Comparative microRNA Transcriptome in Domestic Goats Reveals Adaptation to High Altitude
Ontology highlight
ABSTRACT:
PROVIDER: PRJNA517133 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR8487380.fastq.gz | Fastqsanger.gz | |||
| SRR8487390.fastq.gz | Fastqsanger.gz | |||
| SRR8487400.fastq.gz | Fastqsanger.gz | |||
| SRR8487410.fastq.gz | Fastqsanger.gz | |||
| SRR8487381.fastq.gz | Fastqsanger.gz |
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Project description:High-altitude adaptation is a representative example of vertebrates getting adapted to harsh and extreme environments. To investigate the miRNA expression alterations of goats that were induced by high altitude stress, we performed comparative miRNA transcriptome analysis on six hypoxia-sensitive tissues (heart, kidney, liver, lung, skeletal muscle and spleen) in two indigenous goat populations from distinct altitudes (600 m and 3000 m). We obtained the expression of 1391 mature miRNAs and identified 138 differentially expressed miRNAs between altitudes. Combined with tissue specificity analysis, we illustrated alterations of expression levels between altitudes and among tissues, which suggested the coexisting tissue-specific and tissue-conserved mechanism for hypoxia adaptation. Notably, the interplay between DE miRNA and DE target genes strongly indicated post-transcriptional regulation in HIF-1 signaling pathway, insulin signaling pathway and p53 signaling pathway, which might play a significant role in high altitude adaptation in domestic goats. These results provide insights into the complicated miRNA expression pattern and regulatory mechanism of high altitude adaptation in domestic goats.
2020-07-23 | GSE125665 | GEO
Project description:Purpose: Domestic goats distributed in a wide range of habitats and have evolved genetic adaptations to their local environmental conditions. The goal of this study s to investigate the dramatic gene expression changes of goats that are shaped by high altitude adaptation. Methods: We performed RNA-seq on 27 samples from the three hypoxia-sensitive tissues (heart, lung and skeletal muscle) in three indigenous populations residing in distinct altitudes (600 m, 2,000 m and 3,000 m). Results: We identified numerous differentially expressed genes which exhibited distinct expression patterns, and nonsynonymous SNVs-containing genes which highly differentiated between the high- and low-altitude populations. Conclusions: These identified genes have known or potential roles in hypoxia response, and enriched in functional gene categories potentially responsible for high altitude adaptation, are appealing candidates for further investigation of the adaptive evolution in harsh high-altitude environment.
2017-09-06 | GSE66242 | GEO
Project description:Purpose: The goal of this study was to reveal epigenetic differences in the microRNA transcriptomes of two organs (heart and lung) between yak and cattle. Methods: Three unrelated 2-year old adult females for both of yaks and cattle (Luxi Huang cattle) were used in this study. Two of significant hypoxia-responsive tissues (heart and lung) were rapidly collected from each carcass, washed three times with physiological saline, immediately frozen in liquid nitrogen. All frozen samples were stored at –80 °C until RNA extraction.The total RNA were extracted with Trizol (Ambion, USA). NanoDrop ND-2000 spectrophotometer (Nano Drop, DE, USA) and Bioanalyzer 2100 (Agilent Technologies, Santa Clara, CA, USA) were used to monitor the concentration and integrity of RNA, respectively. In brief, several successive steps consist the Illumina sequencing. The small RNA with length of 14-40 nt were first purified by polyacrylamide gel electrophoresis (PAGE), and then specific adapters were ligated to the purified small RNA. The ligated RNA were reverse transcribed to cDNA libraries. Finally, each library were sequenced on Genome Analyzer. Results: We identified 808 widely-expressed conserved and 697 species-specific novel miRNAs in two species. In addition, although two organs showed similar high expression miRNAs, larger differentiation was present in lung than heart between two species. In addition, miRNAs with significantly differentiated patterns of expression in two organs exhibited obvious co-operation effect in high altitude adaptation in form of miRNA family and cluster. Functional analysis revealed that a large amount of differentially expressed miRNAs were enriched in hypoxia-related pathways, such as VEGF signaling pathway, HIF-1α signaling pathway, insulin signaling pathway, DNA damage response, apoptosis, fatty acid metabolism and glucose metabolism. These results suggested the diverse degrees of epigenetic variation in different tissues between yak and cattle, and revealed extensive roles of miRNAs in high altitude adaptation. Conclusions: In this study, we illustrated the differences in the microRNA transcriptomes level for heart and lung between yak and cattle, and suggested extensive roles of miRNAs in high altitude adaptation. The work performed here will provide a typical demonstration for future deciphering the mechanism of high altitude adaptation
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Project description:High-altitude acclimatization is a representative example of vertebrates' acclimatization to harsh and extreme environments. Previous studies reported sufficient evidence for a molecular genetic basis of high-altitude acclimatization, and genomic patterns of genetic variation among populations and species have been widely elucidated in recent years. However, understanding of the miRNA role in high-altitude acclimatization have lagged behind, especially in non-model species. To investigate miRNA expression alterations of goats that were induced by high-altitude stress, we performed comparative miRNA transcriptome analysis on six hypoxia-sensitive tissues (heart, kidney, liver, lung, skeletal muscle, and spleen) in two goat populations from distinct altitudes (600 and 3000 m). We obtained the expression value of 1391 mature miRNAs and identified 138 differentially expressed (DE) miRNAs between high and low altitudes. Combined with tissue specificity analysis, we illustrated alterations of expression levels among altitudes and tissues, and found that there were coexisting tissue-specific and -conserved mechanisms for hypoxia acclimatization. Notably, the interplay between DE miRNA and DE target genes strongly indicated post-transcriptional regulation in the hypoxia inducible factor 1, insulin, and p53 signaling pathways, which might play significant roles in high-altitude acclimatization in domestic goats. It's also worth noting that we experimentally confirmed miR-106a-5p to have a negative regulation effect on angiogenesis by directly targeting FLT-1. These results provide insight into the complicated miRNA expression patterns and regulatory mechanisms of high-altitude acclimatization in domestic goats.
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Project description:This study evaluates genetic and phenotypic variation in the high altitude Colla population living in the Argentinean Andes above 3500 m. They were compared to the Wichà population living in the nearby lowlands of the Gran Chaco region. This study attempts to pinpoint evolutionary mechanisms underlying adaptation to hypobaric hypoxia. We have genotyped 25 individuals from both populations for 730,525 SNPs. DNA from 25 saliva samples from Collas living >3500 m and 25 saliva samples from Wichà living <500 m from the Province of Salta in Argentina was genotyped
2014-02-20 | E-GEOD-55175 | biostudies-arrayexpress
Project description:Purpose: High-altitude adaptive evolution of transcription, and the convergence and divergence of transcriptional alteration across species in response to high-altitude environments, is an important topic of broad interest to the general biology community. Our study aims to answer this important biological question. Methods: We generated deep transcriptome data of high- and low- altitude populations across four species: chicken, pig, goat and sheep, as well as high-altitude yak and low-altitude cattle, from six tissues (heart, kidney, liver, lung, skeletal muscle and spleen). Results: Here we provide a comprehensive comparative transcriptome landscape of expression and alternative splicing variation between low- and high-altitude populations across multiple species for distinct tissues. Conclusions: Our data serves a valuable resource for further study on adaptive transcription evolution and identification of candidate adaptive genes.
2017-09-06 | GSE93855 | GEO
Project description:This study evaluates genetic and phenotypic variation in the high altitude Colla population living in the Argentinean Andes above 3500 m. They were compared to the Wichí population living in the nearby lowlands of the Gran Chaco region. This study attempts to pinpoint evolutionary mechanisms underlying adaptation to hypobaric hypoxia. We have genotyped 25 individuals from both populations for 730,525 SNPs.
2014-02-20 | GSE55175 | GEO
Project description:Comparative transcriptomic analysis provides insights into high-altitude adaptation
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Project description:<p>Due to a unique adaptation to high altitude, the Tibetan Plateau population has been the subject of much research interest. In this study, we conducted whole genome sequencing of 27 Tibetan individuals. Through our analysis, we inferred a detailed history of demography and revealed the natural selection of Tibetan population. We provided evidence of genetic separation between the two subpopulations of Han and Tibetans as early as 44 to 58 thousand years ago, replicated previously reported high altitude adaptation genes, including <i>EPAS1</i> and <i>EGLN1</i>, and reported three new candidate genes, including <i>PTGIS</i>, <i>VDR</i>, and <i>KCTD12</i>.</p>
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