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Genome-wide profiling of gene expression and DNA methylation provides insight into low-altitude acclimation in Tibetan pigs

ABSTRACT: Genome-wide profiling of gene expression and DNA methylation provides insight into low-altitude acclimation in Tibetan pigs

PROVIDER: PRJNA354939 | ENA |

REPOSITORIES: ENA

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			Action	DRS
	SRR5054330_1.fastq.gz	Fastqsanger.gz
	SRR5054330_2.fastq.gz	Fastqsanger.gz
	SRR5054331_1.fastq.gz	Fastqsanger.gz
	SRR5054331_2.fastq.gz	Fastqsanger.gz
	SRR5054332_1.fastq.gz	Fastqsanger.gz

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Genome-wide profiling of gene expression and DNA methylation provides insight into low-altitude acclimation in Tibetan pigs [RNA-seq]

Project description: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.

2017-11-25 | GSE90511 | GEO

Genome-wide profiling of gene expression and DNA methylation provides insight into low-altitude acclimation in Tibetan pigs [DNA methylation]

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Gene Co-Expression Network Analysis Unraveling Transcriptional Regulation of High-altitude Adaptation of Tibetan Pigs

Project description:To elucidate further molecular mechanisms underlying the regulation of hypoxia-adaptive phenotypes in Tibetan pigs, we used transcriptome microarrays from lung tissues of Tibetan pigs and Duroc pigs both at high and low altitude analyzed differentially expressed genes (DEGs), biological pathway and constructed co-expression regulation network. A total of 3,068 DEGs were identified which involved metabolic process, cellular process, immune biological process and angiogenesis pathway. The regulatory (RIF) and phenotypic (PIF) impact factors analysis identified several known and potentially regulators of hypoxia adaption, including IKBKG, KLF6 and RBPJ (RIF1), SF3B1, EFEMP1, HOXB6 and ATF6 (RIF2).

2016-07-15 | GSE84409 | GEO

Genome-wide profiling of gene expression and DNA methylation provides insight into low-altitude acclimation in Tibetan pigs

Project description:This SuperSeries is composed of the SubSeries listed below.

2017-11-25 | GSE90512 | GEO

Affymetrix SNP array data for 31 Tibetan samples

Project description:This data was used to identify regions of the genome that have undergone positive selection in a high-altitude Tibetan population. Affymetrix SNP arrays were used to genotype DNA extracted from blood samples. This data was used to perform genome-wide scans of positive selection in a native high-altitude Tibetan population.

2010-07-22 | E-GEOD-21661 | biostudies-arrayexpress

Gene expression in Placental Tissue from high altitude European and Tibetan women

Project description:We used in silico analyses to identify the distinct transcriptome signatures of two populations living at high altitudes and identified potential mechanisms that underlie high-altitude adaptation. Data generated in this study indicate that placentas from Tibetan women are genetically distinct from European women at high altitudes, and appear to be protected from hypoxia and stress.

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miRNA expression in Placental Tissue from high altitude European and Tibetan women

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Project description:Long term-exposed to high altitude, the increased numbers of red blood cells tend to stabilize to a certain extend in most people, but someone will occur over-increasing in number of red blood cells, which cause a serious of clinical symptoms and signs, and this is high altitude polycythemia. EPO-EPOR system may be the main reasons for erythroid progenitor cell proliferation and differentiation in early exposion to plateau, but, in the late, there may be other factors involved in the regulation of erythropoiesis in bone marrow, multiple factors working together lead to excessive red blood cell proliferation. We compared gene expression profiling of leukocytes in peripheral blood from high altitude polycythemia patients with those from matched controls. Subjects consisting of 5 masculine Han Chinese patients with HAPC (diagnosed according to international consensus statement on HAPC) and 5 matched controls, were migrants at River of TUOTUO area (Qinghai-Tibetan Plateau, 4550 m). Each of the five HAPC patients was matched to each of the control: gender, nationality, birthplace, duration migrating to plateau, height of location, work intensity. Peripheral blood samples were obtained at 4550m plateau from above subjects. Total RNA was extracted from peripheral blood leucocytes. The gene expression profilings were analysed by Human Genome U133 Plus 2.0 Array.

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Comparative transcriptomic and proteomic analysis provides insight into the key genes involved in high-altitude adaptation in Tibetan pig (RNA-seq)

Project description:In this study, RNA-seq technique was used to identify differentially expressed genes (DEGs) in cardiac muscle of the Tibetan pigs raised at highland (TH), Tibetan pigs raised at lowland (TL), Yorkshire pigs raised at highland (YH) and Yorkshire raised at lowland (YL). We obtained 551M clean reads and detected 18585 genes that were expressed in the eight heart samples. According to a standard of fold-change (FC>2 or FC <0.5) and difference significant (P<0.05), obtained 299, 169, 242 and 368 of significantly differentially expressed genes (DEGs) respectively in TH vs.YH, TH vs.TL, TL vs.YL and YH vs.YL. GO and pathways analysis for DEGs results showed enrichment in HIF-1 signaling pathway, and hypertrophic cardiomyopathy (Hypertrophic cardiomyopathy (HCM), cardiovascular development, immunity, DNA damage and other biological functions. Eight DEGs were randomly selected to validate the veracity of RNA-seq and using real-time PCR. The results showed that the expression corresponds to the trend in RNA-seq, hence the deep-sequencing methods were feasible and efficient. This study expanded the number of hypoxic-adaptation-related genes in pig and indicated that the expression patterns of hypoxia-related genes are significantly altered in the Tibetan pig. DEGs may play important roles in hypoxic adaptation after migration to hypoxic environments.

2016-12-29 | GSE92981 | GEO

Tibetan Population History and High Altitude Adaptation Study

Project description: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 EPAS1 and EGLN1, and reported three new candidate genes, including PTGIS, VDR, and KCTD12.

| phs001338 | dbGaP

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