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Whole transcriptome analyses of six thoroughbred horses before and after exercise using RNA-Seq.

Park KD, Park J, Ko J, Kim BC, Kim HS, Ahn K, Do KT, Choi H, Kim HM, Song S, Lee S, Jho S, Kong HS, Yang YM, Jhun BH, Kim C, Kim TH, Hwang S, Bhak J, Lee HK, Cho BW - BMC Genomics (2012)

Bottom Line: More than 60% (20,428) of the unigene clusters did not match any current equine gene model.Most SNVs (171,558 SNVs; 90.31%) were novel when compared with over 1.1 million equine SNPs from two SNP databases.In addition, we found interesting RNA expression patterns where different alternative splicing forms of the same gene showed reversed expressions before and after exercising.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biotechnology, Hankyong National University, Anseong, Republic of Korea.

ABSTRACT

Background: Thoroughbred horses are the most expensive domestic animals, and their running ability and knowledge about their muscle-related diseases are important in animal genetics. While the horse reference genome is available, there has been no large-scale functional annotation of the genome using expressed genes derived from transcriptomes.

Results: We present a large-scale analysis of whole transcriptome data. We sequenced the whole mRNA from the blood and muscle tissues of six thoroughbred horses before and after exercise. By comparing current genome annotations, we identified 32,361 unigene clusters spanning 51.83 Mb that contained 11,933 (36.87%) annotated genes. More than 60% (20,428) of the unigene clusters did not match any current equine gene model. We also identified 189,973 single nucleotide variations (SNVs) from the sequences aligned against the horse reference genome. Most SNVs (171,558 SNVs; 90.31%) were novel when compared with over 1.1 million equine SNPs from two SNP databases. Using differential expression analysis, we further identified a number of exercise-regulated genes: 62 up-regulated and 80 down-regulated genes in the blood, and 878 up-regulated and 285 down-regulated genes in the muscle. Six of 28 previously-known exercise-related genes were over-expressed in the muscle after exercise. Among the differentially expressed genes, there were 91 transcription factor-encoding genes, which included 56 functionally unknown transcription factor candidates that are probably associated with an early regulatory exercise mechanism. In addition, we found interesting RNA expression patterns where different alternative splicing forms of the same gene showed reversed expressions before and after exercising.

Conclusion: The first sequencing-based horse transcriptome data, extensive analyses results, deferentially expressed genes before and after exercise, and candidate genes that are related to the exercise are provided in this study.

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Switching expressions of alternatively spliced forms before and after exercise. (A) Red bars are the exons of the two transcripts of the DYNC1 gene: ENSECAT00000021919 and ENSECAT00000021863. (B) Each plot shows the gene expression level (FPKM value; fragments per kilobase of exon per million fragments mapped) of the two transcripts (Blue lines represent the ENSECAT00000021919 transcript and red lines represent the ENSECAT00000021863 transcript) in each individual horse, whose name is shown as the plot title. Percentages inside the plots are the coverages of the transcripts.
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Figure 2: Switching expressions of alternatively spliced forms before and after exercise. (A) Red bars are the exons of the two transcripts of the DYNC1 gene: ENSECAT00000021919 and ENSECAT00000021863. (B) Each plot shows the gene expression level (FPKM value; fragments per kilobase of exon per million fragments mapped) of the two transcripts (Blue lines represent the ENSECAT00000021919 transcript and red lines represent the ENSECAT00000021863 transcript) in each individual horse, whose name is shown as the plot title. Percentages inside the plots are the coverages of the transcripts.

Mentions: Four genes (three from muscle, one from blood) showed interesting RNA expression patterns, in which two different alternative splicing forms of the same gene showed reversed expression patterns before and after exercising, similar to that of the SXL gene in Drosophila[45]. This observation suggested a cost-effective method of regulation: the cells do not have to produce completely new exons and proteins, but merely change the composition of the existing exons[46]. The genes with reversed expression are: AXL, DYNC1, PLEKHG1, and COBLL1 (Additional file1: Table S22 and Additional file1: Figure S11). Figure 2 shows cytoplasmic dynein intermediate chain (ENSECAG00000020218) protein (DYNC1)[47] as an example of the reversed expression pattern in muscle before and after exercising.


Whole transcriptome analyses of six thoroughbred horses before and after exercise using RNA-Seq.

Park KD, Park J, Ko J, Kim BC, Kim HS, Ahn K, Do KT, Choi H, Kim HM, Song S, Lee S, Jho S, Kong HS, Yang YM, Jhun BH, Kim C, Kim TH, Hwang S, Bhak J, Lee HK, Cho BW - BMC Genomics (2012)

Switching expressions of alternatively spliced forms before and after exercise. (A) Red bars are the exons of the two transcripts of the DYNC1 gene: ENSECAT00000021919 and ENSECAT00000021863. (B) Each plot shows the gene expression level (FPKM value; fragments per kilobase of exon per million fragments mapped) of the two transcripts (Blue lines represent the ENSECAT00000021919 transcript and red lines represent the ENSECAT00000021863 transcript) in each individual horse, whose name is shown as the plot title. Percentages inside the plots are the coverages of the transcripts.
© Copyright Policy - open-access
Related In: Results  -  Collection

License
Show All Figures
getmorefigures.php?uid=PMC3472166&req=5

Figure 2: Switching expressions of alternatively spliced forms before and after exercise. (A) Red bars are the exons of the two transcripts of the DYNC1 gene: ENSECAT00000021919 and ENSECAT00000021863. (B) Each plot shows the gene expression level (FPKM value; fragments per kilobase of exon per million fragments mapped) of the two transcripts (Blue lines represent the ENSECAT00000021919 transcript and red lines represent the ENSECAT00000021863 transcript) in each individual horse, whose name is shown as the plot title. Percentages inside the plots are the coverages of the transcripts.
Mentions: Four genes (three from muscle, one from blood) showed interesting RNA expression patterns, in which two different alternative splicing forms of the same gene showed reversed expression patterns before and after exercising, similar to that of the SXL gene in Drosophila[45]. This observation suggested a cost-effective method of regulation: the cells do not have to produce completely new exons and proteins, but merely change the composition of the existing exons[46]. The genes with reversed expression are: AXL, DYNC1, PLEKHG1, and COBLL1 (Additional file1: Table S22 and Additional file1: Figure S11). Figure 2 shows cytoplasmic dynein intermediate chain (ENSECAG00000020218) protein (DYNC1)[47] as an example of the reversed expression pattern in muscle before and after exercising.

Bottom Line: More than 60% (20,428) of the unigene clusters did not match any current equine gene model.Most SNVs (171,558 SNVs; 90.31%) were novel when compared with over 1.1 million equine SNPs from two SNP databases.In addition, we found interesting RNA expression patterns where different alternative splicing forms of the same gene showed reversed expressions before and after exercising.

View Article: PubMed Central - HTML - PubMed

Affiliation: Department of Biotechnology, Hankyong National University, Anseong, Republic of Korea.

ABSTRACT

Background: Thoroughbred horses are the most expensive domestic animals, and their running ability and knowledge about their muscle-related diseases are important in animal genetics. While the horse reference genome is available, there has been no large-scale functional annotation of the genome using expressed genes derived from transcriptomes.

Results: We present a large-scale analysis of whole transcriptome data. We sequenced the whole mRNA from the blood and muscle tissues of six thoroughbred horses before and after exercise. By comparing current genome annotations, we identified 32,361 unigene clusters spanning 51.83 Mb that contained 11,933 (36.87%) annotated genes. More than 60% (20,428) of the unigene clusters did not match any current equine gene model. We also identified 189,973 single nucleotide variations (SNVs) from the sequences aligned against the horse reference genome. Most SNVs (171,558 SNVs; 90.31%) were novel when compared with over 1.1 million equine SNPs from two SNP databases. Using differential expression analysis, we further identified a number of exercise-regulated genes: 62 up-regulated and 80 down-regulated genes in the blood, and 878 up-regulated and 285 down-regulated genes in the muscle. Six of 28 previously-known exercise-related genes were over-expressed in the muscle after exercise. Among the differentially expressed genes, there were 91 transcription factor-encoding genes, which included 56 functionally unknown transcription factor candidates that are probably associated with an early regulatory exercise mechanism. In addition, we found interesting RNA expression patterns where different alternative splicing forms of the same gene showed reversed expressions before and after exercising.

Conclusion: The first sequencing-based horse transcriptome data, extensive analyses results, deferentially expressed genes before and after exercise, and candidate genes that are related to the exercise are provided in this study.

Show MeSH