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Bakhtiarizadeh MR. Deciphering the role of alternative splicing as a potential regulator in fat-tail development of sheep: a comprehensive RNA-seq based study. Sci Rep 2024; 14:2361. [PMID: 38287039 PMCID: PMC10825154 DOI: 10.1038/s41598-024-52855-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Accepted: 01/24/2024] [Indexed: 01/31/2024] Open
Abstract
Although research on alternative splicing (AS) has been widely conducted in mammals, no study has investigated the splicing profiles of genes involved in fat-tail formation in sheep. Here, for the first time, a comprehensive study was designed to investigate the profile of AS events and their involvement in fat-tail development of sheep. In total, 45 RNA-Seq samples related to seven different studies, which have compared the fat-tailed vs thin-tailed sheep breeds, were analyzed. Two independent tools, rMATS and Whippet, along with a set of stringent filters were applied to identify differential AS (DAS) events between the breeds per each study. Only DAS events that were detected by both tools as well as in at least three datasets with the same ΔPSI trend (percent spliced in), were considered as the final high-confidence set of DAS genes. Final results revealed 130 DAS skipped exon events (69 negative and 61 positive ΔPSI) belonged to 124 genes. Functional enrichment analysis highlighted the importance of the genes in the underlying molecular mechanisms of fat metabolism. Moreover, protein-protein interaction network analysis revealed that DAS genes are significantly connected. Of DAS genes, five transcription factors were found that were enriched in the biological process associated with lipid metabolism like "Fat Cell Differentiation". Further investigations of the findings along with a comprehensive literature review provided a reliable list of candidate genes that may potentially contribute to fat-tail formation including HSD11B1, SIRT2, STRN3 and TCF7L2. Based on the results, it can be stated that the AS patterns may have evolved, during the evolution of sheep breeds, as another layer of regulation to contribute to biological complexity by reprogramming the gene regulatory networks. This study provided the theoretical basis of the molecular mechanisms behind the sheep fat-tail development in terms of AS.
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Berenjian A, Bakhtiarizadeh MR, Mohammadi-Sangcheshmeh A, Sharifi SD. A nutrigenomics approach to study the effects of ω-3 fatty acids in laying hens under physiological stress. Front Physiol 2023; 14:1198247. [PMID: 37560158 PMCID: PMC10407228 DOI: 10.3389/fphys.2023.1198247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2023] [Accepted: 07/11/2023] [Indexed: 08/11/2023] Open
Abstract
Supplement of ω-3 fatty acids can decrease the harmful effects of stress. However, the potential molecular mechanisms that are modulated by dietary ω-3 fatty acids in laying hens under stress remain unknown. Hence, RNA-sequencing (RNA-Seq) technology was used to gain new insights into different gene expression profiles and potential pathways involved in response to stress in the liver of 35-week-old Lohmann LSL-Lite laying hens supplemented with ω-3. Three groups including control (non-stress), stress, and stress_ω-3 fatty acids (three layers per each group) were applied. A total of 1,321 genes were detected as differentially expressed genes of which 701, 1,049, and 86 DEGs belonged to stress vs. control, stress_ω-3 vs. control, and stress vs. stress_ω-3 pairwise comparisons, respectively. Gene ontology and KEGG pathway analysis indicated that the DEGs were enriched in particular regulation of steroid and cholesterol biosynthetic process, fatty acid degradation, AMPK signaling pathway, fatty acid biosynthesis, and immune response. Our data represented a promising approach regarding the importance of ω-3 as anxiolytic and anti-stress. In this context, UNC13B and ADRA1B genes were downregulated in the stress_ω-3 group compared to the stress group, which are associated with decreased activity of glutamatergic stimulatory neurons and probably play important role in facilitating the response to stress. This study extends the current understanding of the liver transcriptome response to physiological stress, and provides new insights into the molecular responses to stress in laying hens fed a diet supplemented with ω-3 fatty acids.
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Affiliation(s)
| | | | | | - Seyed Davood Sharifi
- Department of Animal and Poultry Science, Faculty of Agricultural Technology, College of Agriculture and Natural Resources, University of Tehran, Tehran, Iran
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Chen M, Lian D, Li Y, Zhao Y, Xu X, Liu Z, Zhang J, Zhang X, Wu S, Qi S, Deng S, Yu K, Lian Z. Global Long Noncoding RNA Expression Profiling of MSTN and FGF5 Double-Knockout Sheep Reveals the Key Gatekeepers of Skeletal Muscle Development. DNA Cell Biol 2023; 42:163-175. [PMID: 36917699 DOI: 10.1089/dna.2022.0574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023] Open
Abstract
Improving livestock and poultry growth rates and increasing meat production are urgently needed worldwide. Previously, we produced a myostatin (MSTN) and fibroblast growth factor 5 (FGF5) double-knockout (MF-/-) sheep by CRISPR Cas9 system to improve meat production, and also wool production. Both MF-/- sheep and the F1 generation (MF+/-) sheep showed an obvious "double-muscle" phenotype. In this study, we identified the expression profiles of long noncoding RNAs (lncRNAs) in wild-type and MF+/- sheep, then screened out the key candidate lncRNAs that can regulate myogenic differentiation and skeletal muscle development. These key candidate lncRNAs can serve as critical gatekeepers for muscle contraction, calcium ion transport and skeletal muscle cell differentiation, apoptosis, autophagy, and skeletal muscle inflammation, further revealing that lncRNAs play crucial roles in regulating muscle phenotype in MF+/- sheep. In conclusion, our newly identified lncRNAs may emerge as novel molecules for muscle development or muscle disease and provide a new reference for MSTN-mediated regulation of skeletal muscle development.
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Affiliation(s)
- Mingming Chen
- Beijing Key Laboratory for Animal Genetic Improvement, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Di Lian
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Yan Li
- Laboratory Animal Center of the Academy of Military Medical Sciences, Beijing, China
| | - Yue Zhao
- Beijing Key Laboratory for Animal Genetic Improvement, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xueling Xu
- Beijing Key Laboratory for Animal Genetic Improvement, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Zhimei Liu
- Beijing Key Laboratory for Animal Genetic Improvement, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Jinlong Zhang
- Institute of Animal Husbandry and Veterinary Medicine, Tianjin Academy of Agricultural Sciences, Tianjin, China
| | - Xiaosheng Zhang
- Institute of Animal Husbandry and Veterinary Medicine, Tianjin Academy of Agricultural Sciences, Tianjin, China
| | - Sujun Wu
- Beijing Key Laboratory for Animal Genetic Improvement, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Shiyu Qi
- Beijing Key Laboratory for Animal Genetic Improvement, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Shoulong Deng
- NHC Key Laboratory of Human Disease Comparative Medicine, Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College, Beijing, China
| | - Kun Yu
- Beijing Key Laboratory for Animal Genetic Improvement, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Zhengxing Lian
- Beijing Key Laboratory for Animal Genetic Improvement, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
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Bai Y, Chen X, Qu A, Liu Y, Zhao J, Ke Q, Pu F, Wu L, Chi H, Gong H, Zhou T, Xu P. Identification and Expression Analysis of LncRNAs Reveal the Immune Mechanism of Visceral White-Nodules Disease Resistance in Large Yellow Croaker. MARINE BIOTECHNOLOGY (NEW YORK, N.Y.) 2023; 25:57-69. [PMID: 36401080 DOI: 10.1007/s10126-022-10181-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 11/01/2022] [Indexed: 06/16/2023]
Abstract
Long non-coding RNAs (lncRNAs) have several known functions in fish growth processes and signal transduction, but their possible roles in response to bacterial diseases remain largely unresolved. In this study, we report a comprehensive cold-water bacterial disease-responsive lncRNA expression profile for understanding the transcriptional regulatory mechanisms of visceral white-nodules disease resistance in large yellow croaker. A total of 2534 high-confidence lncRNAs were identified by a rigorous filtering pipeline as a basic sequence set for comparative transcriptional analysis. In addition, a total of 10,200 lncRNA-mRNA pairs with high correlation coefficients were identified by expressions level correlation analysis, including non-redundant 381 DE lncRNAs and 2590 differential expressed genes. MSTRG_11084_1 and MSTRG_20402_1 were linked to a large number of target genes and may be involved in important functions in immune regulation. We further revealed the conserved and idiosyncratic features of the disease response process between the technical control strain (TCS) and the resistant strain (RS). Immune-related pathways were enriched in GO terms and KEGG pathways, among which cytokine-cytokine receptor interaction, MAPK signaling pathway, and NF-kappa B signaling pathway may play a key role in VWND resistance in large yellow croaker. Protein-protein interaction network (PPI) analysis revealed that immune-related target genes such as il-10, met, acta2, myc, cav1, and ntrk1, as well as growth and metabolism-related target genes such as pik3r2, igf1, sc5d, hmgcr, and lss were considered the main hub genes. This study represents the first characterization of lncRNAs involved in VWND resistance in large yellow croaker and provides new clues for elucidating the disease response mechanism of large yellow croaker.
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Affiliation(s)
- Yulin Bai
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Xintong Chen
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Ang Qu
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Yue Liu
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Ji Zhao
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Qiaozhen Ke
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
- State Key Laboratory of Large Yellow Croaker Breeding, Ningde Fufa Fisheries Company Limited, Ningde, 352130, China
| | - Fei Pu
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Linni Wu
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Hongshu Chi
- Biotechnology Institute, Fujian Academy of Agricultural Sciences, Fuzhou, 350003, China
| | - Hui Gong
- Biotechnology Institute, Fujian Academy of Agricultural Sciences, Fuzhou, 350003, China
| | - Tao Zhou
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
- State Key Laboratory of Large Yellow Croaker Breeding, Ningde Fufa Fisheries Company Limited, Ningde, 352130, China
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China
| | - Peng Xu
- Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China.
- State Key Laboratory of Large Yellow Croaker Breeding, Ningde Fufa Fisheries Company Limited, Ningde, 352130, China.
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, 361102, China.
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Liu X, Tian W, Wang L, Zhang L, Liang J, Wang L. Integrated Analysis of Long Non-Coding RNA and mRNA to Reveal Putative Candidate Genes Associated with Backfat Quality in Beijing Black Pig. Foods 2022; 11:foods11223654. [PMID: 36429246 PMCID: PMC9689697 DOI: 10.3390/foods11223654] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2022] [Revised: 11/07/2022] [Accepted: 11/09/2022] [Indexed: 11/17/2022] Open
Abstract
Pigs' backfat quality has an important impact on the quality of pork and pork products and has a strong relationship with nutrition and sensory characteristics. This study aimed to identify the related candidate genes of backfat quality and to preliminary clarify the molecular regulatory mechanism underlying pig backfat quality phenotypes. Expression assessments of long non-coding RNA (lncRNA) and mRNA profiling in backfat from high-quality (firm and white) and low-quality (soft and yellow) Beijing Black pigs were performed by RNA sequencing. Significantly different expressions were observed in 610 protein-coding genes and 290 lncRNAs between the two groups. Gene Ontology and Kyoto Encyclopedia of Genes and Genomes pathway annotation showed that some candidate differentially expressed genes that participate in lipid-related pathways and pigmentation terms may play a role in backfat quality in pigs. The cis-target and trans-target genes were predicted to explore the regulatory function of lncRNAs, and integrative analyses of different expression lncRNAs targets and different expression genes were performed. The results showed the regulatory networks of lncRNA-mRNA related to backfat quality, and our study obtained strong candidate genes for backfat quality: ELOVL5, SCD, DGAT2, SLC24A5, and TYRP1, which were involved in fat metabolism, adipogenesis regulation, and pigmentation. To our knowledge, this study is the first to demonstrate the molecular genetic mechanisms of backfat quality in pigs, and these findings improve the current understanding of backfat quality mechanisms and provide a foundation for further studies.
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Affiliation(s)
- Xin Liu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Weilong Tian
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China
| | - Ligang Wang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Longchao Zhang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Jing Liang
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China
| | - Lixian Wang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Correspondence: ; Tel.: +86-010-62818771
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He X, Wu R, Yun Y, Qin X, Huang Y, Chen L, Han Y, Wu J, Sha L, Borjigin G. MicroRNA and circular RNA profiling in the deposited fat tissue of Sunite sheep. Front Vet Sci 2022; 9:954882. [DOI: 10.3389/fvets.2022.954882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 10/20/2022] [Indexed: 11/06/2022] Open
Abstract
As the most typical deposited fat, tail fat is an important energy reservoir for sheep adapted to harsh environments and plays an important role as a raw material in daily life. However, the regulatory mechanisms of microRNA (miRNA) and circular RNA (circRNA) in tail fat development remain unclear. In this study, we characterized the miRNA and circRNA expression profiles in the tail fat of sheep at the ages of 6, 18, and 30 months. We identified 219 differentially expressed (DE) miRNAs (including 12 novel miRNAs), which exhibited a major tendency to be downregulated, and 198 DE circRNAs, which exhibited a tendency to be upregulated. Target gene prediction analysis was performed for the DE miRNAs. Functional analysis revealed that their target genes were mainly involved in cellular interactions, while the host genes of DE circRNAs were implicated in lipid and fatty acid metabolism. Subsequently, we established a competing endogenous RNA (ceRNA) network based on the negative regulatory relationship between miRNAs and target genes. The network revealed that upregulated miRNAs play a leading role in the development of tail fat. Finally, the ceRNA relationship network with oar-miR-27a_R-1 and oar-miR-29a as the core was validated, suggesting possible involvement of these interactions in tail fat development. In summary, DE miRNAs were negatively correlated with DE circRNAs during sheep tail fat development. The multiple ceRNA regulatory network dominated by upregulated DE miRNAs may play a key role in this developmental process.
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Kalds P, Zhou S, Gao Y, Cai B, Huang S, Chen Y, Wang X. Genetics of the phenotypic evolution in sheep: a molecular look at diversity-driving genes. Genet Sel Evol 2022; 54:61. [PMID: 36085023 PMCID: PMC9463822 DOI: 10.1186/s12711-022-00753-3] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Accepted: 08/29/2022] [Indexed: 12/22/2022] Open
Abstract
BACKGROUND After domestication, the evolution of phenotypically-varied sheep breeds has generated rich biodiversity. This wide phenotypic variation arises as a result of hidden genomic changes that range from a single nucleotide to several thousands of nucleotides. Thus, it is of interest and significance to reveal and understand the genomic changes underlying the phenotypic variation of sheep breeds in order to drive selection towards economically important traits. REVIEW Various traits contribute to the emergence of variation in sheep phenotypic characteristics, including coat color, horns, tail, wool, ears, udder, vertebrae, among others. The genes that determine most of these phenotypic traits have been investigated, which has generated knowledge regarding the genetic determinism of several agriculturally-relevant traits in sheep. In this review, we discuss the genomic knowledge that has emerged in the past few decades regarding the phenotypic traits in sheep, and our ultimate aim is to encourage its practical application in sheep breeding. In addition, in order to expand the current understanding of the sheep genome, we shed light on research gaps that require further investigation. CONCLUSIONS Although significant research efforts have been conducted in the past few decades, several aspects of the sheep genome remain unexplored. For the full utilization of the current knowledge of the sheep genome, a wide practical application is still required in order to boost sheep productive performance and contribute to the generation of improved sheep breeds. The accumulated knowledge on the sheep genome will help advance and strengthen sheep breeding programs to face future challenges in the sector, such as climate change, global human population growth, and the increasing demand for products of animal origin.
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Affiliation(s)
- Peter Kalds
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
- Department of Animal and Poultry Production, Faculty of Environmental Agricultural Sciences, Arish University, El-Arish, 45511 Egypt
| | - Shiwei Zhou
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
- College of Veterinary Medicine, Northwest A&F University, Yangling, 712100 China
| | - Yawei Gao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
| | - Bei Cai
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
| | - Shuhong Huang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
| | - Yulin Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
- International Joint Agriculture Research Center for Animal Bio-Breeding, Ministry of Agriculture and Rural Affairs, Yangling, 712100 China
| | - Xiaolong Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, 712100 China
- International Joint Agriculture Research Center for Animal Bio-Breeding, Ministry of Agriculture and Rural Affairs, Yangling, 712100 China
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Heidari M, Pakdel A, Bakhtiarizadeh MR, Dehghanian F. A framework for non-preserved consensus gene module detection in Johne's disease. Front Vet Sci 2022; 9:974444. [PMID: 35968017 PMCID: PMC9363878 DOI: 10.3389/fvets.2022.974444] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2022] [Accepted: 07/08/2022] [Indexed: 11/29/2022] Open
Abstract
Johne's disease caused by Mycobacterium avium subsp. paratuberculosis (MAP) is a major concern in dairy industry. Since, the pathogenesis of the disease is not clearly known, it is necessary to develop an approach to discover molecular mechanisms behind this disease with high confidence. Biological studies often suffer from issues with reproducibility. Lack of a method to find stable modules in co-expression networks from different datasets related to Johne's disease motivated us to present a computational pipeline to identify non-preserved consensus modules. Two RNA-Seq datasets related to MAP infection were analyzed, and consensus modules were detected and were subjected to the preservation analysis. The non-preserved consensus modules in both datasets were determined as they are modules whose connectivity and density are affected by the disease. Long non-coding RNAs (lncRNAs) and TF genes in the non-preserved consensus modules were identified to construct integrated networks of lncRNA-mRNA-TF. These networks were confirmed by protein-protein interactions (PPIs) networks. Also, the overlapped hub genes between two datasets were considered hub genes of the consensus modules. Out of 66 consensus modules, 21 modules were non-preserved consensus modules, which were common in both datasets and 619 hub genes were members of these modules. Moreover, 34 lncRNA and 152 TF genes were identified in 12 and 19 non-preserved consensus modules, respectively. The predicted PPIs in 17 non-preserved consensus modules were significant, and 283 hub genes were commonly identified in both co-expression and PPIs networks. Functional enrichment analysis revealed that eight out of 21 modules were significantly enriched for biological processes associated with Johne's disease including “inflammatory response,” “interleukin-1-mediated signaling pathway”, “type I interferon signaling pathway,” “cytokine-mediated signaling pathway,” “regulation of interferon-beta production,” and “response to interferon-gamma.” Moreover, some genes (hub mRNA, TF, and lncRNA) were introduced as potential candidates for Johne's disease pathogenesis such as TLR2, NFKB1, IRF1, ATF3, TREM1, CDH26, HMGB1, STAT1, ISG15, CASP3. This study expanded our knowledge of molecular mechanisms involved in Johne's disease, and the presented pipeline enabled us to achieve more valid results.
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Affiliation(s)
- Maryam Heidari
- Department of Animal Science, College of Agriculture, Isfahan University of Technology, Isfahan, Iran
| | - Abbas Pakdel
- Department of Animal Science, College of Agriculture, Isfahan University of Technology, Isfahan, Iran
- *Correspondence: Abbas Pakdel
| | - Mohammad Reza Bakhtiarizadeh
- Department of Animal and Poultry Science, College of Aburaihan, University of Tehran, Tehran, Iran
- Mohammad Reza Bakhtiarizadeh
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Jin M, Fei X, Li T, Lu Z, Chu M, Di R, He X, Wang X, Wei C. Transcriptome study digs out BMP2 involved in adipogenesis in sheep tails. BMC Genomics 2022; 23:457. [PMID: 35725366 PMCID: PMC9210821 DOI: 10.1186/s12864-022-08657-8] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/09/2022] [Accepted: 05/25/2022] [Indexed: 12/22/2022] Open
Abstract
Background Hu sheep and Tibetan sheep in China are characterized by fat tails and thin tails, respectively. Several transcriptomes have been conducted in different sheep breeds to identify the differentially expressed genes (DEGs) underlying this trait. However, these studies identified different DEGs in different sheep breeds. Results Hence, RNA sequencing was performed on Hu sheep and Tibetan sheep. We obtained a total of 45.57 and 43.82 million sequencing reads, respectively. Two libraries mapped reads from 36.93 and 38.55 million reads after alignment to the reference sequences. 2108 DEGs were identified, including 1247 downregulated and 861 upregulated DEGs. GO and KEGG analyses of all DEGs demonstrated that pathways were enriched in the regulation of lipolysis in adipocytes and terms related to the chemokine signalling pathway, lysosomes, and glycosaminoglycan degradation. Eight genes were selected for validation by RT–qPCR. In addition, the transfection of BMP2 overexpression into preadipocytes resulted in increased PPAR-γ expression and expression. BMP2 potentially induces adipogenesis through LOX in preadipocytes. The number of lipid drops in BMP2 overexpression detected by oil red O staining was also greater than that in the negative control. Conclusion In summary, these results showed that significant genes (BMP2, HOXA11, PPP1CC and LPIN1) are involved in the regulation of adipogenesis metabolism and suggested novel insights into metabolic molecules in sheep fat tails. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08657-8.
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Affiliation(s)
- Meilin Jin
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.,College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xiaojuan Fei
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Taotao Li
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zengkui Lu
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, Gansu, China
| | - Mingxing Chu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ran Di
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaoyun He
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiangyu Wang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Caihong Wei
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
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10
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Jin M, Fei X, Li T, Lu Z, Chu M, Di R, He X, Wang X, Wang Y, Yuan Z, Quan K, Wang H, Wei C. Oar-miR-432 Regulates Fat Differentiation and Promotes the Expression of BMP2 in Ovine Preadipocytes. Front Genet 2022; 13:844747. [PMID: 35559046 PMCID: PMC9087340 DOI: 10.3389/fgene.2022.844747] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2022] [Accepted: 03/11/2022] [Indexed: 11/13/2022] Open
Abstract
The fat tail is a unique characteristic of sheep that represents energy reserves and is a complex adaptative mechanism of fat-tailed sheep to environmental stress. MicroRNA plays a significant role as regulators at the posttranscriptional level, but no studies have explained the molecular mechanisms of miRNA which regulate fat deposition in sheep tails. In this study, mRNA and miRNA analysis examined tail fat tissue from three Hu fat-tailed and three Tibetan thin-tailed sheep. After aligning to the reference sequences, 2,108 differentially expressed genes and 105 differential expression miRNAs were identified, including 1,247 up- and 861 downregulated genes and 43 up- and 62 downregulated miRNAs. Among these differentially expressed miRNAs, oar-miR-432 was one of the most downregulated miRNAs between Hu sheep and Tibetan sheep, and 712 genes were predicted to be targeted by oar-miR-432, 80 of which overlapped with DEGs. The Gene Ontology analysis on these genes showed that BMP2, LEP, GRK5, BMP7, and RORC were enriched in fat cell differentiation terms. The genes for BMP2 targeted by oar-miR-432 were examined using dual-luciferase assay. The oar-miR-432 mimic transfected into preadipocytes resulted in increased expression of BMP2. The marker gene PPAR-γ of fat differentiation had a lower expression than the negative control on days 0, 2, and 4 after induced differentiation. The decrease in the number of lipids in the oar-miR-432 mimic group detected by oil red O stain was also less than that in the negative control. This is the first study to reveal the fat mechanisms by which oar-miR-432 inhibits fat differentiation and promotes the expression of BMP2 in sheep tails.
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Affiliation(s)
- Meilin Jin
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.,College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xiaojuan Fei
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Taotao Li
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Zengkui Lu
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Mingxing Chu
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Ran Di
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaoyun He
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiangyu Wang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Yuqing Wang
- College of Animal Science and Technology, Henan University of Science and Technology, Luoyang, China
| | - Zehu Yuan
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Kai Quan
- College of Animal Science and Technology, Henan University of Animal Husbandry and Economy, Zhengzhou, China
| | - Huihua Wang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Caihong Wei
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
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11
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Transcriptome reveals key microRNAs involved in fat deposition between different tail sheep breeds. PLoS One 2022; 17:e0264804. [PMID: 35231067 PMCID: PMC8887763 DOI: 10.1371/journal.pone.0264804] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2021] [Accepted: 02/16/2022] [Indexed: 12/11/2022] Open
Abstract
MicroRNA (miRNA) is a kind of noncoding RNA whose function involved in various biological processes in neuronal maturation and adipocyte cells, such as differentiation, proliferation, development, apoptosis, and metabolism. Herein, miRNA-Seq was used to identify miRNAs in the tail fat tissue of Hu sheep (short-fat-tailed) and Tibetan sheep (short-thin-tailed). In this study, 155 differentially expression miRNAs (DE miRNAs) were identified, including 78 up-regulated and 77 down-regulated. Among these DE miRNAs, 17 miRNAs were reported and related with lipid metabolism. MiRanda and RNAhybrid software were used to predict the target genes of DE miRNAs, obtaining the number of targeting relationships is 38553. Target genes were enriched by Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG). 742 terms and 302 single pathways are enriched, including lipid metabolic process, response to lipid, cellular lipid catabolic process, lipid catabolic process, cellular lipid metabolic process, inositol lipid-mediated signaling, calcium channel activity, PI3K-Akt signaling pathway, MAPK signaling pathway, ECM-receptor interaction, AMPK signaling pathway, Wnt signaling pathway and TGF-beta signaling pathway. Notably, miR-379-5p was associated with tail fat deposition of sheep. Dual-Luciferase reporter assays showed miR-379-5p and HOXC9 had targeted relationship. The result of RT-qPCR showed that the expression trend of miR-379-5p and HOXC9 was opposite. miR-379-5p was down-regulated and highly expressed in tail adipose tissue of Tibetan sheep. HOXC9 was highly expressed in adipose tissue of Hu sheep. These results could provide a meaningful theoretical basis for studying the molecular mechanisms of sheep tail adipogenesis.
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12
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Wang F, Liu J, Zeng Q, Zhuoga D. Comparative analysis of long noncoding RNA and mRNA expression provides insights into adaptation to hypoxia in Tibetan sheep. Sci Rep 2022; 12:6597. [PMID: 35449433 PMCID: PMC9023463 DOI: 10.1038/s41598-022-08625-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2021] [Accepted: 03/03/2022] [Indexed: 01/21/2023] Open
Abstract
Tibetan sheep have lived on the Qinghai-Tibetan Plateau for thousands of years and have good adaptability to the hypoxic environment and strong disease resistance. However, the molecular mechanism by which Tibetan sheep adapt to this extreme environment, especially the role of genetic regulation, is still unknown. Emerging evidence suggests that long noncoding RNAs (lncRNAs) participate in the regulation of a diverse range of biological processes. To explore the potential lncRNAs involved in the adaptation to high-altitude hypoxia of Tibetan sheep, we analysed the expression profile of lncRNAs and mRNAs in the liver and lung tissues of sheep using comparative transcriptome analysis between four Tibetan sheep populations (high altitude) and one Hu sheep population (low altitude). The results showed a total of 7848 differentially expressed (DE) lncRNA transcripts, and 22,971 DE mRNA transcripts were detected by pairwise comparison. The expression patterns of selected mRNAs and lncRNAs were validated by qRT-PCR, and the results correlated well with the transcriptome data. Moreover, the functional annotation analysis based on the Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) databases showed that DE mRNAs and the target genes of the lncRNAs were significantly enriched in organ morphogenesis, response to stimulus, haem binding, the immune system, arginine and proline metabolism, and fatty acid biosynthesis. The prediction of mRNA–mRNA and lncRNA–mRNA interaction networks further revealed transcripts potentially involved in adaptation to high-altitude hypoxia, and the hub genes DDX24, PDCD11, EIF4A3, NDUFA11, SART1, PRPF8 and TCONS_00306477, TCONS_00306029, TCONS_00139593, TCONS_00293272, and TCONS_00313398 were selected. Additionally, a set of target genes, PIK3R1, IGF1R, FZD6, IFNB2, ATF3, MB, CYP2B4, PSMD13, and TGFB1, were also identified as candidate genes associated with high-altitude hypoxia adaptation. In conclusion, a collection of novel expressed lncRNAs, a set of target genes and biological pathways known to be relevant for altitude adaptation were identified by comparative transcriptome analysis between Tibetan sheep and Hu sheep. Our results are the first to identify the characterization and expression profile of lncRNAs between Tibetan sheep and Hu sheep and provide insights into the genetic regulation mechanisms by which Tibetan sheep adapt to high-altitude hypoxic environments.
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Affiliation(s)
- Fan Wang
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, 730070, China.,China Agricultural Veterinary Biological Science and Technology Co., Ltd., Lanzhou, 730046, China
| | - Jianbin Liu
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China.,Sheep Breeding Engineering Technology Research Center, Chinese Academy of Agricultural Sciences, Lanzhou, 730050, China
| | - Qiaoying Zeng
- College of Veterinary Medicine, Gansu Agricultural University, Lanzhou, 730070, China.
| | - Deqing Zhuoga
- Institute of Livestock Research, Tibet Academy of Agriculture and Animal Science, Lhasa, 850000, China.
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13
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Han J, Ma S, Liang B, Bai T, Zhao Y, Ma Y, MacHugh DE, Ma L, Jiang L. Transcriptome Profiling of Developing Ovine Fat Tail Tissue Reveals an Important Role for MTFP1 in Regulation of Adipogenesis. Front Cell Dev Biol 2022; 10:839731. [PMID: 35350385 PMCID: PMC8957931 DOI: 10.3389/fcell.2022.839731] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2021] [Accepted: 02/18/2022] [Indexed: 02/05/2023] Open
Abstract
Fat-tail sheep exhibit a unique trait whereby substantial adipose tissue accumulates in the tail, a phenotype that is advantageous in many agroecological environments. In this study, we conducted histological assays, transcriptome analysis and functional assays to examine morphogenesis, characterize gene expression, and elucidate mechanisms that regulate fat tail development. We obtained the microstructure of tail before and after fat deposition, and demonstrated that measurable fat deposition occurred by the 80-day embryo (E80) stage, earlier than other tissues. Transcriptome profiling revealed 1,058 differentially expressed genes (DEGs) with six markedly different expression trends. GSEA enrichment and other downstream analyses showed important roles for genes and pathways involving in metabolism and that mitochondrial components were specifically overexpressed in the fat tail tissue of the 70-day embryo (E70). One hundred and eighty-three genes were further identified by leading edge gene analysis, among which, 17 genes have been reported in previous studies, including EEF1D, MTFP1, PPP1CA, PDGFD. Notably, the MTFP1 gene was highly correlated with the expression of other genes and with the highest enrichment score and gene expression change. Knockdown of MTFP1 in isolated adipose derived stem cells (ADSCs) inhibited cell proliferation and migration ability, besides, promoted the process of adipogenesis in vitro.
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Affiliation(s)
- Jiangang Han
- Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China.,Animal Genomics Laboratory, UCD School of Agriculture and Food Science, UCD College of Health and Agricultural Sciences, University College Dublin, Dublin, Ireland
| | - Sijia Ma
- Agricultural College, Ningxia University, Yinchuan, China
| | - Benmeng Liang
- Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China.,National Germplasm Center of Domestic Animal Resources, Ministry of Technology, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Tianyou Bai
- Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China.,National Germplasm Center of Domestic Animal Resources, Ministry of Technology, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Yuhetian Zhao
- Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China.,National Germplasm Center of Domestic Animal Resources, Ministry of Technology, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - Yuehui Ma
- Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China.,National Germplasm Center of Domestic Animal Resources, Ministry of Technology, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
| | - David E MacHugh
- Animal Genomics Laboratory, UCD School of Agriculture and Food Science, UCD College of Health and Agricultural Sciences, University College Dublin, Dublin, Ireland.,UCD Conway Institute of Biomolecular and Biomedical Research, University College Dublin, Dublin, Ireland
| | - Lina Ma
- Institute of Animal Science, Ningxia Academy of Agriculture and Forestry Sciences, Yinchuan, China
| | - Lin Jiang
- Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China.,National Germplasm Center of Domestic Animal Resources, Ministry of Technology, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing, China
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14
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Karimi P, Bakhtiarizadeh MR, Salehi A, Izadnia HR. Transcriptome analysis reveals the potential roles of long non-coding RNAs in feed efficiency of chicken. Sci Rep 2022; 12:2558. [PMID: 35169237 PMCID: PMC8847365 DOI: 10.1038/s41598-022-06528-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2021] [Accepted: 02/02/2022] [Indexed: 12/13/2022] Open
Abstract
Feed efficiency is an important economic trait and reduces the production costs per unit of animal product. Up to now, few studies have conducted transcriptome profiling of liver tissue in feed efficiency-divergent chickens (Ross vs native breeds). Also, molecular mechanisms contributing to differences in feed efficiency are not fully understood, especially in terms of long non-coding RNAs (lncRNAs). Hence, transcriptome profiles of liver tissue in commercial and native chicken breeds were analyzed. RNA-Seq data along with bioinformatics approaches were applied and a series of lncRNAs and target genes were identified. Furthermore, protein-protein interaction network construction, co-expression analysis, co-localization analysis of QTLs and functional enrichment analysis were used to functionally annotate the identified lncRNAs. In total, 2,290 lncRNAs were found (including 1,110 annotated, 593 known and 587 novel), of which 53 (including 39 known and 14 novel), were identified as differentially expressed genes between two breeds. The expression profile of lncRNAs was validated by RT-qPCR. The identified novel lncRNAs showed a number of characteristics similar to those of known lncRNAs. Target prediction analysis showed that these lncRNAs have the potential to act in cis or trans mode. Functional enrichment analysis of the predicted target genes revealed that they might affect the differences in feed efficiency of chicken by modulating genes associated with lipid metabolism, carbohydrate metabolism, growth, energy homeostasis and glucose metabolism. Some gene members of significant modules in the constructed co-expression networks were reported as important genes related to feed efficiency. Co-localization analysis of QTLs related to feed efficiency and the identified lncRNAs suggested several candidates to be involved in residual feed intake. The findings of this study provided valuable resources to further clarify the genetic basis of regulation of feed efficiency in chicken from the perspective of lncRNAs.
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Affiliation(s)
- Parastoo Karimi
- Department of Animal and Poultry Science, College of Aburaihan, University of Tehran, Tehran, Iran
| | | | - Abdolreza Salehi
- Department of Animal and Poultry Science, College of Aburaihan, University of Tehran, Tehran, Iran
| | - Hamid Reza Izadnia
- Animal Science Improvement Research Department, Agricultural and Natural Resources Research and Education Center, Safiabad AREEO, Dezful, Iran
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15
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Emerging Roles of Non-Coding RNAs in the Feed Efficiency of Livestock Species. Genes (Basel) 2022; 13:genes13020297. [PMID: 35205343 PMCID: PMC8872339 DOI: 10.3390/genes13020297] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/27/2022] [Accepted: 01/31/2022] [Indexed: 01/27/2023] Open
Abstract
A global population of already more than seven billion people has led to an increased demand for food and water, and especially the demand for meat. Moreover, the cost of feed used in animal production has also increased dramatically, which requires animal breeders to find alternatives to reduce feed consumption. Understanding the biology underlying feed efficiency (FE) allows for a better selection of feed-efficient animals. Non-coding RNAs (ncRNAs), especially micro RNAs (miRNAs) and long non-coding RNAs (lncRNAs), play important roles in the regulation of bio-logical processes and disease development. The functions of ncRNAs in the biology of FE have emerged as they participate in the regulation of many genes and pathways related to the major FE indicators, such as residual feed intake and feed conversion ratio. This review provides the state of the art studies related to the ncRNAs associated with FE in livestock species. The contribution of ncRNAs to FE in the liver, muscle, and adipose tissues were summarized. The research gap of the function of ncRNAs in key processes for improved FE, such as the nutrition, heat stress, and gut–brain axis, was examined. Finally, the potential uses of ncRNAs for the improvement of FE were discussed.
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16
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Su XH, He HY, Fang C, Liu LL, Liu WJ. Transcriptome profiling of LncRNAs in sheep tail fat deposition. Anim Biotechnol 2021:1-11. [PMID: 34865605 DOI: 10.1080/10495398.2021.2002882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
LncRNAs have recently received special attention due to their critical role in many important biological processes. There are few reports on its regulatory function in sheep fat deposition. In this study, two sheep populations with different tail types in Xinjiang, Bashibai sheep (fat-tailed) and the hybrid population of Bashibai sheep and wild argali (small-tailed) were selected for whole transcriptome sequencing from their tail tissues. First, 728 differentially expressed LncRNAs of tail fat between Bashibai and F2 sheep were identified by RNA-seq. Second, the tissue expression profile and relative expression difference between Bashibai and F2 sheep of 2 of 728 DE LncRNAs were analyzed by RT-PCR. LncRNA-MSTRG.24995 was highly expressed in tail fat, while lncRNA-MSTRG.36913 was highly expressed in subcutaneous fat. In addition, the expressions of LncRNA-MSTRG.24995 and LncRNA-MSTRG.36913 in tail fat of F2 sheep were significantly lower than that of Bashibai sheep, while those patterns in longissimus dorsi, quadriceps femoris and rumen were reversed. Third, the expression pattern of target genes FASN and THRSP in each tissue was similar with that of corresponding LncRNAs. The LncRNA-MSTRG.24995 directly affects tail fat deposition by FASN gene, while the LncRNA-MSTRG.36913 indirectly affects that by THRSP gene. This will help us to understand molecular mechanism of fat tail deposition from transcriptomic perspectives.
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Affiliation(s)
- Xiao-Hui Su
- Faculty of Animal Science, Xinjiang Agricultural University, Urumqi, China
| | - Hai-Ying He
- Faculty of Animal Science, Xinjiang Agricultural University, Urumqi, China
| | - Chao Fang
- Faculty of Animal Science, Xinjiang Agricultural University, Urumqi, China
| | - Ling-Ling Liu
- Faculty of Animal Science, Xinjiang Agricultural University, Urumqi, China
| | - Wu-Jun Liu
- Faculty of Animal Science, Xinjiang Agricultural University, Urumqi, China
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17
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Yuan Z, Ge L, Sun J, Zhang W, Wang S, Cao X, Sun W. Integrative analysis of Iso-Seq and RNA-seq data reveals transcriptome complexity and differentially expressed transcripts in sheep tail fat. PeerJ 2021; 9:e12454. [PMID: 34760406 PMCID: PMC8571958 DOI: 10.7717/peerj.12454] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Accepted: 10/18/2021] [Indexed: 01/22/2023] Open
Abstract
Background Nowadays, both customers and producers prefer thin-tailed fat sheep. To effectively breed for this phenotype, it is important to identify candidate genes and uncover the genetic mechanism related to tail fat deposition in sheep. Accumulating evidence suggesting that post-transcriptional modification events of precursor-messenger RNA (pre-mRNA), including alternative splicing (AS) and alternative polyadenylation (APA), may regulate tail fat deposition in sheep. Differentially expressed transcripts (DETs) analysis is a way to identify candidate genes related to tail fat deposition. However, due to the technological limitation, post-transcriptional modification events in the tail fat of sheep and DETs between thin-tailed and fat-tailed sheep remains unclear. Methods In the present study, we applied pooled PacBio isoform sequencing (Iso-Seq) to generate transcriptomic data of tail fat tissue from six sheep (three thin-tailed sheep and three fat-tailed sheep). By comparing with reference genome, potential gene loci and novel transcripts were identified. Post-transcriptional modification events, including AS and APA, and lncRNA in sheep tail fat were uncovered using pooled Iso-Seq data. Combining Iso-Seq data with six RNA-sequencing (RNA-Seq) data, DETs between thin- and fat-tailed sheep were identified. Protein protein interaction (PPI) network, Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses were implemented to investigate the potential functions of DETs. Results In the present study, we revealed the transcriptomic complexity of the tail fat of sheep, result in 9,001 potential novel gene loci, 17,834 AS events, 5,791 APA events, and 3,764 lncRNAs. Combining Iso-Seq data with RNA-Seq data, we identified hundreds of DETs between thin- and fat-tailed sheep. Among them, 21 differentially expressed lncRNAs, such as ENSOART00020036299, ENSOART00020033641, ENSOART00020024562, ENSOART00020003848 and 9.53.1 may regulate tail fat deposition. Many novel transcripts were identified as DETs, including 15.527.13 (DGAT2), 13.624.23 (ACSS2), 11.689.28 (ACLY), 11.689.18 (ACLY), 11.689.14 (ACLY), 11.660.12 (ACLY), 22.289.6 (SCD), 22.289.3 (SCD) and 22.289.14 (SCD). Most of the identified DETs have been enriched in GO and KEGG pathways related to extracellular matrix (ECM). Our result revealed the transcriptome complexity and identified many candidate transcripts in tail fat, which could enhance the understanding of molecular mechanisms behind tail fat deposition.
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Affiliation(s)
- Zehu Yuan
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education, Yangzhou University, Yangzhou, China
| | - Ling Ge
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Jingyi Sun
- College of Veterinary Medicine, Yangzhou University, Yangzhou, China
| | - Weibo Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Shanhe Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Xiukai Cao
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education, Yangzhou University, Yangzhou, China
| | - Wei Sun
- Joint International Research Laboratory of Agriculture and Agri-Product Safety of Ministry of Education, Yangzhou University, Yangzhou, China.,College of Animal Science and Technology, Yangzhou University, Yangzhou, China
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18
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He X, Wu R, Yun Y, Qin X, Chen L, Han Y, Wu J, Sha L, Borjigin G. Transcriptome analysis of messenger RNA and long noncoding RNA related to different developmental stages of tail adipose tissues of sunite sheep. Food Sci Nutr 2021; 9:5722-5734. [PMID: 34646540 PMCID: PMC8498062 DOI: 10.1002/fsn3.2537] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/11/2021] [Revised: 08/03/2021] [Accepted: 08/09/2021] [Indexed: 12/18/2022] Open
Abstract
The tail fat of sheep is the most typical deposited fat, and it can be widely used in human daily life, such as diet, cosmetics, and industrial raw materials. To understand the potential regulatory mechanism of different growth stages of tail fat in Sunite sheep, we performed high-throughput RNA sequencing to characterize the long noncoding RNA (lncRNA) and messenger RNA (mRNA) expression profiles of the sheep tail fat at the age of 6, 18, and 30 months. A total of 223 differentially expressed genes (DEGs) and 148 differentially expressed lncRNAs were found in the tail fat of 6-, 18-, and 30-month-old sheep. Based on functional analysis, we found that fat-related DEGs were mainly expressed at 6 months of age and gradually decreased at 18 and 30 months of age. The target gene prediction analysis shows that most of the lncRNAs target more than 20 mRNAs as their transregulators. Further, we obtained several fat-related differentially expressed target genes; these target genes interact with different differentially expressed lncRNAs at various ages and play an important role in the development of tail fat. Based on the DEGs and differentially expressed lncRNAs, we established three co-expression networks for each comparison group. Finally, we concluded that the development of the sheep tail fat is more active during the early stage of growth and gradually decreases with the increase in age. The mutual regulation of lncRNAs and mRNAs may play a key role in this complex biological process.
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Affiliation(s)
- Xige He
- College of Food Science and EngineeringInner Mongolia Agricultural UniversityHohhotChina
| | - Rihan Wu
- College of Biochemistry and EngineeringHohhot Vocational CollegeHohhotChina
| | - Yueying Yun
- College of Food Science and EngineeringInner Mongolia Agricultural UniversityHohhotChina
- School of Life Science and TechnologyInner Mongolia University of Science and TechnologyBaotouChina
| | - Xia Qin
- College of Food Science and EngineeringInner Mongolia Agricultural UniversityHohhotChina
| | - Lu Chen
- College of Food Science and EngineeringInner Mongolia Agricultural UniversityHohhotChina
| | - Yunfei Han
- College of Food Science and EngineeringInner Mongolia Agricultural UniversityHohhotChina
| | - Jindi Wu
- College of Food Science and EngineeringInner Mongolia Agricultural UniversityHohhotChina
| | - Lina Sha
- College of Food Science and EngineeringInner Mongolia Agricultural UniversityHohhotChina
| | - Gerelt Borjigin
- College of Food Science and EngineeringInner Mongolia Agricultural UniversityHohhotChina
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19
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Wiener P, Robert C, Ahbara A, Salavati M, Abebe A, Kebede A, Wragg D, Friedrich J, Vasoya D, Hume DA, Djikeng A, Watson M, Prendergast JGD, Hanotte O, Mwacharo JM, Clark EL. Whole-Genome Sequence Data Suggest Environmental Adaptation of Ethiopian Sheep Populations. Genome Biol Evol 2021; 13:evab014. [PMID: 33501931 PMCID: PMC7955157 DOI: 10.1093/gbe/evab014] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/19/2021] [Indexed: 12/13/2022] Open
Abstract
Great progress has been made over recent years in the identification of selection signatures in the genomes of livestock species. This work has primarily been carried out in commercial breeds for which the dominant selection pressures are associated with artificial selection. As agriculture and food security are likely to be strongly affected by climate change, a better understanding of environment-imposed selection on agricultural species is warranted. Ethiopia is an ideal setting to investigate environmental adaptation in livestock due to its wide variation in geo-climatic characteristics and the extensive genetic and phenotypic variation of its livestock. Here, we identified over three million single nucleotide variants across 12 Ethiopian sheep populations and applied landscape genomics approaches to investigate the association between these variants and environmental variables. Our results suggest that environmental adaptation for precipitation-related variables is stronger than that related to altitude or temperature, consistent with large-scale meta-analyses of selection pressure across species. The set of genes showing association with environmental variables was enriched for genes highly expressed in human blood and nerve tissues. There was also evidence of enrichment for genes associated with high-altitude adaptation although no strong association was identified with hypoxia-inducible-factor (HIF) genes. One of the strongest altitude-related signals was for a collagen gene, consistent with previous studies of high-altitude adaptation. Several altitude-associated genes also showed evidence of adaptation with temperature, suggesting a relationship between responses to these environmental factors. These results provide a foundation to investigate further the effects of climatic variables on small ruminant populations.
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Affiliation(s)
- Pamela Wiener
- Roslin Institute, University of Edinburgh, Midlothian, United Kingdom
| | - Christelle Robert
- Roslin Institute, University of Edinburgh, Midlothian, United Kingdom
- Centre for Tropical Livestock Genetics and Health (CTLGH), Midlothian, United Kingdom
| | - Abulgasim Ahbara
- School of Life Sciences, University of Nottingham, United Kingdom
- Department of Zoology, Misurata University, Misurata, Libya
| | - Mazdak Salavati
- Roslin Institute, University of Edinburgh, Midlothian, United Kingdom
- Centre for Tropical Livestock Genetics and Health (CTLGH), Midlothian, United Kingdom
| | - Ayele Abebe
- Debre Berhan Research Centre, Debre Berhan, Ethiopia
| | - Adebabay Kebede
- Amhara Regional Agricultural Research Institute, Bahir Dar, Ethiopia
- LiveGene, International Livestock Research Institute, Addis Ababa, Ethiopia
| | - David Wragg
- Roslin Institute, University of Edinburgh, Midlothian, United Kingdom
- Centre for Tropical Livestock Genetics and Health (CTLGH), Midlothian, United Kingdom
| | - Juliane Friedrich
- Roslin Institute, University of Edinburgh, Midlothian, United Kingdom
| | - Deepali Vasoya
- Roslin Institute, University of Edinburgh, Midlothian, United Kingdom
| | - David A Hume
- Mater Research Institute-University of Queensland, Translational Research Institute, Brisbane, Australia
| | - Appolinaire Djikeng
- Roslin Institute, University of Edinburgh, Midlothian, United Kingdom
- Centre for Tropical Livestock Genetics and Health (CTLGH), Midlothian, United Kingdom
| | - Mick Watson
- Roslin Institute, University of Edinburgh, Midlothian, United Kingdom
- Centre for Tropical Livestock Genetics and Health (CTLGH), Midlothian, United Kingdom
| | - James G D Prendergast
- Roslin Institute, University of Edinburgh, Midlothian, United Kingdom
- Centre for Tropical Livestock Genetics and Health (CTLGH), Midlothian, United Kingdom
| | - Olivier Hanotte
- Centre for Tropical Livestock Genetics and Health (CTLGH), Midlothian, United Kingdom
- School of Life Sciences, University of Nottingham, United Kingdom
- LiveGene, International Livestock Research Institute, Addis Ababa, Ethiopia
| | - Joram M Mwacharo
- Centre for Tropical Livestock Genetics and Health (CTLGH), Midlothian, United Kingdom
- Animal and Veterinary Sciences Group, Scotland’s Rural College (SRUC), Midlothian, United Kingdom
- Small Ruminant Genomics, International Centre for Agricultural Research in the Dry Areas (ICARDA), Addis Ababa, Ethiopia
| | - Emily L Clark
- Roslin Institute, University of Edinburgh, Midlothian, United Kingdom
- Centre for Tropical Livestock Genetics and Health (CTLGH), Midlothian, United Kingdom
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20
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Han J, Guo T, Yue Y, Lu Z, Liu J, Yuan C, Niu C, Yang M, Yang B. Quantitative proteomic analysis identified differentially expressed proteins with tail/rump fat deposition in Chinese thin- and fat-tailed lambs. PLoS One 2021; 16:e0246279. [PMID: 33529214 PMCID: PMC7853479 DOI: 10.1371/journal.pone.0246279] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/05/2020] [Accepted: 01/17/2021] [Indexed: 11/19/2022] Open
Abstract
Tail adipose as one of the important functional tissues can enhance hazardous environments tolerance for sheep. The objective of this study was to gain insight into the underlying development mechanisms of this trait. A quantitative analysis of protein abundance in ovine tail/rump adipose tissue was performed between Chinese local fat- (Kazakh, Hu and Lanzhou) and thin-tailed (Alpine Merino, Tibetan) sheep in the present study by using lable-free approach. Results showed that 3400 proteins were identified in the five breeds, and 804 were differentially expressed proteins, including 638 up regulated proteins and 83 down regulated proteins in the tail adipose tissues between fat- and thin-tailed sheep, and 8 clusters were distinguished for all the DEPs’ expression patterns. The differentially expressed proteins are mainly associated with metabolism pathways and peroxisome proliferator activated receptor signaling pathway. Furthermore, the proteomics results were validated by quantitative real-time PCR and Western Blot. Our research has also suggested that the up-regulated proteins ACSL1, HSD17β4, FABP4 in the tail adipose tissue might contribute to tail fat deposition by facilitating the proliferation of adipocytes and fat accumulation in tail/rump of sheep. Particularly, FABP4 highly expressed in the fat-tail will play an important role for tail fat deposition. Our study might provide a novel view to understanding fat accumulation in special parts of the body in sheep and other animals.
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Affiliation(s)
- Jilong Han
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences (CAAS), Lanzhou, China
- College of Animal Science and Technology, Shihezi University, Shihezi, China
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, CAAS, Beijing, China
| | - Tingting Guo
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences (CAAS), Lanzhou, China
- Engineering Research Center of Sheep and Goat Breeding, CAAS, Lanzhou, China
| | - Yaojing Yue
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences (CAAS), Lanzhou, China
- Engineering Research Center of Sheep and Goat Breeding, CAAS, Lanzhou, China
| | - Zengkui Lu
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences (CAAS), Lanzhou, China
- Engineering Research Center of Sheep and Goat Breeding, CAAS, Lanzhou, China
| | - Jianbin Liu
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences (CAAS), Lanzhou, China
- Engineering Research Center of Sheep and Goat Breeding, CAAS, Lanzhou, China
| | - Chao Yuan
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences (CAAS), Lanzhou, China
- Engineering Research Center of Sheep and Goat Breeding, CAAS, Lanzhou, China
| | - Chune Niu
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences (CAAS), Lanzhou, China
- Engineering Research Center of Sheep and Goat Breeding, CAAS, Lanzhou, China
| | - Min Yang
- College of Animal Science and Technology, Shihezi University, Shihezi, China
- Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Science, CAAS, Beijing, China
- * E-mail: (MY); (BY)
| | - Bohui Yang
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences (CAAS), Lanzhou, China
- Engineering Research Center of Sheep and Goat Breeding, CAAS, Lanzhou, China
- * E-mail: (MY); (BY)
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21
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Azlan A, Obeidat SM, Theva Das K, Yunus MA, Azzam G. Genome-wide identification of Aedes albopictus long noncoding RNAs and their association with dengue and Zika virus infection. PLoS Negl Trop Dis 2021; 15:e0008351. [PMID: 33481791 PMCID: PMC7872224 DOI: 10.1371/journal.pntd.0008351] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Revised: 02/09/2021] [Accepted: 11/20/2020] [Indexed: 12/14/2022] Open
Abstract
The Asian tiger mosquito, Aedes albopictus (Ae. albopictus), is an important vector that transmits arboviruses such as dengue (DENV), Zika (ZIKV) and Chikungunya virus (CHIKV). Long noncoding RNAs (lncRNAs) are known to regulate various biological processes. Knowledge on Ae. albopictus lncRNAs and their functional role in virus-host interactions are still limited. Here, we identified and characterized the lncRNAs in the genome of an arbovirus vector, Ae. albopictus, and evaluated their potential involvement in DENV and ZIKV infection. We used 148 public datasets, and identified a total of 10, 867 novel lncRNA transcripts, of which 5,809, 4,139, and 919 were intergenic, intronic and antisense respectively. The Ae. albopictus lncRNAs shared many characteristics with other species such as short length, low GC content, and low sequence conservation. RNA-sequencing of Ae. albopictus cells infected with DENV and ZIKV showed that the expression of lncRNAs was altered upon virus infection. Target prediction analysis revealed that Ae. albopictus lncRNAs may regulate the expression of genes involved in immunity and other metabolic and cellular processes. To verify the role of lncRNAs in virus infection, we generated mutations in lncRNA loci using CRISPR-Cas9, and discovered that two lncRNA loci mutations, namely XLOC_029733 (novel lncRNA transcript id: lncRNA_27639.2) and LOC115270134 (known lncRNA transcript id: XR_003899061.1) resulted in enhancement of DENV and ZIKV replication. The results presented here provide an important foundation for future studies of lncRNAs and their relationship with virus infection in Ae. albopictus. Ae. albopictus is an important vector of arboviruses such as dengue and Zika viruses. Studies on virus-host interaction at gene expression and molecular level are crucial especially in devising methods to inhibit virus replication in Aedes mosquitoes. Previous reports have shown that, besides protein-coding genes, noncoding RNAs such as lncRNAs are also involved in virus-host interaction. In this study, we report a comprehensive catalog of novel lncRNA transcripts in the genome of Ae. albopictus. We also show that the expression of lncRNAs was altered upon infection with dengue and Zika. Additionally, depletion of certain lncRNAs resulted in increased replication of dengue and Zika; hence, suggesting potential association of lncRNAs in virus infection. Results of this study provide a new avenue to the investigation of mosquito-virus interactions, especially in the aspect of noncoding genes.
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Affiliation(s)
- Azali Azlan
- School of Biological Sciences, Universiti Sains Malaysia, Penang, Malaysia
| | - Sattam M. Obeidat
- School of Biological Sciences, Universiti Sains Malaysia, Penang, Malaysia
| | - Kumitaa Theva Das
- Infectomics Cluster, Advanced Medical & Dental Institute, Universiti Sains Malaysia, Bertam, Kepala Batas, Pulau Pinang, Malaysia
| | - Muhammad Amir Yunus
- Infectomics Cluster, Advanced Medical & Dental Institute, Universiti Sains Malaysia, Bertam, Kepala Batas, Pulau Pinang, Malaysia
| | - Ghows Azzam
- School of Biological Sciences, Universiti Sains Malaysia, Penang, Malaysia
- * E-mail:
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22
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Zhang X, Zhou T, Chen B, Bai H, Bai Y, Zhao J, Pu F, Wu Y, Chen L, Shi Y, Ke Q, Zheng W, Chen J, Xu P. Identification and Expression Analysis of Long Non-coding RNA in Large Yellow Croaker ( Larimichthys crocea) in Response to Cryptocaryon irritans Infection. Front Genet 2020; 11:590475. [PMID: 33281881 PMCID: PMC7689269 DOI: 10.3389/fgene.2020.590475] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2020] [Accepted: 09/18/2020] [Indexed: 12/19/2022] Open
Abstract
Large-scale transcription studies have revealed numerous lncRNAs (long non-coding RNAs). lncRNAs have been proposed to participate in the regulation of a diverse range of biological processes, including transcriptional regulation. Although lncRNAs have attracted increasing attention, the studies in large yellow croaker (Larimichthys crocea) are still rare, and they lack systematic analysis. In this study, 101 RNA-seq datasets varied in ages, sexes, and tissues were retrieved from the NCBI database to generate a comprehensive catalog of large yellow croaker transcriptome database. A set of 14,599 high-confidence lncRNAs from 13,673 loci were identified and characterized. Furthermore, RNA-seq datasets obtained from the infection of C. irritans were employed to investigate the differential expression pattern of lncRNAs and analyze potential biological functions. A total of 77 differentially expressed lncRNAs targeting to 567 protein-coding genes were identified by using expression analysis. Several immune genes, including TLR5, CD2AP, and MMP9, were highlighted. With GO enrichment and KEGG pathway analysis, the immune-related terms or pathways were enriched. This study created a comprehensive dataset of lncRNAs for large yellow croaker, which would be helpful for the researches of functional roles of lncRNAs in large yellow croaker.
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Affiliation(s)
- Xinyi Zhang
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Tao Zhou
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Baohua Chen
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Huaqiang Bai
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Yulin Bai
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Ji Zhao
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Fei Pu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Yidi Wu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Lin Chen
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Yue Shi
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China
| | - Qiaozhen Ke
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China.,State Key Laboratory of Large Yellow Croaker Breeding, Ningde Fufa Fisheries Company Limited, Ningde, China
| | - Weiqiang Zheng
- State Key Laboratory of Large Yellow Croaker Breeding, Ningde Fufa Fisheries Company Limited, Ningde, China
| | - Jia Chen
- State Key Laboratory of Large Yellow Croaker Breeding, Ningde Fufa Fisheries Company Limited, Ningde, China
| | - Peng Xu
- State Key Laboratory of Marine Environmental Science, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China.,State Key Laboratory of Large Yellow Croaker Breeding, Ningde Fufa Fisheries Company Limited, Ningde, China.,Fujian Key Laboratory of Genetics and Breeding of Marine Organisms, College of Ocean and Earth Sciences, Xiamen University, Xiamen, China.,Xiamen Key Laboratory of Urban Sea Ecological Conservation and Restoration (USER), Xiamen University, Xiamen, China
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23
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Nolte W, Weikard R, Brunner RM, Albrecht E, Hammon HM, Reverter A, Kühn C. Identification and Annotation of Potential Function of Regulatory Antisense Long Non-Coding RNAs Related to Feed Efficiency in Bos taurus Bulls. Int J Mol Sci 2020; 21:ijms21093292. [PMID: 32384694 PMCID: PMC7247587 DOI: 10.3390/ijms21093292] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2020] [Revised: 05/02/2020] [Accepted: 05/04/2020] [Indexed: 12/18/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) can influence transcriptional and translational processes in mammalian cells and are associated with various developmental, physiological and phenotypic conditions. However, they remain poorly understood and annotated in livestock species. We combined phenotypic, metabolomics and liver transcriptomic data of bulls divergent for residual feed intake (RFI) and fat accretion. Based on a project-specific transcriptome annotation for the bovine reference genome ARS-UCD.1.2 and multiple-tissue total RNA sequencing data, we predicted 3590 loci to be lncRNAs. To identify lncRNAs with potential regulatory influence on phenotype and gene expression, we applied the regulatory impact factor algorithm on a functionally prioritized set of loci (n = 4666). Applying the algorithm of partial correlation and information theory, significant and independent pairwise correlations were calculated and co-expression networks were established, including plasma metabolites correlated with lncRNAs. The network hub lncRNAs were assessed for potential cis-actions and subjected to biological pathway enrichment analyses. Our results reveal a prevalence of antisense lncRNAs positively correlated with adjacent protein-coding genes and suggest their participation in mitochondrial function, acute phase response signalling, TCA-cycle, fatty acid β-oxidation and presumably gluconeogenesis. These antisense lncRNAs indicate a stabilizing function for their cis-correlated genes and a putative regulatory role in gene expression.
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Affiliation(s)
- Wietje Nolte
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany; (W.N.); (R.W.); (R.M.B.)
| | - Rosemarie Weikard
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany; (W.N.); (R.W.); (R.M.B.)
| | - Ronald M. Brunner
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany; (W.N.); (R.W.); (R.M.B.)
| | - Elke Albrecht
- Institute of Muscle Biology and Growth, Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany;
| | - Harald M. Hammon
- Institute of Nutritional Physiology “Oskar Kellner”, Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany;
| | - Antonio Reverter
- Commonwealth Scientific and Industrial Research Organisation (CSIRO) Agriculture and Food, Queensland Bioscience Precinct, St Lucia 4067 QLD, Australia;
| | - Christa Kühn
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany; (W.N.); (R.W.); (R.M.B.)
- Faculty of Agricultural and Environmental Sciences, University Rostock, 18059 Rostock, Germany
- Correspondence:
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24
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Genome-wide identification and characterization of long non-coding RNAs during differentiation of visceral preadipocytes in rabbit. Funct Integr Genomics 2019; 20:409-419. [PMID: 31745672 DOI: 10.1007/s10142-019-00729-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Revised: 11/06/2019] [Accepted: 11/07/2019] [Indexed: 12/14/2022]
Abstract
Emerging evidence suggests that long non-coding RNAs (lncRNAs) are critical regulators of diverse biological processes, including adipogenesis. Despite being considered an ideal animal model for studying adipogenesis, little is known about the roles of lncRNAs in the regulation of rabbit preadipocyte differentiation. In the present study, visceral preadipocytes isolated from newborn rabbits were cultured in vitro and induced for differentiation, and global lncRNA expression profiles of adipocytes collected at days 0, 3, and 9 of differentiation were analyzed by RNA-seq. A total of 2066 lncRNAs were identified from nine RNA-seq libraries. Compared to protein-coding transcripts, lncRNA transcripts exhibited characteristics of a longer length and lower expression level. Furthermore, 486 and 357 differentially expressed (DE) lncRNAs were identified when comparing day 3 vs. day 0 and day 9 vs. day 3, respectively. Target genes of DE lncRNAs were predicted by the cis-regulating approach. Prediction of functions revealed that DE lncRNAs when comparing day 3 vs. day 0 were involved in gene ontology (GO) terms of developmental growth, growth, developmental cell growth, and stem cell proliferation, and involved in Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways of PI3K-Akt signaling pathway, fatty acid biosynthesis, and the insulin signaling pathway. The DE lncRNAs when comparing day 9 vs. day 3 were involved in GO terms that associated with epigenetic modification and were involved in the KEGG pathway of cAMP signaling pathway. This study provides further insight into the regulatory function of lncRNAs in rabbit visceral adipose and facilitates a better understanding of different stages of preadipocyte differentiation.
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25
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Bakhtiarizadeh MR, Salehi A, Alamouti AA, Abdollahi-Arpanahi R, Salami SA. Deep transcriptome analysis using RNA-Seq suggests novel insights into molecular aspects of fat-tail metabolism in sheep. Sci Rep 2019; 9:9203. [PMID: 31235755 PMCID: PMC6591244 DOI: 10.1038/s41598-019-45665-3] [Citation(s) in RCA: 34] [Impact Index Per Article: 6.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 06/12/2019] [Indexed: 12/11/2022] Open
Abstract
Fat-tail content of sheep breeds is varied and the molecular mechanisms regulating fat-tail development have not been well characterized. Aiming at better identifying the important candidate genes and their functional pathways contributing to fat deposition in the tail, a comparative transcriptome analysis was performed between fat- (Lori-Bakhtiari) and thin-tailed (Zel) Iranian sheep breeds using RNA-seq. The experiment was conducted on six male lambs (three lambs per each breed) at seven months of age. Four different combinations of aligners and statistical methods including Hisat2 + edgeR, Hisat2 + DESeq2, STAR + edgeR and STAR + DESeq2 were used to identify the differentially expressed genes (DEGs). The DEGs were selected for functional enrichment analysis and protein-protein interaction (PPI) network construction. Module analysis was also conducted to mine the functional sub-networks from the PPI network. In total, 264 genes including 80 up- and 184 down-regulated genes were identified as DEGs. The RNA-Seq results were validated by Q-RT-PCR. Functional analysis of DEGs and the module analysis of PPI network demonstrated that in addition to pathways affecting lipid metabolism, a series of enriched functional terms related to "response to interleukin", "MAPK signaling pathways", "Wnt signaling pathway", "ECM-receptor interaction", "regulation of actin cytoskeleton", and "response to cAMP" might contribute to the deposition of fat in tails of sheep. Overall results using RNA-Seq analysis characterized important candidate genes involved in the fatty acid metabolism and regulation of fat deposition, suggesting novel insights into molecular aspects of fat-tail metabolism in sheep. Selected DEGs should be further investigated as potential markers associated with the fat-tail development in sheep breeds.
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Affiliation(s)
| | - Abdolreza Salehi
- Department of Animal and Poultry Science, College of Aburaihan, University of Tehran, Tehran, Iran
| | - Ali A Alamouti
- Department of Animal and Poultry Science, College of Aburaihan, University of Tehran, Tehran, Iran
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26
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Wang S, Fan Y, Xu Y, Zhang L, Cai L, Lv B. GDNFOS1 knockdown decreases the invasion and viability of glioblastoma cells. Exp Ther Med 2019; 18:1315-1322. [PMID: 31316623 DOI: 10.3892/etm.2019.7670] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/22/2018] [Accepted: 05/10/2019] [Indexed: 01/12/2023] Open
Abstract
Glioblastoma multiforme is the most aggressive primary brain cancer in adults. Therefore, it is important to investigate the mechanisms associated with cell viability and invasion ability of the cells in glioblastoma multiforme. The opposite strand of the glial cell line-derived neurotrophic factor (GDNF) gene is used to transcribe the cis-antisense GDNF opposite strand (GDNFOS) gene, which belongs to the long noncoding RNAs. The current study assessed the effects of GDNFOS1 overexpression and interference on GDNF expression, cell viability and invasion ability in U87 and U251 MG glioblastoma cells. Overexpression and interference were performed using constructed lentiviral vectors, including long non-coding RNA GDNFOS1 overexpression vector, pL-short hairpin RNA (shRNA)-GDNFOS1-9, pL-shRNA-GDNFOS1-49, pL-shRNA-GDNFOS1-248, pL-shRNA-GDNFOS1-9+49, pL-shRNA-GDNFOS1-9+248 and pL-shRNA-GDNFOS1-49+248. Reverse transcription-quantitative PCR was used to determine the efficiency of interference and overexpression of GDNFOS1 in U87 and U251 MG cells. GDNF protein expression in U87 and U251 MG cells was detected using western blot analysis. In addition, cell viability was detected using a cell counting kit-8 assay at 24, 48 and 72 h after GDNFOS1 overexpression or interference. A transwell invasion assay was used to detect invasion ability. Different shRNA sequences were tested and the results revealed that a combination (pL-shRNA-GDNFOS1-49+248) was most effective in the knock-down GDNFOS1. Compared with the control group, GDNF expression in U87 MG cells was significantly increased in the GDNFOS1 overexpression group and decreased in the shRNA-GDNFOS1-248 group. U87 MG cell viability was significantly increased in the GDNFOS1 overexpression group at 24, 48 and 72 h compared with the negative control group. The viability of U87 MG cells was decreased in the GDNFOS1 interference group at 72 h when compared with the control group. The relative invasive ability was significantly increased in the GDNFOS1 overexpression group when compared with the negative control group. The invasive ability was significantly decreased in the GDNFOS1 interference group when compared with the negative control group. Similar results were exhibited by the U251 MG cells. Overall, GDNF expression, cell viability and invasion ability of glioblastoma cells significantly increased with GDNFOS1 overexpression and decreased with GDNFOS1 interference.
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Affiliation(s)
- Shiyi Wang
- Department of Gastroenterology, Ningbo Hospital of TCM Affiliated to Zhejiang Chinese Medical University, Ningbo, Zhejiang 315000, P.R. China.,Department of Gastroenterology, The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310006, P.R. China
| | - Yihong Fan
- Department of Gastroenterology, The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310006, P.R. China
| | - Yi Xu
- Department of Gastroenterology, The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310006, P.R. China
| | - Lu Zhang
- Department of Gastroenterology, The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310006, P.R. China
| | - Lijun Cai
- Department of Gastroenterology, The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310006, P.R. China
| | - Bin Lv
- Department of Gastroenterology, The First Affiliated Hospital of Zhejiang Chinese Medical University, Hangzhou, Zhejiang 310006, P.R. China
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