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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

Plot of linear regression and correlation. Plot of linear regression and correlation of gene expression and deletion status of copy number variations (CNVs) in all four conditions (blood and skeletal muscle, before and after exercise) is shown. The position relationships between CNVs and linked genes are shown in (a). The ‘cover’ indicates that the genes cover CNV regions, ‘inside’ indicates that the genes are located in CNV regions, ‘front’ indicates that the genes span the front part of the CNV regions, and ‘rear’ indicates that the genes span the rear part of the CNV regions. The characters C, D, E, and F on the right side of the position relationships matches (c), (d), (e), and (f). To indicate each sampling condition of (c–f), a simple sampling condition diagram using the same color scheme is shown in (b) (red for blood and blue for muscle).
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f2-ajas-27-9-1345: Plot of linear regression and correlation. Plot of linear regression and correlation of gene expression and deletion status of copy number variations (CNVs) in all four conditions (blood and skeletal muscle, before and after exercise) is shown. The position relationships between CNVs and linked genes are shown in (a). The ‘cover’ indicates that the genes cover CNV regions, ‘inside’ indicates that the genes are located in CNV regions, ‘front’ indicates that the genes span the front part of the CNV regions, and ‘rear’ indicates that the genes span the rear part of the CNV regions. The characters C, D, E, and F on the right side of the position relationships matches (c), (d), (e), and (f). To indicate each sampling condition of (c–f), a simple sampling condition diagram using the same color scheme is shown in (b) (red for blood and blue for muscle).

Mentions: We identified 2,648 possible CNVs from 10,094 CNV candidates using GenomeSTRiP (Handsaker et al., 2011). We retained 1,246 CNVs of deletion calls after applying the genotype quality threshold for further analysis. These plausible CNVs of deletion polymorphisms were linked to the gene expression profiles of four Thoroughbred horses depending on their start-end position. There were four possible position classifications: ‘cover’ indicates that the genes cover CNV regions, ‘inside’ indicates that the genes are located in CNV regions, ‘front’ indicates that the genes span the front part of the CNV regions, and ‘rear’ indicates that the genes span the rear part of the CNV regions (Figure 2a). Genes not expressed in all four conditions (i.e., blood and skeletal muscle, before and after exercise) were removed from the expression profiles of the four Thoroughbred horses. Finally, we obtained a total of 252 pairs of CNVs and associated genes, including 229 pairs in the ‘cover’ group, 14 in the ‘inside’ group, 5 in the ‘front’ group, and 4 in the ‘rear’ group.


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)

Plot of linear regression and correlation. Plot of linear regression and correlation of gene expression and deletion status of copy number variations (CNVs) in all four conditions (blood and skeletal muscle, before and after exercise) is shown. The position relationships between CNVs and linked genes are shown in (a). The ‘cover’ indicates that the genes cover CNV regions, ‘inside’ indicates that the genes are located in CNV regions, ‘front’ indicates that the genes span the front part of the CNV regions, and ‘rear’ indicates that the genes span the rear part of the CNV regions. The characters C, D, E, and F on the right side of the position relationships matches (c), (d), (e), and (f). To indicate each sampling condition of (c–f), a simple sampling condition diagram using the same color scheme is shown in (b) (red for blood and blue for muscle).
© Copyright Policy
Related In: Results  -  Collection

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

f2-ajas-27-9-1345: Plot of linear regression and correlation. Plot of linear regression and correlation of gene expression and deletion status of copy number variations (CNVs) in all four conditions (blood and skeletal muscle, before and after exercise) is shown. The position relationships between CNVs and linked genes are shown in (a). The ‘cover’ indicates that the genes cover CNV regions, ‘inside’ indicates that the genes are located in CNV regions, ‘front’ indicates that the genes span the front part of the CNV regions, and ‘rear’ indicates that the genes span the rear part of the CNV regions. The characters C, D, E, and F on the right side of the position relationships matches (c), (d), (e), and (f). To indicate each sampling condition of (c–f), a simple sampling condition diagram using the same color scheme is shown in (b) (red for blood and blue for muscle).
Mentions: We identified 2,648 possible CNVs from 10,094 CNV candidates using GenomeSTRiP (Handsaker et al., 2011). We retained 1,246 CNVs of deletion calls after applying the genotype quality threshold for further analysis. These plausible CNVs of deletion polymorphisms were linked to the gene expression profiles of four Thoroughbred horses depending on their start-end position. There were four possible position classifications: ‘cover’ indicates that the genes cover CNV regions, ‘inside’ indicates that the genes are located in CNV regions, ‘front’ indicates that the genes span the front part of the CNV regions, and ‘rear’ indicates that the genes span the rear part of the CNV regions (Figure 2a). Genes not expressed in all four conditions (i.e., blood and skeletal muscle, before and after exercise) were removed from the expression profiles of the four Thoroughbred horses. Finally, we obtained a total of 252 pairs of CNVs and associated genes, including 229 pairs in the ‘cover’ group, 14 in the ‘inside’ group, 5 in the ‘front’ group, and 4 in the ‘rear’ group.

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