hypomethylation pattern, compared to other tissues. We also examined DMRs within the repeat region, and found that SINE and LINE elements showed a high level of methylation in skeletal muscle compared to that of JH. The satellite regions indicated a high hypermethylation density in lung tissue compared to that of JH (Figure 2C). Here, based on our DMR data, we provide the DMRs associated with comprehensive maps of the DNA methylome of TH and JH (Figure 3).Figure 2


Genome-wide analysis of DNA methylation patterns in horse.

Lee JR, Hong CP, Moon JW, Jung YD, Kim DS, Kim TH, Gim JA, Bae JH, Choi Y, Eo J, Kwon YJ, Song S, Ko J, Yang YM, Lee HK, Park KD, Ahn K, Do KT, Ha HS, Han K, Yi JM, Cha HJ, Cho BW, Bhak J, Kim HS - BMC Genomics (2014)

Genomic distribution of differentially methylated regions (DMRs) in the thoroughbred horse compared to the Jeju horse. (A) The number of hyper- and hypomethylated DMRs in 4 different tissues of thoroughbred horses. (B) Distribution of hyper- and hypomethylation density in different genomic regions such as intergenic, gene body, and promoter regions. (C) Hyper- and hypomethylation density in repeat regions, classified according to the family.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4117963&req=5

Fig2: Genomic distribution of differentially methylated regions (DMRs) in the thoroughbred horse compared to the Jeju horse. (A) The number of hyper- and hypomethylated DMRs in 4 different tissues of thoroughbred horses. (B) Distribution of hyper- and hypomethylation density in different genomic regions such as intergenic, gene body, and promoter regions. (C) Hyper- and hypomethylation density in repeat regions, classified according to the family.
Mentions: We observed a total of 35,467 differentially methylated regions (DMRs) in the four different TH and JH tissues, indicating differences in their methylation profiles (Additional file 1: Table S2). The TH’s skeletal muscle was hypermethylated compared to that of JH, whereas the heart, lung, and cerebrum of TH showed a hypomethylated pattern compared to those of JH (Figure 2A). We also analyzed methylation events in the intergenic, gene body, and promoter regions in the four tissues of TH and JH. As shown in Figure 2B, the gene body region in the skeletal muscle of TH showed a relatively high level of methylation, whereas the gene body in the heart of TH showed a high hypomethylation pattern, compared to other tissues. We also examined DMRs within the repeat region, and found that SINE and LINE elements showed a high level of methylation in skeletal muscle compared to that of JH. The satellite regions indicated a high hypermethylation density in lung tissue compared to that of JH (Figure 2C). Here, based on our DMR data, we provide the DMRs associated with comprehensive maps of the DNA methylome of TH and JH (Figure 3).Figure 2

Bottom Line: The analysis of the DNA methylation patterns indicated that the average methylation density was the lowest in the promoter region, while the density in the coding DNA sequence region was the highest.Among repeat elements, a relatively high density of methylation was observed in long interspersed nuclear elements compared to short interspersed nuclear elements or long terminal repeat elements.We also successfully identified differential methylated regions through a comparative analysis of corresponding tissues from TH and JH, indicating that the gene body regions showed a high methylation density.

View Article: PubMed Central - PubMed

Affiliation: Department of Biological Sciences, College of Natural Sciences, Pusan National University, Busan 609-735, Republic of Korea. jongbhak@genomics.org.

ABSTRACT

Background: DNA methylation is an epigenetic regulatory mechanism that plays an essential role in mediating biological processes and determining phenotypic plasticity in organisms. Although the horse reference genome and whole transcriptome data are publically available the global DNA methylation data are yet to be known.

Results: We report the first genome-wide DNA methylation characteristics data from skeletal muscle, heart, lung, and cerebrum tissues of thoroughbred (TH) and Jeju (JH) horses, an indigenous Korea breed, respectively by methyl-DNA immunoprecipitation sequencing. The analysis of the DNA methylation patterns indicated that the average methylation density was the lowest in the promoter region, while the density in the coding DNA sequence region was the highest. Among repeat elements, a relatively high density of methylation was observed in long interspersed nuclear elements compared to short interspersed nuclear elements or long terminal repeat elements. We also successfully identified differential methylated regions through a comparative analysis of corresponding tissues from TH and JH, indicating that the gene body regions showed a high methylation density.

Conclusions: We provide report the first DNA methylation landscape and differentially methylated genomic regions (DMRs) of thoroughbred and Jeju horses, providing comprehensive DMRs maps of the DNA methylome. These data are invaluable resource to better understanding of epigenetics in the horse providing information for the further biological function analyses.

Show MeSH