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| Status |
Public on Nov 25, 2017 |
| Title |
Genome-wide profiling of gene expression and DNA methylation provides insight into low-altitude acclimation in Tibetan pigs [RNA-seq] |
| Organism |
Sus scrofa |
| Experiment type |
Expression profiling by high throughput sequencing
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| Summary |
To explore the exceptional mechanisms of gene expression and DNA methylation that are induced by low altitude environments in Tibetan pigs, we performed a comparative transcriptomic analysis of skeletal muscle in indigenous Tibetan pigs that reside in high altitude regions (～4,000 m) and their counterparts that migrated to the geographically neighboring low-altitude regions (～500 m) for nearly ten generations. We identified protein coding genes that related to hypoxia response (EGLN3 and FLT1), oxygen transport and energy metabolism (TFB2M), and two long non-coding RNAs (TCONS_00039686 and TCONS_00084992) that associated with the regulation of transcription and various nucleolus and organelle lumen, were differentially expressed between Tibetan pigs and their counterparts in low-altitude regions, thus might be the potential candidate regulators in skeletal muscle of low-altitude acclimation in Tibetan pigs. We also found genes embedded in differentially methylated regions between Tibetan pigs and their counterparts in low-altitude regions were mainly involved in ‘Starch and sucrose metabolism’, ‘glucuronosyltransferase activity’ processes, hypoxia and energy metabolism. We envision that this study will serve as a valuable resource for mammal acclimatization research and agricultural food industry.
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| Overall design |
A total of six healthy female Tibetan pigs were used in this study: three free-ranging individuals in Tibetan highland with the average altitude of 4,000 m (high-altitude); three counterparts under experimental conditions with normal daily feeding in geographically neighboring low-altitude regions (Chengdu plain) with average altitude of 500 m (low-altitude), these pigs were descendants of Tibetan pigs that have been raised in lowland for nearly ten generations.
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| Contributor(s) |
Jin L |
| Citation(s) |
29197588 |
| |
| Submission date |
Nov 25, 2016 |
| Last update date |
May 15, 2019 |
| Contact name |
jin long |
| E-mail(s) |
longjin8806@163.com
|
| Organization name |
Sichuan Agricultural University
|
| Street address |
Hui ming
|
| City |
Chengdu |
| ZIP/Postal code |
611130 |
| Country |
China |
| |
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| Platforms (1) |
| GPL11429 |
Illumina HiSeq 2000 (Sus scrofa) |
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| Samples (6)
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| This SubSeries is part of SuperSeries: |
| GSE90512 |
Genome-wide profiling of gene expression and DNA methylation provides insight into low-altitude acclimation in Tibetan pigs |
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| Relations |
| BioProject |
PRJNA354943 |
| SRA |
SRP093916 |
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