That PCK2 may be a key gene for tail fat deposition in Altay sheep under different energy intake
Ontology highlight
ABSTRACT:
ORGANISM(S): Ovis Aries
SUBMITTER: 
Shuzhen Song
PROVIDER: PXD078096 | iProX | Wed May 06 00:00:00 GMT+01:00 2026
REPOSITORIES: iProX
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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.
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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:Chinese indigenous sheep can be classified into two types according to their tail morphology: fat-rumped and thin-tailed sheep, of which the typical breeds are Altay sheep and Tibetan sheep, respectively. To identify the differentially expressed proteins (DEPs) underlying the phenotypic differences between tail types, we used iTRAQ combined with multi-dimensional liquid chromatography tandem mass spectrometry (LC-MS/MS) technology to detect candidate proteins. We then subjected these to a database search, and identified the DEPs. Finally, bioinformatics technology was used to carry out GO functional and KEGG pathway analyses. A total of 3248 proteins were identified, of which 44 were up-regulated and 40 were down-regulated DEPs. Analyzing their GO function terms and KEGG pathways revealed that the functions of these DEPs are mainly binding, catalytic activity, structural molecule activity, molecular function regulator, and transporter activity. Among the genes encoding the DEPs, APOA2, GALK1, ADIPOQ, and NDUFS4 are associated with fat formation and metabolism.
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Project description:Background: Genomic imprinting is an epigenetic phenomenon of differential allelic expression based on parental origin. To date a total of 255 imprinted genes have been identified or predicted among all investigated mammal species. However, only 21 have been described in sheep and 11 are annotated in current ovine genome. Results: Here we aim to use DNA/RNA throughput sequencing to identify monoallelically expressed and imprinted genes in organs of day 135 fetal sheep, and 2) to determine whether different levels of maternal energy intake (100% of NRC energy requirement or control, 140% or over-, and 60% or under-fed) influence genomic imprinting. We report strategies to solve technical challenges in the next-generation sequencing data analysis pipeline, including alignment bias of RNA sequencing reads and filtering potential false positives. We identified 80 monoallelically expressed and 18 putatively imprinted genes using the list of 255 stated above as a guide. Five (45.6% of 11) were already known imprinted genes in sheep, the other 13 were known imprinted in other mammals. Sanger sequencing confirmed four putative sheep imprinted genes INPP5F, PLAGL1, CASD1 and PPP1R9A. Among the 13 putative imprinted genes, five localized in the known sheep imprinting clusters of MEST domain on chromosome 4, DLK1/GTL2 domain on chromosome 18 and IGF2/H19 domain on chromosome 21, three were in a novel sheep imprinted cluster on chromosome 4 known in other species as PEG10/SGCE. Additionally, we found that the imprinted genes PHLDA2, SLC22A18, DIRAS3, and IGF2 were differentially expressed, albeit without allelic expression reversal, among the three maternal nutritional groups. Conclusions: Together, our results expanded the sheep imprinted gene list to 34 and demonstrated the influence of maternal diet on fetal imprinting under the conditions studied.
2018-08-29 | GSE111306 | GEO
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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:Body axis patterning in vertebrates is controlled by HOX genes during embryogenesis, with their expression gradients defining spatial identity along the anterior–posterior axis. While their developmental roles are well known, less is understood about their persistence and function in adult tissues. Tail length in sheep provides a model for studying the phenotypic effects of HOX gene variants. We used Improved Jezersko–Solčava sheep, which segregate for both tail length and HOXB13 promoter variants, to examine genotype–phenotype associations. The HOXB13 genotype was the main determinant of adult tail length, acting primarily by modulating caudal vertebral number. RNA‑seq and qPCR analyses revealed a clear anterior–posterior HOXB13 expression gradient in adult tail skin and bones, with stronger distal expression in short‑tailed animals. These results provide in vivo evidence that spatially patterned HOX gene expression persists in adulthood, suggesting that residual developmental programs may maintain regional identity in adult tissues.
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Project description:In this study, we selected differentially expressed miRNAs through construcing and analyzing the miRNA expression profile during 2-, 6-, and 12- month-old Small Tail Han Sheep ovaries, which provided a theoretical basis for the study of miRNAs regulating the reproduction of Small Tail Han Sheep. RNASeq techniques were used to perform profile analysis for these ovaries. The results showed that 11, 13 and 19 DE miRNAs were identified in 2- vs 6-, 6- vs 12-, and 2- vs 12-month-old ovaries, respectively. In total, 54, 37, and 198 predicted target genes of DE miRNAs were obtained from these three groups, respectively. GO and KEGG analyses showed that, in 2- vs 6-month-olds, the target genes of DE known sheep miRNAs were involved in 102 GO terms and 7 signaling pathways; in 6- vs 12-month-olds, the target genes of DE known sheep miRNAs were involved in 52 GO terms and 3 signaling pathways; and in 2- vs 12-month-olds, the target genes of DE known sheep miRNAs were involved in 88 GO terms and 6 signaling pathways. Three miR–target regulatory networks were constructed based on these DE miRNA–targets. 9 miRNAs were selected to validate the accuracy of miRNA sequencing data by qRT-PCR. The binding sites of oar-miR-432 with RPS6KA1 was validated by a dual luciferase reporter gene detection system. This is the first integrative analysis of miRNA and mRNA expression profiles in Small Tail Han Sheep ovarian development. These data help elucidate the molecular regulatory mechanisms in sheep ovarian development and identify the biomarkers that influence reproductive performance of Small Tail Han Sheep ewe.
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