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Copy number deletion has little impact on gene expression levels in racehorses.

Park KD, Kim H, Hwang JY, Lee CK, Do KT, Kim HS, Yang YM, Kwon YJ, Kim J, Kim HJ, Song KD, Oh JD, Kim H, Cho BW, Cho S, Lee HK - Asian-australas. J. Anim. Sci. (2014)

Bottom Line: Indeed, it is widely accepted that CNVs are associated with differential disease susceptibility.We did not observe a clear and consistent relationship between the deletion status of CNVs and gene expression levels before and after exercise in blood and muscle.However, we found some pairs of CNVs and associated genes that indicated relationships with gene expression levels: a positive relationship with genes responsible for membrane structure or cytoskeleton and a negative relationship with genes involved in disease.

View Article: PubMed Central - PubMed

Affiliation: Genomic Informatics Center, Hankyong National University, Anseong 456-749, Korea.

ABSTRACT
Copy number variations (CNVs), important genetic factors for study of human diseases, may have as large of an effect on phenotype as do single nucleotide polymorphisms. Indeed, it is widely accepted that CNVs are associated with differential disease susceptibility. However, the relationships between CNVs and gene expression have not been characterized in the horse. In this study, we investigated the effects of copy number deletion in the blood and muscle transcriptomes of Thoroughbred racing horses. We identified a total of 1,246 CNVs of deletion polymorphisms using DNA re-sequencing data from 18 Thoroughbred racing horses. To discover the tendencies between CNV status and gene expression levels, we extracted CNVs of four Thoroughbred racing horses of which RNA sequencing was available. We found that 252 pairs of CNVs and genes were associated in the four horse samples. We did not observe a clear and consistent relationship between the deletion status of CNVs and gene expression levels before and after exercise in blood and muscle. However, we found some pairs of CNVs and associated genes that indicated relationships with gene expression levels: a positive relationship with genes responsible for membrane structure or cytoskeleton and a negative relationship with genes involved in disease. This study will lead to conceptual advances in understanding the relationship between CNVs and global gene expression in the horse.

No MeSH data available.


Related in: MedlinePlus

The skeletal Box and Whisker plots show the relationships between copy number variations (CNVs) and ‘cover’ position linked gene expression in blood and muscle before and after exercise of four Thoroughbred horses. The ‘cover’ means that the genes cover CNV regions. In each box plot, x-axis shows the deletion status of CNVs and y-axis shows the gene expression level (FPKM). The deletion status of CNVs are denoted by 0/0, 0/1, and 1/1. The 0/0 indicates that the individual or population is homozygous for the wild-type, and the 0/1 indicates that the individual or population is heterozygous for the CNV, and the 0/1 indicates that the individual or population is homozygous for the CNV. The sampling conditions in four horses are shown on the top of the figure, which are blood (red rectangles in the box plot) and muscle (blue rectangles in the box plot) before and after exercise. On the right side of the panel individual horse number was shown.
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f1-ajas-27-9-1345: The skeletal Box and Whisker plots show the relationships between copy number variations (CNVs) and ‘cover’ position linked gene expression in blood and muscle before and after exercise of four Thoroughbred horses. The ‘cover’ means that the genes cover CNV regions. In each box plot, x-axis shows the deletion status of CNVs and y-axis shows the gene expression level (FPKM). The deletion status of CNVs are denoted by 0/0, 0/1, and 1/1. The 0/0 indicates that the individual or population is homozygous for the wild-type, and the 0/1 indicates that the individual or population is heterozygous for the CNV, and the 0/1 indicates that the individual or population is homozygous for the CNV. The sampling conditions in four horses are shown on the top of the figure, which are blood (red rectangles in the box plot) and muscle (blue rectangles in the box plot) before and after exercise. On the right side of the panel individual horse number was shown.

Mentions: For each pair of CNVs and associated genes in the skeletal Box-and-Whisker plot was used to display the relationship between CNV status and its position-linked gene expression levels. Figure 1 and Supplementary Figure 2 to 4 depict the relationship between CNVs and gene expression in the ‘cover’, ‘inside’, ‘front’ and ‘rear’ groups. The deletion status of CNVs was denoted by 0/0 for no deletion at the population- or individual-based CNV region, 0/1 for one allele deletion at the CNV region, or 1/1 for two allele deletions at the CNV region. From the plots, we observed only a reduced gene expression pattern according to allele deletion in the blood of the ‘inside’ group. For the other groups, we observed no common tendency of positive or negative correlation patterns between the deletion status of CNVs and gene expression levels in blood and muscle before and after exercise.


Copy number deletion has little impact on gene expression levels in racehorses.

Park KD, Kim H, Hwang JY, Lee CK, Do KT, Kim HS, Yang YM, Kwon YJ, Kim J, Kim HJ, Song KD, Oh JD, Kim H, Cho BW, Cho S, Lee HK - Asian-australas. J. Anim. Sci. (2014)

The skeletal Box and Whisker plots show the relationships between copy number variations (CNVs) and ‘cover’ position linked gene expression in blood and muscle before and after exercise of four Thoroughbred horses. The ‘cover’ means that the genes cover CNV regions. In each box plot, x-axis shows the deletion status of CNVs and y-axis shows the gene expression level (FPKM). The deletion status of CNVs are denoted by 0/0, 0/1, and 1/1. The 0/0 indicates that the individual or population is homozygous for the wild-type, and the 0/1 indicates that the individual or population is heterozygous for the CNV, and the 0/1 indicates that the individual or population is homozygous for the CNV. The sampling conditions in four horses are shown on the top of the figure, which are blood (red rectangles in the box plot) and muscle (blue rectangles in the box plot) before and after exercise. On the right side of the panel individual horse number was shown.
© Copyright Policy
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC4150202&req=5

f1-ajas-27-9-1345: The skeletal Box and Whisker plots show the relationships between copy number variations (CNVs) and ‘cover’ position linked gene expression in blood and muscle before and after exercise of four Thoroughbred horses. The ‘cover’ means that the genes cover CNV regions. In each box plot, x-axis shows the deletion status of CNVs and y-axis shows the gene expression level (FPKM). The deletion status of CNVs are denoted by 0/0, 0/1, and 1/1. The 0/0 indicates that the individual or population is homozygous for the wild-type, and the 0/1 indicates that the individual or population is heterozygous for the CNV, and the 0/1 indicates that the individual or population is homozygous for the CNV. The sampling conditions in four horses are shown on the top of the figure, which are blood (red rectangles in the box plot) and muscle (blue rectangles in the box plot) before and after exercise. On the right side of the panel individual horse number was shown.
Mentions: For each pair of CNVs and associated genes in the skeletal Box-and-Whisker plot was used to display the relationship between CNV status and its position-linked gene expression levels. Figure 1 and Supplementary Figure 2 to 4 depict the relationship between CNVs and gene expression in the ‘cover’, ‘inside’, ‘front’ and ‘rear’ groups. The deletion status of CNVs was denoted by 0/0 for no deletion at the population- or individual-based CNV region, 0/1 for one allele deletion at the CNV region, or 1/1 for two allele deletions at the CNV region. From the plots, we observed only a reduced gene expression pattern according to allele deletion in the blood of the ‘inside’ group. For the other groups, we observed no common tendency of positive or negative correlation patterns between the deletion status of CNVs and gene expression levels in blood and muscle before and after exercise.

Bottom Line: Indeed, it is widely accepted that CNVs are associated with differential disease susceptibility.We did not observe a clear and consistent relationship between the deletion status of CNVs and gene expression levels before and after exercise in blood and muscle.However, we found some pairs of CNVs and associated genes that indicated relationships with gene expression levels: a positive relationship with genes responsible for membrane structure or cytoskeleton and a negative relationship with genes involved in disease.

View Article: PubMed Central - PubMed

Affiliation: Genomic Informatics Center, Hankyong National University, Anseong 456-749, Korea.

ABSTRACT
Copy number variations (CNVs), important genetic factors for study of human diseases, may have as large of an effect on phenotype as do single nucleotide polymorphisms. Indeed, it is widely accepted that CNVs are associated with differential disease susceptibility. However, the relationships between CNVs and gene expression have not been characterized in the horse. In this study, we investigated the effects of copy number deletion in the blood and muscle transcriptomes of Thoroughbred racing horses. We identified a total of 1,246 CNVs of deletion polymorphisms using DNA re-sequencing data from 18 Thoroughbred racing horses. To discover the tendencies between CNV status and gene expression levels, we extracted CNVs of four Thoroughbred racing horses of which RNA sequencing was available. We found that 252 pairs of CNVs and genes were associated in the four horse samples. We did not observe a clear and consistent relationship between the deletion status of CNVs and gene expression levels before and after exercise in blood and muscle. However, we found some pairs of CNVs and associated genes that indicated relationships with gene expression levels: a positive relationship with genes responsible for membrane structure or cytoskeleton and a negative relationship with genes involved in disease. This study will lead to conceptual advances in understanding the relationship between CNVs and global gene expression in the horse.

No MeSH data available.


Related in: MedlinePlus