Transcriptome sequencing unveils a novel mechanism underlying breed distinctions between thin- and fat-tailed sheep
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ABSTRACT:
PROVIDER: PRJNA1227916 | ENA |
REPOSITORIES: ENA
Dataset's files
| Action | DRS | |||
|---|---|---|---|---|
| SRR32480081.fastq.gz | Fastqsanger.gz | |||
| SRR32480082.fastq.gz | Fastqsanger.gz | |||
| SRR32480083.fastq.gz | Fastqsanger.gz | |||
| SRR32480084.fastq.gz | Fastqsanger.gz | |||
| SRR32480085.fastq.gz | Fastqsanger.gz |
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Project description:Tail fat in sheep (Ovis aries), has evolved mainly in response to cold weather for better energy storage. As things stand, too much tail fat in sheep can lead to a reduction in feed utilisation and is also unpopular with consumers due to the excessive fat content in the tail of sheep. Therefore, the need to find the mechanism of tail fat formation is obvious. In this study, we elected to utilise Kazakh sheep, prolific Suffolk sheep, and their hybrid F2 generation as research objects. Sheep transcriptome sequencing technology was employed to screen and explore target candidate genes related to sheep tail fat deposition. Comparison with RNA-seq data from fat-tailed and thin-tailed tissue, the LncRNA-mRNA-miRNA axis was identified as main functional pathway in the formation of fat in tail. Our results offer valuable insights into the fat deposition of sheep and provide a significant genomic resource for future genetic studies and the enhancement of genome-assisted breeding in sheep and other domestic animals.
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Project description:An essential tissue involved in the development and regulation of lipid metabolism in animals is adipose tissue. The “fat-tail” can supply energy for sheep during migration and winter when a low amount of dry matter intake is available. Tail fat content affects meat quality and varies significantly among the different breeds of sheep. Ghezel (fat-tailed) and Zel (thin-tailed) are two important local Iranian sheep breeds that show different patterns of fat storage. The current study presents the transcriptome characterization of tail fat using RNA-sequencing in order to get a better comprehension of the molecular mechanism of lipid storage in the two sheep breeds. The results of sequencing were analyzed with bioinformatics methods, including differentially expressed genes (DEGs) identification, functional enrichment analysis, structural classification of proteins, protein–protein interaction (PPI), network analysis and module analysis. The results revealed a total of332 DEGs between the Zel and Ghezel breed, with78 up-regulated and 254 down-regulated DEGs in the Zel breed. Identification of differential genes showed that some DEGs, such as IL-6, LIPG, SAA1, SOCS3 and HIF-1α, with the largest fold change had close association with lipid deposition. Also, important lipid storage genes such as FASN and SCPEP1 had high levels of expression. Furthermore, functional enrichment analysis revealed some pathways associated with fat deposition, such as “Fatty acid metabolism”, “Fatty acid biosynthesis” and“HIF-1 signaling pathway”. In addition, structural classification of proteins showed major DEGs in transcription factor classes such as JUNB, NR4A3, FOSL1, MAFF, NR4A1, CREB3L1 and ATF3 were up-regulated in the Zel breed. IL-6, JUNB, and related DEGs were up-regulated in the PPI network.HMGCS1, SUCLA2 and STT3B and related DEGs were down-regulated in the PPI network and had high topology scores as hub genes. This implies the DEGs of these modules are important candidate genes for tail fat metabolism and, therefore, can be further studied.
2023-01-01 | GSE143407 | GEO
Project description:Transcriptome comparison of adipose tissue in Iranian fat and thin-tailed sheep breeds using RNA-seq technique
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Project description:Ovis aries breed:Small-tailed Han sheep Raw sequence reads
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Project description:With climate change bound to affect food and feed production, emphasis will shift to resilient and adapted indigenous livestock to sustain animal production. However, indigenous livestock comprise several varieties, strains and ecotypes whose genomes are poorly characterized. Here, we investigated genomic variation in an African thin-tailed Desert Sheep sampled in Sudan, using 600K genotype data generated from 92 individuals representing five ecotypes. We included data from 18 fat-tailed and 45 thin-tailed sheep from China, to investigate shared ancestry and perform comparative genomic analysis. We observed a clear genomic differentiation between the African thin-tailed Desert Sheep and the Chinese thin-tailed and fat-tailed sheep, suggesting a broad genetic structure between the fat-tailed and thin-tailed sheep in general, and that at least two autosomal gene pools comprise the genome profile of the thin-tailed sheep. Further analysis detected two distinct genetic clusters in both the African thin-tailed Desert Sheep and the Chinese thin-tailed sheep, suggesting a fine-scale and complex genome architecture in thin-tailed sheep. Selection signature analysis suggested differences in adaptation, production, reproduction and morphology likely underly the fine-scale genetic structure in the African thin-tailed Desert Sheep. This may need to be considered in designing breeding programs and genome-wide association studies.
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Project description:Melanoma is the fifth-most common cancer diagnosed in the United States with a dramatic increase in incidence among both men and women. Most melanomas present as thin lesions (≤1.0mm) and have a good prognosis. However a small percentage of patients (5-10%) with thin lesions recur or metastasize. The aim of our study was to elucidate which thin melanomas (< 1.0 mm thickness) have the propensity to metastasize to regional lymph nodes or distant sites. Our focus was analyzing gene expression as a whole. We sought to identify a distinct pattern of gene expression within thin melanomas that were known to have eventually metastasized to regional lymph nodes or distant sites, from those that followed the typical course with good response to wide local excision alone. While gene expression differences were observed between nine thin melanoma patients with poor clinical outcome compared to ten patients with a good clinical outcome, neither the number of genes nor the magnitude of the fold difference was very substantial or significant. Although cluster analysis was able to use this subset of genes to definitively separate a subset of the poor responders from the good responders, there remained a mixed group of tumors which could not be predicted from gene expression alone. Pathway analysis did identify cellular processes that were regulated based upon response, including categories commonly associated with melanoma progression The goal of this pilot study was to identify gene expression changes within the tumor cells of thin melanomas that have a poor outcome that would discriminate them from thin melanomas that do not recur or metastasize . Our results conclude that there were very few differences between these groups. Future research will be required and investigation of the mutational landscape of these different tumor sub-types may be another strategy to uncover genomic changes that drive recurrence and metastasis.
2017-01-15 | GSE79662 | GEO
Project description:Significant efforts have been made to understand how fat deposition in sheep tail is regulated in genetic, transcriptomic, physiologic, biochemical, and metabolic levels in order to elucidate the complex mechanisms underlying the energy storage, lipid metabolism in adipose tissue, adaptability to harsh environments, and evolutionary domestication. Through RNA-seq data analysis, we are able to compare the gene expression of fat-tailed sheep versus thin-tailed sheep breeds in an acceptable resolution at transcriptome level. The purpose of this study was to compare the transcriptomes of Ghezel (fat-tailed) and Zel (thin-tailed) sheep. Total RNA from subcutaneous and tail tissue samples from healthy lambs was sequenced (150b PE) to identify differentially expressed genes (DEGs) between the two mentioned tissues and between the Ghezel and Zel sheep breeds. Further downstream pathway and network analyses were conducted afterwards. The results uncovered the association of the most important DEGs such as CAV1, ALB, and SOCS3 with cellular signaling pathways of lipids metabolism. It seems that the SOCS3 gene plays an important role in the differential deposition of lipid in the tails of two phenotypically different sheep breeds. Although the detail of gene expression in the tail and subcutaneous tissues of two morphologically different breeds was decoded here, to fully understand how differential expression of the SOCS3 gene affects the fat synthesis, further studies are needed.
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Project description:In the ribosome-associated quality control acting on nuclear-encoded mitochondrial proteins (mitoRQC), Vms1 protects mitochondria from toxic effects of Rqc2-generated C-terminal alanyl and threonyl (CAT) tailed proteins that escaped proteosomal degradation facilitated by E3 ubiquitin ligase Ltn1. Here, we performed a genome-wide screen in yeast to identify novel proteins involved in mitoRQC. We found that Pth2, a peptidyl-tRNA hydrolase in the outer mitochondrial membrane, influences aggregation of mitochondrial-targeted CAT-tailed proteins without majorly affecting the CAT-tailing process itself. Peptidyl-tRNA hydrolase activity is essential during this process, however, the activity of Pth2 can be substituted by another peptidyl-tRNA hydrolase, upon proper localization. Our data suggest that Pth2 acts through modulating protein import into mitochondria, enabling CAT-tailed proteins to get access to the cytosolic chaperones and thus relieving the mitochondrial proteostasis network. Other hits obtained in the screen show that, in general, slowing down protein translocation protects mitochondria against toxic CAT-tailed proteins.
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