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Chitneedi PK, Hadlich F, Moreira GCM, Espinosa-Carrasco J, Li C, Plastow G, Fischer D, Charlier C, Rocha D, Chamberlain AJ, Kuehn C. eQTL-Detect: nextflow-based pipeline for eQTL detection in modular format with sharable and parallelizable scripts. NAR Genom Bioinform 2024; 6:lqae122. [PMID: 39318506 PMCID: PMC11420669 DOI: 10.1093/nargab/lqae122] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 07/26/2024] [Accepted: 09/02/2024] [Indexed: 09/26/2024] Open
Abstract
Bioinformatic pipelines are becoming increasingly complex with the ever-accumulating amount of Next-generation sequencing (NGS) data. Their orchestration is difficult with a simple Bash script, but bioinformatics workflow managers such as Nextflow provide a framework to overcome respective problems. This study used Nextflow to develop a bioinformatic pipeline for detecting expression quantitative trait loci (eQTL) using a DSL2 Nextflow modular syntax, to enable sharing the huge demand for computing power as well as data access limitation across different partners often associated with eQTL studies. Based on the results from a test run with pilot data by measuring the required runtime and computational resources, the new pipeline should be suitable for eQTL studies in large scale analyses.
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Affiliation(s)
| | - Frieder Hadlich
- Research Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany
| | - Gabriel C M Moreira
- Unit of Animal Genomics, GIGA Institute, University of Liège, 4000 Liège, Belgium
| | - Jose Espinosa-Carrasco
- Centre for Genomic Regulation (CRG), The Barcelona Institute of Science and Technology, Dr. Aiguader 88, Barcelona 08003, Spain
| | - Changxi Li
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton T6G 2P5, Canada
- Lacombe Research and Development Centre, Agriculture and Agri-Food Canada, T4L 1W1 Lacombe, Canada
| | - Graham Plastow
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton T6G 2P5, Canada
| | - Daniel Fischer
- Natural Resources Institute Finland (Luke), Green Technology, Animal and Plant Genomics and Breeding, FI-31600 Jokioinen, Finland
| | - Carole Charlier
- Unit of Animal Genomics, GIGA Institute, University of Liège, 4000 Liège, Belgium
| | - Dominique Rocha
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | - Amanda J Chamberlain
- Agriculture Victoria Research, AgriBio, Centre for AgriBiosciences, Bundoora, VIC 3083, Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, VIC 3083, Australia
| | - Christa Kuehn
- Research Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, 18196 Dummerstorf, Germany
- Faculty of Agricultural and Environmental Science, University Rostock, Justus-von-Liebig-Weg 6, 18059 Rostock, Germany
- Friedrich-Loeffler-Institut (FLI), Federal Research Institute for Animal Health, 17493 Greifswald, Insel Riems, Germany
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2
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Kuraz Abebe B, Wang J, Guo J, Wang H, Li A, Zan L. A review of the role of epigenetic studies for intramuscular fat deposition in beef cattle. Gene 2024; 908:148295. [PMID: 38387707 DOI: 10.1016/j.gene.2024.148295] [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: 10/26/2023] [Revised: 01/23/2024] [Accepted: 02/15/2024] [Indexed: 02/24/2024]
Abstract
Intramuscular fat (IMF) deposition profoundly influences meat quality and economic value in beef cattle production. Meanwhile, contemporary developments in epigenetics have opened new outlooks for understanding the molecular basics of IMF regulation, and it has become a key area of research for world scholars. Therefore, the aim of this paper was to provide insight and synthesis into the intricate relationship between epigenetic mechanisms and IMF deposition in beef cattle. The methodology involves a thorough analysis of existing literature, including pertinent books, academic journals, and online resources, to provide a comprehensive overview of the role of epigenetic studies in IMF deposition in beef cattle. This review summarizes the contemporary studies in epigenetic mechanisms in IMF regulation, high-resolution epigenomic mapping, single-cell epigenomics, multi-omics integration, epigenome editing approaches, longitudinal studies in cattle growth, environmental epigenetics, machine learning in epigenetics, ethical and regulatory considerations, and translation to industry practices from perspectives of IMF deposition in beef cattle. Moreover, this paper highlights DNA methylation, histone modifications, acetylation, phosphorylation, ubiquitylation, non-coding RNAs, DNA hydroxymethylation, epigenetic readers, writers, and erasers, chromatin immunoprecipitation followed by sequencing, whole genome bisulfite sequencing, epigenome-wide association studies, and their profound impact on the expression of crucial genes governing adipogenesis and lipid metabolism. Nutrition and stress also have significant influences on epigenetic modifications and IMF deposition. The key findings underscore the pivotal role of epigenetic studies in understanding and enhancing IMF deposition in beef cattle, with implications for precision livestock farming and ethical livestock management. In conclusion, this review highlights the crucial significance of epigenetic pathways and environmental factors in affecting IMF deposition in beef cattle, providing insightful information for improving the economics and meat quality of cattle production.
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Affiliation(s)
- Belete Kuraz Abebe
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China; Department of Animal Science, Werabe University, P.O. Box 46, Werabe, Ethiopia
| | - Jianfang Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Juntao Guo
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Hongbao Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Anning Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Linsen Zan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China; National Beef Cattle Improvement Center, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China.
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3
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Schneider H, Krizanac AM, Falker-Gieske C, Heise J, Tetens J, Thaller G, Bennewitz J. Genomic dissection of the correlation between milk yield and various health traits using functional and evolutionary information about imputed sequence variants of 34,497 German Holstein cows. BMC Genomics 2024; 25:265. [PMID: 38461236 PMCID: PMC11385139 DOI: 10.1186/s12864-024-10115-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/17/2023] [Accepted: 02/13/2024] [Indexed: 03/11/2024] Open
Abstract
BACKGROUND Over the last decades, it was subject of many studies to investigate the genomic connection of milk production and health traits in dairy cattle. Thereby, incorporating functional information in genomic analyses has been shown to improve the understanding of biological and molecular mechanisms shaping complex traits and the accuracies of genomic prediction, especially in small populations and across-breed settings. Still, little is known about the contribution of different functional and evolutionary genome partitioning subsets to milk production and dairy health. Thus, we performed a uni- and a bivariate analysis of milk yield (MY) and eight health traits using a set of ~34,497 German Holstein cows with 50K chip genotypes and ~17 million imputed sequence variants divided into 27 subsets depending on their functional and evolutionary annotation. In the bivariate analysis, eight trait-combinations were observed that contrasted MY with each health trait. Two genomic relationship matrices (GRM) were included, one consisting of the 50K chip variants and one consisting of each set of subset variants, to obtain subset heritabilities and genetic correlations. In addition, 50K chip heritabilities and genetic correlations were estimated applying merely the 50K GRM. RESULTS In general, 50K chip heritabilities were larger than the subset heritabilities. The largest heritabilities were found for MY, which was 0.4358 for the 50K and 0.2757 for the subset heritabilities. Whereas all 50K genetic correlations were negative, subset genetic correlations were both, positive and negative (ranging from -0.9324 between MY and mastitis to 0.6662 between MY and digital dermatitis). The subsets containing variants which were annotated as noncoding related, splice sites, untranslated regions, metabolic quantitative trait loci, and young variants ranked highest in terms of their contribution to the traits` genetic variance. We were able to show that linkage disequilibrium between subset variants and adjacent variants did not cause these subsets` high effect. CONCLUSION Our results confirm the connection of milk production and health traits in dairy cattle via the animals` metabolic state. In addition, they highlight the potential of including functional information in genomic analyses, which helps to dissect the extent and direction of the observed traits` connection in more detail.
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Affiliation(s)
- Helen Schneider
- Institute of Animal Science, University of Hohenheim, 70599, Stuttgart, Germany.
| | - Ana-Marija Krizanac
- Department of Animal Sciences, University of Göttingen, 37077, Göttingen, Germany
| | | | - Johannes Heise
- Vereinigte Informationssysteme Tierhaltung w.V. (VIT), 27283, Verden, Germany
| | - Jens Tetens
- Department of Animal Sciences, University of Göttingen, 37077, Göttingen, Germany
| | - Georg Thaller
- Institute of Animal Breeding and Husbandry, Christian-Albrechts University of Kiel, 24098, Kiel, Germany
| | - Jörn Bennewitz
- Institute of Animal Science, University of Hohenheim, 70599, Stuttgart, Germany
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4
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Yang Y, Wu J, Liu W, Zhao Y, Chen H. The Function and Regulation Mechanism of Non-Coding RNAs in Muscle Development. Int J Mol Sci 2023; 24:14534. [PMID: 37833983 PMCID: PMC10572267 DOI: 10.3390/ijms241914534] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 08/25/2023] [Accepted: 08/28/2023] [Indexed: 10/15/2023] Open
Abstract
Animal skeletal muscle growth is regulated by a complex molecular network including some non-coding RNAs (ncRNAs). In this paper, we review the non-coding RNAs related to the growth and development of common animal skeletal muscles, aiming to provide a reference for the in-depth study of the role of ncRNAs in the development of animal skeletal muscles, and to provide new ideas for the improvement of animal production performance.
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Affiliation(s)
- Yaling Yang
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China; (Y.Y.); (W.L.)
| | - Jian Wu
- Key Laboratory of Beef Cattle Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Academy of Agricultural Sciences of Jilin Province, Changchun 136100, China;
| | - Wujun Liu
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China; (Y.Y.); (W.L.)
| | - Yumin Zhao
- Key Laboratory of Beef Cattle Genetics and Breeding, Ministry of Agriculture and Rural Affairs, Academy of Agricultural Sciences of Jilin Province, Changchun 136100, China;
| | - Hong Chen
- College of Animal Science, Xinjiang Agricultural University, Urumqi 830052, China; (Y.Y.); (W.L.)
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5
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Marceau A, Wang J, Iqbal V, Jiang J, Liu GE, Ma L. Investigation of lncRNA in Bos taurus Mammary Tissue during Dry and Lactation Periods. Genes (Basel) 2023; 14:1789. [PMID: 37761929 PMCID: PMC10531232 DOI: 10.3390/genes14091789] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2023] [Revised: 09/01/2023] [Accepted: 09/08/2023] [Indexed: 09/29/2023] Open
Abstract
This study aims to collect RNA-Seq data from Bos taurus samples representing dry and lactating mammary tissue, identify lncRNA transcripts, and analyze findings for their features and functional annotation. This allows for connections to be drawn between lncRNA and the lactation process. RNA-Seq data from 103 samples of Bos taurus mammary tissue were gathered from publicly available databases (60 dry, 43 lactating). The samples were filtered to reveal 214 dry mammary lncRNA transcripts and 517 lactating mammary lncRNA transcripts. The lncRNAs met common lncRNA characteristics such as shorter length, fewer exons, lower expression levels, and less sequence conservation when compared to the genome. Interestingly, several lncRNAs showed sequence similarity to genes associated with strong hair keratin intermediate filaments. Human breast cancer research has associated strong hair keratin filaments with mammary tissue cellular resilience. The lncRNAs were also associated with several genes/proteins that linked to pregnancy using expression correlation and gene ontology. Such findings indicate that there are crucial relationships between the lncRNAs found in mammary tissue and the development of the tissue, to meet both the animal's needs and our own production needs; these relationships should be further investigated to ensure that we continue to breed the most resilient, efficient dairy cattle.
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Affiliation(s)
- Alexis Marceau
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742, USA; (A.M.); (V.I.)
| | - Junjian Wang
- Department of Animal Science, North Carlonina State University, Raleigh, NC 27695, USA; (J.W.); (J.J.)
| | - Victoria Iqbal
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742, USA; (A.M.); (V.I.)
| | - Jicai Jiang
- Department of Animal Science, North Carlonina State University, Raleigh, NC 27695, USA; (J.W.); (J.J.)
| | - George E. Liu
- Animal Genomics and Improvemennt Laboratory, BARC, USDA-ARS, Beltsville, MD 20705, USA;
| | - Li Ma
- Department of Animal and Avian Sciences, University of Maryland, College Park, MD 20742, USA; (A.M.); (V.I.)
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6
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Dehghanian Reyhan V, Ghafouri F, Sadeghi M, Miraei-Ashtiani SR, Kastelic JP, Barkema HW, Shirali M. Integrated Comparative Transcriptome and circRNA-lncRNA-miRNA-mRNA ceRNA Regulatory Network Analyses Identify Molecular Mechanisms Associated with Intramuscular Fat Content in Beef Cattle. Animals (Basel) 2023; 13:2598. [PMID: 37627391 PMCID: PMC10451991 DOI: 10.3390/ani13162598] [Citation(s) in RCA: 6] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 08/05/2023] [Accepted: 08/08/2023] [Indexed: 08/27/2023] Open
Abstract
Intramuscular fat content (IMF), one of the most important carcass traits in beef cattle, is controlled by complex regulatory factors. At present, molecular mechanisms involved in regulating IMF and fat metabolism in beef cattle are not well understood. Our objective was to integrate comparative transcriptomic and competing endogenous RNA (ceRNA) network analyses to identify candidate messenger RNAs (mRNAs) and regulatory RNAs involved in molecular regulation of longissimus dorsi muscle (LDM) tissue for IMF and fat metabolism of 5 beef cattle breeds (Angus, Chinese Simmental, Luxi, Nanyang, and Shandong Black). In total, 34 circRNAs, 57 lncRNAs, 15 miRNAs, and 374 mRNAs were identified by integrating gene ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses. Furthermore, 7 key subnets with 16 circRNAs, 43 lncRNAs, 7 miRNAs, and 237 mRNAs were detected through clustering analyses, whereas GO enrichment analysis of identified RNAs revealed 48, 13, and 28 significantly enriched GO terms related to IMF in biological process, molecular function, and cellular component categories, respectively. The main metabolic-signaling pathways associated with IMF and fat metabolism that were enriched included metabolic, calcium, cGMP-PKG, thyroid hormone, and oxytocin signaling pathways. Moreover, MCU, CYB5R1, and BAG3 genes were common among the 10 comparative groups defined as important candidate marker genes for fat metabolism in beef cattle. Contributions of transcriptome profiles from various beef breeds and a competing endogenous RNA (ceRNA) regulatory network underlying phenotypic differences in IMF provided novel insights into molecular mechanisms associated with meat quality.
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Affiliation(s)
- Vahid Dehghanian Reyhan
- Department of Animal Science, University College of Agriculture and Natural Resources, University of Tehran, Karaj 77871-31587, Iran; (V.D.R.); (F.G.); (S.R.M.-A.)
| | - Farzad Ghafouri
- Department of Animal Science, University College of Agriculture and Natural Resources, University of Tehran, Karaj 77871-31587, Iran; (V.D.R.); (F.G.); (S.R.M.-A.)
| | - Mostafa Sadeghi
- Department of Animal Science, University College of Agriculture and Natural Resources, University of Tehran, Karaj 77871-31587, Iran; (V.D.R.); (F.G.); (S.R.M.-A.)
| | - Seyed Reza Miraei-Ashtiani
- Department of Animal Science, University College of Agriculture and Natural Resources, University of Tehran, Karaj 77871-31587, Iran; (V.D.R.); (F.G.); (S.R.M.-A.)
| | - John P. Kastelic
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; (J.P.K.); (H.W.B.)
| | - Herman W. Barkema
- Faculty of Veterinary Medicine, University of Calgary, Calgary, AB T2N 4N1, Canada; (J.P.K.); (H.W.B.)
| | - Masoud Shirali
- Agri-Food and Biosciences Institute, Hillsborough BT26 6DR, UK
- School of Biological Sciences, Queen’s University Belfast, Belfast BT9 5AJ, UK
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7
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Zhang H, Mi S, Brito LF, Hu L, Wang L, Ma L, Xu Q, Guo G, Yu Y, Wang Y. Genomic and transcriptomic analyses enable the identification of important genes associated with subcutaneous fat deposition in Holstein cows. J Genet Genomics 2023:S1673-8527(23)00026-7. [PMID: 36738887 DOI: 10.1016/j.jgg.2023.01.011] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 01/18/2023] [Accepted: 01/20/2023] [Indexed: 02/05/2023]
Abstract
Subcutaneous fat deposition has many important roles in dairy cattle, including immunological defense and mechanical protection. The main objectives of this study are to identify key candidate genes regulating subcutaneous fat deposition in high-producing dairy cows by integrating genomic and transcriptomic datasets. A total of 1,654 genotyped Holstein cows are used to perform a genome-wide association study (GWAS) aiming to identify genes associated with subcutaneous fat deposition. Subsequently, weighted gene co-expression network analyses (WGCNA) are conducted based on RNA-sequencing data of 34 cows and de-regressed estimated breeding values of subcutaneous fat deposition. Lastly, differentially expressed (DE) mRNA, lncRNA, and differentially alternative splicing genes are obtained for 12 Holstein cows with extreme and divergent phenotypes for subcutaneous fat deposition. Forty-six protein-coding genes are identified as candidate genes regulating subcutaneous fat deposition in Holstein cattle based on the GWAS. Eleven overlapping genes are identified based on the analyses of DE genes and WGCNA. Furthermore, the candidate genes identified based on the GWAS, WGCNA, and analyses of DE genes are significantly enriched for pathways involved in metabolism, oxidative phosphorylation, thermogenesis, fatty acid degradation, and glycolysis/gluconeogenesis pathways. Integrating all findings, the NID2, STARD3, UFC1, DEDD, PPP1R1B, and USP21 genes are considered to be the most important candidate genes influencing subcutaneous fat deposition traits in Holstein cows. This study provides novel insights into the regulation mechanism underlying fat deposition in high-producing dairy cows, which will be useful when designing management and breeding strategies.
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Affiliation(s)
- Hailiang Zhang
- Laboratory of Animal Genetics, Breeding, and Reproduction, Ministry of Agriculture of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Siyuan Mi
- Laboratory of Animal Genetics, Breeding, and Reproduction, Ministry of Agriculture of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Luiz F Brito
- Department of Animal Sciences, Purdue University, West Lafayette, IN, 47907, USA
| | - Lirong Hu
- Laboratory of Animal Genetics, Breeding, and Reproduction, Ministry of Agriculture of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Lei Wang
- Laboratory of Animal Genetics, Breeding, and Reproduction, Ministry of Agriculture of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Longgang Ma
- Laboratory of Animal Genetics, Breeding, and Reproduction, Ministry of Agriculture of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China
| | - Qing Xu
- Institute of Life Sciences and Bioengineering, Beijing Jiaotong University, Beijing, China
| | - Gang Guo
- Beijing Sunlon Livestock Development Co. Ltd, Beijing, 100176, China
| | - Ying Yu
- Laboratory of Animal Genetics, Breeding, and Reproduction, Ministry of Agriculture of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
| | - Yachun Wang
- Laboratory of Animal Genetics, Breeding, and Reproduction, Ministry of Agriculture of China, National Engineering Laboratory of Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, 100193, China.
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8
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Kutchy NA, Morenikeji OB, Memili A, Ugur MR. Deciphering sperm functions using biological networks. Biotechnol Genet Eng Rev 2023:1-25. [PMID: 36722689 DOI: 10.1080/02648725.2023.2168912] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2022] [Indexed: 02/02/2023]
Abstract
The global human population is exponentially increasing, which requires the production of quality food through efficient reproduction as well as sustainable production of livestock. Lack of knowledge and technology for assessing semen quality and predicting bull fertility is hindering advances in animal science and food animal production and causing millions of dollars of economic losses annually. The intent of this systemic review is to summarize methods from computational biology for analysis of gene, metabolite, and protein networks to identify potential markers that can be applied to improve livestock reproduction, with a focus on bull fertility. We provide examples of available gene, metabolic, and protein networks and computational biology methods to show how the interactions between genes, proteins, and metabolites together drive the complex process of spermatogenesis and regulate fertility in animals. We demonstrate the use of the National Center for Biotechnology Information (NCBI) and Ensembl for finding gene sequences, and then use them to create and understand gene, protein and metabolite networks for sperm associated factors to elucidate global cellular processes in sperm. This study highlights the value of mapping complex biological pathways among livestock and potential for conducting studies on promoting livestock improvement for global food security.
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Affiliation(s)
- Naseer A Kutchy
- Department of Anatomy, Physiology and Pharmacology, School of Veterinary Medicine, St. George's University, St. George's, Grenada
- Department of Animal Sciences, School of Environmental and Biological Sciences Rutgers, The State University of New Jersey, New Brunswick, NJ, USA
| | - Olanrewaju B Morenikeji
- Division of Biological and Health Sciences, University of Pittsburgh at Bradford, Bradford, PA, USA
| | - Aylin Memili
- Department of Nutrition, Gillings School of Global Public Health, University of North Carolina-Chapel Hill, Chapel Hill, NC, USA
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9
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Transcriptome Profiling of the Liver in Nellore Cattle Phenotypically Divergent for RFI in Two Genetic Groups. Animals (Basel) 2023; 13:ani13030359. [PMID: 36766249 PMCID: PMC9913155 DOI: 10.3390/ani13030359] [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: 12/01/2022] [Revised: 01/14/2023] [Accepted: 01/16/2023] [Indexed: 01/24/2023] Open
Abstract
The identification and selection of genetically superior animals for residual feed intake (RFI) could enhance productivity and minimize environmental impacts. The aim of this study was to use RNA-seq data to identify the differentially expressed genes (DEGs), known non-coding RNAs (ncRNAs), specific biomarkers and enriched biological processes associated with RFI of the liver in Nellore cattle in two genetic groups. In genetic group 1 (G1), 24 extreme RFI animals (12 low RFI (LRFI) versus 12 high RFI (HRFI)) were selected from a population of 60 Nellore bulls. The RNA-seq of the samples from their liver tissues was performed using an Illumina HiSeq 2000. In genetic group 2 (G2), 20 samples of liver tissue of Nellore bulls divergent for RFI (LRFI, n = 10 versus HRFI, n = 10) were selected from 83 animals. The raw data of the G2 were chosen from the ENA repository. A total of 1811 DEGs were found for the G1 and 2054 for the G2 (p-value ≤ 0.05). We detected 88 common genes in both genetic groups, of which 33 were involved in the immune response and in blocking oxidative stress. In addition, seven (B2M, ADSS, SNX2, TUBA4A, ARHGAP18, MECR, and ABCF3) possible gene biomarkers were identified through a receiver operating characteristic analysis (ROC) considering an AUC > 0.70. The B2M gene was overexpressed in the LRFI group. This gene regulates the lipid metabolism protein turnover and inhibits cell death. We also found non-coding RNAs in both groups. MIR25 was up-regulated and SNORD16 was down-regulated in the LRFI for G1. For G2, up-regulated RNase_MRP and SCARNA10 were found. We highlight MIR25 as being able to act by blocking cytotoxicity and oxidative stress and RMRP as a blocker of mitochondrial damage. The biological pathways associated with RFI of the liver in Nellore cattle in the two genetic groups were for energy metabolism, protein turnover, redox homeostasis and the immune response. The common transcripts, biomarkers and metabolic pathways found in the two genetic groups make this unprecedented work even more relevant, since the results are valid for different herds raised in different ways. The results reinforce the biological importance of these known processes but also reveal new insights into the complexity of the liver tissue transcriptome of Nellore cattle.
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10
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Machado PC, Brito LF, Martins R, Pinto LFB, Silva MR, Pedrosa VB. Genome-Wide Association Analysis Reveals Novel Loci Related with Visual Score Traits in Nellore Cattle Raised in Pasture-Based Systems. Animals (Basel) 2022; 12:ani12243526. [PMID: 36552446 PMCID: PMC9774243 DOI: 10.3390/ani12243526] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 12/06/2022] [Accepted: 12/10/2022] [Indexed: 12/15/2022] Open
Abstract
Body conformation traits assessed based on visual scores are widely used in Zebu cattle breeding programs. The aim of this study was to identify genomic regions and biological pathways associated with body conformation (CONF), finishing precocity (PREC), and muscling (MUSC) in Nellore cattle. The measurements based on visual scores were collected in 20,807 animals raised in pasture-based systems in Brazil. In addition, 2775 animals were genotyped using a 35 K SNP chip, which contained 31,737 single nucleotide polymorphisms after quality control. Single-step GWAS was performed using the BLUPF90 software while candidate genes were identified based on the Ensembl Genes 69. PANTHER and REVIGO platforms were used to identify key biological pathways and STRING to create gene networks. Novel candidate genes were revealed associated with CONF, including ALDH9A1, RXRG, RAB2A, and CYP7A1, involved in lipid metabolism. The genes associated with PREC were ELOVL5, PID1, DNER, TRIP12, and PLCB4, which are related to the synthesis of long-chain fatty acids, lipid metabolism, and muscle differentiation. For MUSC, the most important genes associated with muscle development were SEMA6A, TIAM2, UNC5A, and UIMC1. The polymorphisms identified in this study can be incorporated in commercial genotyping panels to improve the accuracy of genomic evaluations for visual scores in beef cattle.
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Affiliation(s)
- Pamela C. Machado
- Department of Animal Sciences, State University of Ponta Grossa, Ponta Grossa 84030-900, PR, Brazil
| | - Luiz F. Brito
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Rafaela Martins
- Department of Animal Sciences, State University of Ponta Grossa, Ponta Grossa 84030-900, PR, Brazil
| | - Luis Fernando B. Pinto
- Department of Animal Science, Federal University of Bahia, Av. Adhemar de Barros 500, Ondina, Salvador 40170-110, BA, Brazil
| | - Marcio R. Silva
- Melhore Animal and Katayama Agropecuaria Lda, Guararapes 16700-000, SP, Brazil
| | - Victor B. Pedrosa
- Department of Animal Sciences, State University of Ponta Grossa, Ponta Grossa 84030-900, PR, Brazil
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907, USA
- Correspondence:
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11
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Marceau A, Gao Y, Baldwin RL, Li CJ, Jiang J, Liu GE, Ma L. Investigation of rumen long noncoding RNA before and after weaning in cattle. BMC Genomics 2022; 23:531. [PMID: 35869425 PMCID: PMC9308236 DOI: 10.1186/s12864-022-08758-4] [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: 12/16/2021] [Accepted: 07/12/2022] [Indexed: 11/10/2022] Open
Abstract
Background This study aimed to identify long non-coding RNA (lncRNA) from the rumen tissue in dairy cattle, explore their features including expression and conservation levels, and reveal potential links between lncRNA and complex traits that may indicate important functional impacts of rumen lncRNA during the transition to the weaning period. Results A total of six cattle rumen samples were taken with three replicates from before and after weaning periods, respectively. Total RNAs were extracted and sequenced with lncRNA discovered based on size, coding potential, sequence homology, and known protein domains. As a result, 404 and 234 rumen lncRNAs were identified before and after weaning, respectively. However, only nine of them were shared under two conditions, with 395 lncRNAs found only in pre-weaning tissues and 225 only in post-weaning samples. Interestingly, none of the nine common lncRNAs were differentially expressed between the two weaning conditions. LncRNA averaged shorter length, lower expression, and lower conservation scores than the genome overall, which is consistent with general lncRNA characteristics. By integrating rumen lncRNA before and after weaning with large-scale GWAS results in cattle, we reported significant enrichment of both pre- and after-weaning lncRNA with traits of economic importance including production, reproduction, health, and body conformation phenotypes. Conclusions The majority of rumen lncRNAs are uniquely expressed in one of the two weaning conditions, indicating a functional role of lncRNA in rumen development and transition of weaning. Notably, both pre- and post-weaning lncRNA showed significant enrichment with a variety of complex traits in dairy cattle, suggesting the importance of rumen lncRNA for cattle performance in the adult stage. These relationships should be further investigated to better understand the specific roles lncRNAs are playing in rumen development and cow performance. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08758-4.
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Becker D, Weikard R, Heimes A, Hadlich F, Hammon HM, Meyerholz MM, Petzl W, Zerbe H, Schuberth HJ, Hoedemaker M, Schmicke M, Engelmann S, Kühn C. Allele-biased expression of the bovine APOB gene associated with the cholesterol deficiency defect suggests cis-regulatory enhancer effects of the LTR retrotransposon insertion. Sci Rep 2022; 12:13469. [PMID: 35931741 PMCID: PMC9355974 DOI: 10.1038/s41598-022-17798-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2022] [Accepted: 07/31/2022] [Indexed: 11/09/2022] Open
Abstract
The insertion of an endogenous retroviral long terminal repeat (LTR) sequence into the bovine apolipoprotein B (APOB) gene is causal to the inherited genetic defect cholesterol deficiency (CD) observed in neonatal and young calves. Affected calves suffer from developmental abnormalities, symptoms of incurable diarrhoea and often die within weeks to a few months after birth. Neither the detailed effects of the LTR insertion on APOB expression profile nor the specific mode of inheritance nor detailed phenotypic consequences of the mutation are undisputed. In our study, we analysed German Holstein dairy heifers at the peak of hepatic metabolic load and exposed to an additional pathogen challenge for clinical, metabolic and hepatic transcriptome differences between wild type (CDF) and heterozygote carriers of the mutation (CDC). Our data revealed that a divergent allele-biased expression pattern of the APOB gene in heterozygous CDC animals leads to a tenfold higher expression of exons upstream and a decreased expression of exons downstream of the LTR insertion compared to expression levels of CDF animals. This expression pattern could be a result of enhancer activity induced by the LTR insertion, in addition to a previously reported artificial polyadenylation signal. Thus, our data support a regulatory potential of mobile element insertions. With regard to the phenotype generated by the LTR insertion, heterozygote CDC carriers display significantly differential hepatic expression of genes involved in cholesterol biosynthesis and lipid metabolism. Phenotypically, CDC carriers show a significantly affected lipomobilization compared to wild type animals. These results reject a completely recessive mode of inheritance for the CD defect, which should be considered for selection decisions in the affected population. Exemplarily, our results illustrate the regulatory impact of mobile element insertions not only on specific host target gene expression but also on global transcriptome profiles with subsequent biological, functional and phenotypic consequences in a natural in-vivo model of a non-model mammalian organism.
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Affiliation(s)
- Doreen Becker
- Institute of Genome Biology, Research Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Rosemarie Weikard
- Institute of Genome Biology, Research Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Annika Heimes
- Institute of Genome Biology, Research Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Frieder Hadlich
- Institute of Genome Biology, Research Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Harald M Hammon
- Institute of Nutritional Physiology, Research Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Marie M Meyerholz
- Clinic for Ruminants with Ambulatory and Herd Health Services, Centre for Clinical Veterinary Medicine, Ludwig-Maximilians-University Munich, Oberschleißheim, Germany
- Institute for Immunology, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Wolfram Petzl
- Clinic for Ruminants with Ambulatory and Herd Health Services, Centre for Clinical Veterinary Medicine, Ludwig-Maximilians-University Munich, Oberschleißheim, Germany
| | - Holm Zerbe
- Clinic for Ruminants with Ambulatory and Herd Health Services, Centre for Clinical Veterinary Medicine, Ludwig-Maximilians-University Munich, Oberschleißheim, Germany
| | | | - Martina Hoedemaker
- Clinic for Cattle, University of Veterinary Medicine Hannover, Hannover, Germany
| | - Marion Schmicke
- Faculty of Natural Sciences III, Martin-Luther University Halle-Wittenberg, Halle, Germany
| | - Susanne Engelmann
- Institute for Microbiology, Technical University Braunschweig, Brunswick, Germany
- Microbial Proteomics, Helmholtz Centre for Infection Research, Brunswick, Germany
| | - Christa Kühn
- Institute of Genome Biology, Research Institute for Farm Animal Biology (FBN), Dummerstorf, Germany.
- Agricultural and Environmental Faculty, University of Rostock, Rostock, Germany.
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Toro-Ospina AM, Herrera Rios AC, Pimenta Schettini G, Vallejo Aristizabal VH, Bizarria dos Santos W, Zapata CA, Ortiz Morea EG. Identification of Runs of Homozygosity Islands and Genomic Estimated Inbreeding Values in Caqueteño Creole Cattle (Colombia). Genes (Basel) 2022; 13:genes13071232. [PMID: 35886015 PMCID: PMC9318017 DOI: 10.3390/genes13071232] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2022] [Revised: 06/29/2022] [Accepted: 07/01/2022] [Indexed: 02/04/2023] Open
Abstract
The Caqueteño Creole (CAQ) is a native breed of cattle from the Caquetá department (Colombia), adapted to tropical conditions, which is extremely important to production systems in those regions. However, CAQ is poorly studied. In this sense, population structure studies associated with runs of homozygosity (ROH) analysis would allow for a better understanding of CAQ. Through ROH analysis, it is possible to reveal genetic relationships between individuals, measure genome inbreeding levels, and identify regions associated with traits of economic interest. Samples from a CAQ population (n = 127) were genotyped with the Bovine HD BeadChip (777,000 SNPs) and analyzed with the PLINK 1.9 program to estimate FROH and ROH islands. We highlighted a decrease in inbreeding frequency for FROH 4−8 Mb, 8−16 Mb, and >16 Mb classes, indicating inbreeding control in recent matings. We also found genomic hotspot regions on chromosomes 3, 5, 6, 8, 16, 20, and 22, where chromosome 20 harbored four hotspots. Genes in those regions were associated with fertility and immunity traits, muscle development, and environmental resistance, which may be present in the CAQ breed due to natural selection. This indicates potential for production systems in tropical regions. However, further studies are necessary to elucidate the CAQ production objective.
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Affiliation(s)
- Alejandra M. Toro-Ospina
- Amazonian Research Center CIMAZ-MACAGUAL, Laboratory of Agrobiotechnology, University of the Amazon, Florencia 180002, Colombia; (A.C.H.R.); (V.H.V.A.); (C.A.Z.); (E.G.O.M.)
- Correspondence:
| | - Ana C. Herrera Rios
- Amazonian Research Center CIMAZ-MACAGUAL, Laboratory of Agrobiotechnology, University of the Amazon, Florencia 180002, Colombia; (A.C.H.R.); (V.H.V.A.); (C.A.Z.); (E.G.O.M.)
- Science and Humanities Faculty, Digital University Institute of Antioquia, IUDigital, Medellin, Antioquia 50010, Colombia
| | - Gustavo Pimenta Schettini
- Department of Animal and Poultry Science, Virginia Polytechnic Institute and State University, Blacksburg, VA 24061-0002, USA;
| | - Viviana H. Vallejo Aristizabal
- Amazonian Research Center CIMAZ-MACAGUAL, Laboratory of Agrobiotechnology, University of the Amazon, Florencia 180002, Colombia; (A.C.H.R.); (V.H.V.A.); (C.A.Z.); (E.G.O.M.)
| | - Wellington Bizarria dos Santos
- School of Agricultural and Veterinary Sciences (FCAV), São Paulo State University (UNESP), Jaboticabal, Sao Paulo 14884-900, Brazil;
| | - Cesar A. Zapata
- Amazonian Research Center CIMAZ-MACAGUAL, Laboratory of Agrobiotechnology, University of the Amazon, Florencia 180002, Colombia; (A.C.H.R.); (V.H.V.A.); (C.A.Z.); (E.G.O.M.)
| | - Edna Gicela Ortiz Morea
- Amazonian Research Center CIMAZ-MACAGUAL, Laboratory of Agrobiotechnology, University of the Amazon, Florencia 180002, Colombia; (A.C.H.R.); (V.H.V.A.); (C.A.Z.); (E.G.O.M.)
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Construction of a Novel MYC-Associated ceRNA Regulatory Network to Identify Prognostic Biomarkers in Colon Adenocarcinoma. JOURNAL OF ONCOLOGY 2022; 2022:3216285. [PMID: 35847359 PMCID: PMC9277212 DOI: 10.1155/2022/3216285] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 06/07/2022] [Indexed: 11/17/2022]
Abstract
Colorectal cancer (CRC) includes colon adenocarcinoma (COAD) and rectal adenocarcinoma (READ). Competitive endogenous RNA (ceRNA) is crucial for cancer pathogenesis. Abnormal expression of MYC is generally associated with a poor colon adenocarcinoma prognosis. The present study aimed to identify a novel MYC-associated ceRNA regulatory network and identify potential prognostic markers associated with COAD. We obtained the transcriptome sequencing profiles of 462 COAD cases from the TCGA database and analyzed differentially expressed genes (DEGs) in MYC high expression (MYChigh) and MYC low expression (Myclow) tumors. We identified an important lncRNA, LINC00114, which effectively predicts overall survival and plays a protective role in COAD. Moreover, the LINC00114/miR-216a-5p axis was identified as a clinical prognostic model. The predicted target genes of the LINC00114/miR-216a-5p axis include uromodulin Like 1 (UMODL1) and oncoprotein induced transcript 3 (OIT3), which are closely related to the survival and prognosis of COAD patients. In summary, we constructed a novel ceRNA regulatory network and identified potential biomarkers for the targeted therapy and prognosis of COAD.
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15
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Robic A, Cerutti C, Demars J, Kühn C. From the comparative study of a circRNA originating from an mammalian ATXN2L intron to understanding the genesis of intron lariat-derived circRNAs. BIOCHIMICA ET BIOPHYSICA ACTA. GENE REGULATORY MECHANISMS 2022; 1865:194815. [PMID: 35513260 DOI: 10.1016/j.bbagrm.2022.194815] [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: 02/03/2022] [Revised: 04/12/2022] [Accepted: 04/14/2022] [Indexed: 06/14/2023]
Abstract
Circular intronic RNAs (ciRNAs) are still unexplored regarding mechanisms for their emergence. We considered the ATXN2L intron lariat-derived circular RNA (ciRNA-ATXN2L) as an opportunity to conduct a cross-species examination of ciRNA genesis. To this end, we investigated 207 datasets from 4 tissues and from 13 mammalian species. While in eight species, ciRNA-ATXN2L was never detected, in pigs and rabbits, ciRNA-ATXN2L was expressed in all tissues and sometimes at very high levels. Bovine tissues were an intermediate case and in macaques and cats, only ciRNA-ATXN2L traces were detected. The pattern of ciRNA-ATXN2L restricted to only five species is not related to a particular evolution of intronic sequences. To empower our analysis, we considered 221 additional introns including 80 introns where a lariat-derived ciRNA was previously described. The primary driver of micro-ciRNA genesis (< 155 nt as ciRNA-ATXN2L) appears to be the absence of a canonical "A" (i.e. a "tnA" located in the usual branching region) to build the lariat around this adenosine. The balance between available "non canonical-A" (no ciRNA genesis) and "non-A" (ciRNA genesis) for use as a branch point to build the lariat could modify the expression level of ciRNA-ATXN2L. In addition, the rare localization of the 2'-5' bond in an open RNA secondary structure could also negatively affect the lifetime of ciRNAs (macaque ciRNA-ATXN2L). Our analyses suggest that ciRNA-ATXN2L is likely a functionless splice remnant. This study provides a better understanding of the ciRNAs origin, especially drivers for micro ciRNA genesis.
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Affiliation(s)
- Annie Robic
- GenPhySE, Université de Toulouse, INRAE, ENVT, 31326 Castanet Tolosan, France.
| | - Chloé Cerutti
- GenPhySE, Université de Toulouse, INRAE, ENVT, 31326 Castanet Tolosan, France.
| | - Julie Demars
- GenPhySE, Université de Toulouse, INRAE, ENVT, 31326 Castanet Tolosan, France.
| | - Christa Kühn
- Institute of Genome Biology, Research Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany; Faculty of Agricultural and Environmental Sciences, University of Rostock, 18059 Rostock, Germany.
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16
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Vaughn RN, Kochan KJ, Torres AK, Du M, Riley DG, Gill CA, Herring AD, Sanders JO, Riggs PK. Skeletal Muscle Expression of Actinin-3 (ACTN3) in Relation to Feed Efficiency Phenotype of F2Bos indicus - Bos taurus Steers. Front Genet 2022; 13:796038. [PMID: 35186028 PMCID: PMC8850926 DOI: 10.3389/fgene.2022.796038] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/15/2021] [Accepted: 01/10/2022] [Indexed: 01/09/2023] Open
Abstract
In this study, actinin-3 (ACTN3) gene expression was investigated in relation to the feed efficiency phenotype in Bos indicus - Bos taurus crossbred steers. A measure of relative feed efficiency based on residual feed intake relative to predictions from the NRC beef cattle model was analyzed by the use of a mixed linear model that included sire and family nested within sire as fixed effects and age, animal type, sex, condition, and breed as random effects for 173 F2 Nellore-Angus steers. Based on these residual intake observations, individuals were ranked from most efficient to least efficient. Skeletal muscle samples were analyzed from 54 steers in three groups of 18 (high efficiency, low efficiency, and a statistically average group). ACTN3, which encodes a muscle-specific structural protein, was previously identified as a candidate gene from a microarray analysis of RNA extracted from muscle samples obtained from a subset of steers from each of these three efficiency groups. The expression of ACTN3 was evaluated by quantitative reverse transcriptase PCR analysis. The expression of ACTN3 in skeletal muscle was 1.6-fold greater in the inefficient steer group than in the efficient group (p = 0.007). In addition to expression measurements, blocks of SNP haplotypes were assessed for breed or parent of origin effects. A maternal effect was observed for ACTN3 inheritance, indicating that a maternal B. indicus block conferred improved residual feed efficiency relative to the B. taurus copy (p = 0.03). A SNP haplotype analysis was also conducted for m-calpain (CAPN2) and fibronectin 1 (FN1), and a significant breed effect was observed for both genes, with B. indicus and B. taurus alleles each conferring favorable efficiency when inherited maternally (p = 0.03 and p = 0.04). Because the ACTN3 structural protein is specific to fast-twitch (type II) muscle fibers and not present in slow-twitch muscle fibers (type I), muscle samples used for expression analysis were also assayed for fiber type ratio (type II/type I). Inefficient animals had a fast fiber type ratio 1.8-fold greater than the efficient animals (p = 0.027). Because these fiber-types exhibit different metabolic profiles, we hypothesize that animals with a greater proportion of fast-twitch muscle fibers are also less feed efficient.
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Affiliation(s)
- Robert N. Vaughn
- Department of Animal Science, Texas A&M University, College Station, TX, United States
| | - Kelli J. Kochan
- Department of Animal Science, Texas A&M University, College Station, TX, United States
| | - Aline K. Torres
- Department of Animal Science, Texas A&M University, College Station, TX, United States
| | - Min Du
- Department of Animal Sciences, Washington State University, Pullman, WA, United States
| | - David G. Riley
- Department of Animal Science, Texas A&M University, College Station, TX, United States
| | - Clare A. Gill
- Department of Animal Science, Texas A&M University, College Station, TX, United States
| | - Andy D. Herring
- Department of Animal Science, Texas A&M University, College Station, TX, United States
| | - James O. Sanders
- Department of Animal Science, Texas A&M University, College Station, TX, United States
| | - Penny K. Riggs
- Department of Animal Science, Texas A&M University, College Station, TX, United States
- *Correspondence: Penny K. Riggs,
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Nolte W, Weikard R, Albrecht E, Hammon HM, Kühn C. Metabogenomic analysis to functionally annotate the regulatory role of long non-coding RNAs in the liver of cows with different nutrient partitioning phenotype. Genomics 2021; 114:202-214. [PMID: 34923089 DOI: 10.1016/j.ygeno.2021.12.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2020] [Revised: 07/26/2021] [Accepted: 12/13/2021] [Indexed: 11/17/2022]
Abstract
Long non-coding RNAs (lncRNAs) hold gene regulatory potential, but require substantial further functional annotation in livestock. Applying two metabogenomic approaches by combining transcriptomic and metabolomic analyses, we aimed to identify lncRNAs with potential regulatory function for divergent nutrient partitioning of lactating crossbred cows and to establish metabogenomic interaction networks comprising metabolites, genes and lncRNAs. Through correlation analysis of lncRNA expression with transcriptomic and metabolomic data, we unraveled lncRNAs that have a putative regulatory role in energy and lipid metabolism, the urea and tricarboxylic acid cycles, and gluconeogenesis. Especially FGF21, which correlated with a plentitude of differentially expressed genes, differentially abundant metabolites, as well as lncRNAs, suggested itself as a key metabolic regulator. Notably, lncRNAs in close physical proximity to coding-genes as well as lncRNAs with natural antisense transcripts appear to perform a fine-tuning function in gene expression involved in metabolic pathways associated with different nutrient partitioning phenotypes.
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Affiliation(s)
- Wietje Nolte
- Institute of Genome Biology, Research Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany
| | - Rosemarie Weikard
- Institute of Genome Biology, Research Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany
| | - Elke Albrecht
- Institute of Muscle Biology and Growth, Research Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany
| | - Harald M Hammon
- Institute of Nutritional Physiology "Oskar Kellner", Research Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany
| | - Christa Kühn
- Institute of Genome Biology, Research Institute for Farm Animal Biology (FBN), 18196 Dummerstorf, Germany; Faculty of Agricultural and Environmental Sciences, University Rostock, 18059 Rostock, Germany.
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Lagarrigue S, Lorthiois M, Degalez F, Gilot D, Derrien T. LncRNAs in domesticated animals: from dog to livestock species. Mamm Genome 2021; 33:248-270. [PMID: 34773482 PMCID: PMC9114084 DOI: 10.1007/s00335-021-09928-7] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/28/2021] [Accepted: 10/19/2021] [Indexed: 11/29/2022]
Abstract
Animal genomes are pervasively transcribed into multiple RNA molecules, of which many will not be translated into proteins. One major component of this transcribed non-coding genome is the long non-coding RNAs (lncRNAs), which are defined as transcripts longer than 200 nucleotides with low coding-potential capabilities. Domestic animals constitute a unique resource for studying the genetic and epigenetic basis of phenotypic variations involving protein-coding and non-coding RNAs, such as lncRNAs. This review presents the current knowledge regarding transcriptome-based catalogues of lncRNAs in major domesticated animals (pets and livestock species), covering a broad phylogenetic scale (from dogs to chicken), and in comparison with human and mouse lncRNA catalogues. Furthermore, we describe different methods to extract known or discover novel lncRNAs and explore comparative genomics approaches to strengthen the annotation of lncRNAs. We then detail different strategies contributing to a better understanding of lncRNA functions, from genetic studies such as GWAS to molecular biology experiments and give some case examples in domestic animals. Finally, we discuss the limitations of current lncRNA annotations and suggest research directions to improve them and their functional characterisation.
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Affiliation(s)
| | - Matthias Lorthiois
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes) - UMR 6290, 2 av Prof Leon Bernard, F-35000, Rennes, France
| | - Fabien Degalez
- INRAE, INSTITUT AGRO, PEGASE UMR 1348, 35590, Saint-Gilles, France
| | - David Gilot
- CLCC Eugène Marquis, INSERM, Université Rennes, UMR_S 1242, 35000, Rennes, France
| | - Thomas Derrien
- Univ Rennes, CNRS, IGDR (Institut de Génétique et Développement de Rennes) - UMR 6290, 2 av Prof Leon Bernard, F-35000, Rennes, France.
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Micheel J, Safrastyan A, Wollny D. Advances in Non-Coding RNA Sequencing. Noncoding RNA 2021; 7:70. [PMID: 34842804 PMCID: PMC8628893 DOI: 10.3390/ncrna7040070] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2021] [Revised: 10/22/2021] [Accepted: 10/26/2021] [Indexed: 12/11/2022] Open
Abstract
Non-coding RNAs (ncRNAs) comprise a set of abundant and functionally diverse RNA molecules. Since the discovery of the first ncRNA in the 1960s, ncRNAs have been shown to be involved in nearly all steps of the central dogma of molecular biology. In recent years, the pace of discovery of novel ncRNAs and their cellular roles has been greatly accelerated by high-throughput sequencing. Advances in sequencing technology, library preparation protocols as well as computational biology helped to greatly expand our knowledge of which ncRNAs exist throughout the kingdoms of life. Moreover, RNA sequencing revealed crucial roles of many ncRNAs in human health and disease. In this review, we discuss the most recent methodological advancements in the rapidly evolving field of high-throughput sequencing and how it has greatly expanded our understanding of ncRNA biology across a large number of different organisms.
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Affiliation(s)
| | | | - Damian Wollny
- RNA Bioinformatics/High Throughput Analysis, Faculty of Mathematics and Computer Science, Friedrich Schiller University, 07743 Jena, Germany; (J.M.); (A.S.)
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Chitneedi PK, Weikard R, Arranz JJ, Martínez-Valladares M, Kuehn C, Gutiérrez-Gil B. Identification of Regulatory Functions of LncRNAs Associated With T. circumcincta Infection in Adult Sheep. Front Genet 2021; 12:685341. [PMID: 34194481 PMCID: PMC8236958 DOI: 10.3389/fgene.2021.685341] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 05/20/2021] [Indexed: 12/13/2022] Open
Abstract
Several recent studies have demonstrated the role of long non-coding RNAs (lncRNAs) in regulating the defense mechanism against parasite infections, but no studies are available that investigated their relevance for immune response to nematode infection in sheep. Thus, the aim of the current study was to (i) detect putative lncRNAs that are expressed in the abomasal lymph node of adult sheep after an experimental infection with the gastrointestinal nematode (GIN) Teladorsagia circumcincta and (ii) to elucidate their potential functional role associated with the differential host immune response. We hypothesized that putative lncRNAs differentially expressed (DE) between samples from animals that differ in resistance to infection may play a significant regulatory role in response to nematode infection in adult sheep. To obtain further support for our hypothesis, we performed co-expression and functional gene enrichment analyses with the differentially expressed lncRNAs (DE lncRNAs). In a conservative approach, we included for this predictive analysis only those lncRNAs that are confirmed and supported by documentation of expression in gastrointestinal tissues in the current sheep gene atlas. We identified 9,105 putative lncRNA transcripts corresponding to 7,124 gene loci. Of these, 457 were differentially expressed lncRNA loci (DELs) with 683 lncRNA transcripts. Based on a gene co-expression analysis via weighted gene co-expression network analysis, 12 gene network modules (GNMs) were found significantly correlated with at least one of 10 selected target DE lncRNAs. Based on the principle of “guilt-by-association,” the DE genes from each of the three most significantly correlated GNMs were subjected to a gene enrichment analysis. The significant pathways associated with DE lncRNAs included ERK5 Signaling, SAPK/JNK Signaling, RhoGDI Signaling, EIF2 Signaling, Regulation of eIF4 and p70S6K Signaling and Oxidative Phosphorylation pathways. They belong to signaling pathway categories like Cellular Growth, Proliferation and Development, Cellular Stress and Injury, Intracellular and Second Messenger Signaling and Apoptosis. Overall, this lncRNA study conducted in adult sheep after GIN infection provided first insights into the potential functional role of lncRNAs in the differential host response to nematode infection.
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Affiliation(s)
| | - Rosemarie Weikard
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Juan J Arranz
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, León, Spain
| | - María Martínez-Valladares
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad de León, León, Spain.,Instituto de Ganadería de Montaña, CSIC-Universidad de León, León, Spain
| | - Christa Kuehn
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany.,Faculty of Agricultural and Environmental Sciences, University of Rostock, Rostock, Germany
| | - Beatriz Gutiérrez-Gil
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, León, Spain
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21
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Robic A, Cerutti C, Kühn C, Faraut T. Comparative Analysis of the Circular Transcriptome in Muscle, Liver, and Testis in Three Livestock Species. Front Genet 2021; 12:665153. [PMID: 34040640 PMCID: PMC8141914 DOI: 10.3389/fgene.2021.665153] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 04/07/2021] [Indexed: 12/13/2022] Open
Abstract
Circular RNAs have been observed in a large number of species and tissues and are now recognized as a clear component of the transcriptome. Our study takes advantage of functional datasets produced within the FAANG consortium to investigate the pervasiveness of circular RNA transcription in farm animals. We describe here the circular transcriptional landscape in pig, sheep and bovine testicular, muscular and liver tissues using total 66 RNA-seq datasets. After an exhaustive detection of circular RNAs, we propose an annotation of exonic, intronic and sub-exonic circRNAs and comparative analyses of circRNA content to evaluate the variability between individuals, tissues and species. Despite technical bias due to the various origins of the datasets, we were able to characterize some features (i) (ruminant) liver contains more exonic circRNAs than muscle (ii) in testis, the number of exonic circRNAs seems associated with the sexual maturity of the animal. (iii) a particular class of circRNAs, sub-exonic circRNAs, are produced by a large variety of multi-exonic genes (protein-coding genes, long non-coding RNAs and pseudogenes) and mono-exonic genes (protein-coding genes from mitochondrial genome and small non-coding genes). Moreover, for multi-exonic genes there seems to be a relationship between the sub-exonic circRNAs transcription level and the linear transcription level. Finally, sub-exonic circRNAs produced by mono-exonic genes (mitochondrial protein-coding genes, ribozyme, and sno) exhibit a particular behavior. Caution has to be taken regarding the interpretation of the unannotated circRNA proportion in a given tissue/species: clusters of circRNAs without annotation were characterized in genomic regions with annotation and/or assembly problems of the respective animal genomes. This study highlights the importance of improving genome annotation to better consider candidate circRNAs and to better understand the circular transcriptome. Furthermore, it emphasizes the need for considering the relative “weight” of circRNAs/parent genes for comparative analyses of several circular transcriptomes. Although there are points of agreement in the circular transcriptome of the same tissue in two species, it will be not possible to do without the characterization of it in both species.
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Affiliation(s)
- Annie Robic
- INRAE, ENVT, GenPhySE, Université de Toulouse, Castanet-Tolosan, France
| | - Chloé Cerutti
- INRAE, ENVT, GenPhySE, Université de Toulouse, Castanet-Tolosan, France
| | - Christa Kühn
- Institute Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany.,Faculty of Agricultural and Environmental Sciences, University of Rostock, Rostock, Germany
| | - Thomas Faraut
- INRAE, ENVT, GenPhySE, Université de Toulouse, Castanet-Tolosan, France
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22
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de Lima AO, Afonso J, Edson J, Marcellin E, Palfreyman R, Porto-Neto LR, Reverter A, Fortes MRS. Network Analyses Predict Small RNAs That Might Modulate Gene Expression in the Testis and Epididymis of Bos indicus Bulls. Front Genet 2021; 12:610116. [PMID: 33995471 PMCID: PMC8120238 DOI: 10.3389/fgene.2021.610116] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2020] [Accepted: 03/19/2021] [Indexed: 12/16/2022] Open
Abstract
Spermatogenesis relies on complex molecular mechanisms, essential for the genesis and differentiation of the male gamete. Germ cell differentiation starts at the testicular parenchyma and finishes in the epididymis, which has three main regions: head, body, and tail. RNA-sequencing data of the testicular parenchyma (TP), head epididymis (HE), and tail epididymis (TE) from four bulls (three biopsies per bull: 12 samples) were subjected to differential expression analyses, functional enrichment analyses, and co-expression analyses. The aim was to investigate the co-expression and infer possible regulatory roles for transcripts involved in the spermatogenesis of Bos indicus bulls. Across the three pairwise comparisons, 3,826 differentially expressed (DE) transcripts were identified, of which 384 are small RNAs. Functional enrichment analysis pointed to gene ontology (GO) terms related to ion channel activity, detoxification of copper, neuroactive receptors, and spermatogenesis. Using the regulatory impact factor (RIF) algorithm, we detected 70 DE small RNAs likely to regulate the DE transcripts considering all pairwise comparisons among tissues. The pattern of small RNA co-expression suggested that these elements are involved in spermatogenesis regulation. The 3,826 DE transcripts (mRNAs and small RNAs) were further subjected to co-expression analyses using the partial correlation and information theory (PCIT) algorithm for network prediction. Significant correlations underpinned the co-expression network, which had 2,216 transcripts connected by 158,807 predicted interactions. The larger network cluster was enriched for male gamete generation and had 15 miRNAs with significant RIF. The miRNA bta-mir-2886 showed the highest number of connections (601) and was predicted to down-regulate ELOVL3, FEZF2, and HOXA13 (negative co-expression correlations and confirmed with TargetScan). In short, we suggest that bta-mir-2886 and other small RNAs might modulate gene expression in the testis and epididymis, in Bos indicus cattle.
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Affiliation(s)
- Andressa O de Lima
- Department of Production and Animal Health, School of Veterinary Medicine, São Paulo State University (UNESP), Araçatuba, Brazil
| | - Juliana Afonso
- Department of Animal Science, University of São Paulo/ESALQ, Piracicaba, Brazil
| | - Janette Edson
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia
| | - Esteban Marcellin
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St Lucia, QLD, Australia
| | - Robin Palfreyman
- Australian Institute for Bioengineering and Nanotechnology (AIBN), The University of Queensland, St Lucia, QLD, Australia
| | - Laercio R Porto-Neto
- CSIRO Agriculture and Food, Queensland Bioscience Precinct, St. Lucia, QLD, Australia
| | - Antonio Reverter
- CSIRO Agriculture and Food, Queensland Bioscience Precinct, St. Lucia, QLD, Australia
| | - Marina R S Fortes
- School of Chemistry and Molecular Biosciences, The University of Queensland, St Lucia, QLD, Australia
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23
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Luo M, Zhang L, Yang H, Luo K, Qing C. Long non‑coding RNA NEAT1 promotes ovarian cancer cell invasion and migration by interacting with miR‑1321 and regulating tight junction protein 3 expression. Mol Med Rep 2020; 22:3429-3439. [PMID: 32945443 PMCID: PMC7453588 DOI: 10.3892/mmr.2020.11428] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Accepted: 06/17/2020] [Indexed: 12/13/2022] Open
Abstract
Previous studies have reported that long non‑coding RNAs (lncRNAs) have a significant role in the metastasis of tumors, including ovarian cancer (OC). The aim of the present study was to demonstrate the function and working mechanism of lncRNA nuclear enriched abundant transcript 1 (NEAT1) in OC. The expressions of NEAT1 in OC were measured by reverse transcription‑quantitativePCR (RT‑qPCR). The effects of NEAT1 on cell proliferation, invasion, migration and epithelial‑mesenchymal transition (EMT) were detected by Cell Counting Kit‑8, transwell and wound healing assays, and western blotting. Dual‑luciferase reporter assays were performed to confirm the correlated between NEAT and miR‑1321, miR‑1321 and TJP3. The effect of NEAT1 on miR‑1321 and TJP3 was confirmed by RT‑qPCR and western blotting. Elevated expression of NEAT1 was observed in OC cell lines, and NEAT1 expression was found to be positively related to the expression of tight junction protein 3 (TJP3), which is important in cancer development. Moreover, the present results indicated that NEAT1 and TJP3 expression levels were negatively correlated with microRNA (miR)‑1321 expression in OC. Knockdown of NEAT1 attenuated the migration and invasion of OC cells, as well as increased miR‑1321 expression and in turn led to the reduction of TJP3. Thus, the present study demonstrated that NEAT1 regulates TJP3 expression by sponging miR‑1321 and enhances the epithelial‑mesenchymal transition, invasion and migration of OC cells. Overall, the present study identified the function and mechanism of NEAT1 in OC, suggesting that NEAT1 may be a promising therapeutic target for OC metastasis.
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Affiliation(s)
- Min Luo
- School of Medicine, Yunnan University, Kunming, Yunnan 650091, P.R. China
- School of Pharmaceutical Sciences and Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, Kunming, Yunnan 650500, P.R. China
- Yunnan Key Laboratory of Quality Standards for Traditional Chinese Medicine and National Medicine, Yunnan University of Chinese Medicine, Kunming, Yunnan 650500, P.R. China
| | - Lei Zhang
- Department of Gynecology, Yunnan Tumor Hospital & The Third Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650118, P.R. China
| | - Hongying Yang
- Department of Gynecology, Yunnan Tumor Hospital & The Third Affiliated Hospital of Kunming Medical University, Kunming, Yunnan 650118, P.R. China
| | - Kaili Luo
- School of Pharmaceutical Sciences and Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, Kunming, Yunnan 650500, P.R. China
| | - Chen Qing
- School of Pharmaceutical Sciences and Yunnan Key Laboratory of Pharmacology for Natural Products, Kunming Medical University, Kunming, Yunnan 650500, P.R. China
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24
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Alexandre PA, Reverter A, Berezin RB, Porto-Neto LR, Ribeiro G, Santana MHA, Ferraz JBS, Fukumasu H. Exploring the Regulatory Potential of Long Non-Coding RNA in Feed Efficiency of Indicine Cattle. Genes (Basel) 2020; 11:genes11090997. [PMID: 32854445 PMCID: PMC7565090 DOI: 10.3390/genes11090997] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2020] [Revised: 08/19/2020] [Accepted: 08/21/2020] [Indexed: 12/12/2022] Open
Abstract
Long non-coding RNA (lncRNA) can regulate several aspects of gene expression, being associated with complex phenotypes in humans and livestock species. In taurine beef cattle, recent evidence points to the involvement of lncRNA in feed efficiency (FE), a proxy for increased productivity and sustainability. Here, we hypothesized specific regulatory roles of lncRNA in FE of indicine cattle. Using RNA-Seq data from the liver, muscle, hypothalamus, pituitary gland and adrenal gland from Nellore bulls with divergent FE, we submitted new transcripts to a series of filters to confidently predict lncRNA. Then, we identified lncRNA that were differentially expressed (DE) and/or key regulators of FE. Finally, we explored lncRNA genomic location and interactions with miRNA and mRNA to infer potential function. We were able to identify 126 relevant lncRNA for FE in Bos indicus, some with high homology to previously identified lncRNA in Bos taurus and some possible specific regulators of FE in indicine cattle. Moreover, lncRNA identified here were linked to previously described mechanisms related to FE in hypothalamus-pituitary-adrenal axis and are expected to help elucidate this complex phenotype. This study contributes to expanding the catalogue of lncRNA, particularly in indicine cattle, and identifies candidates for further studies in animal selection and management.
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Affiliation(s)
- Pâmela A. Alexandre
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of Sao Paulo, Pirassununga, Sao Paulo 13635-900, Brazil; (R.B.B.); (G.R.); (J.B.S.F.); (H.F.)
- Commonwealth Scientific and Industrial Research Organization, Agriculture & Food, St. Lucia, Brisbane, QLD 4067, Australia; (A.R.); (L.R.P.-N.)
- Correspondence: ; Tel.: +61-7-32142453
| | - Antonio Reverter
- Commonwealth Scientific and Industrial Research Organization, Agriculture & Food, St. Lucia, Brisbane, QLD 4067, Australia; (A.R.); (L.R.P.-N.)
| | - Roberta B. Berezin
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of Sao Paulo, Pirassununga, Sao Paulo 13635-900, Brazil; (R.B.B.); (G.R.); (J.B.S.F.); (H.F.)
| | - Laercio R. Porto-Neto
- Commonwealth Scientific and Industrial Research Organization, Agriculture & Food, St. Lucia, Brisbane, QLD 4067, Australia; (A.R.); (L.R.P.-N.)
| | - Gabriela Ribeiro
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of Sao Paulo, Pirassununga, Sao Paulo 13635-900, Brazil; (R.B.B.); (G.R.); (J.B.S.F.); (H.F.)
| | - Miguel H. A. Santana
- Department of Animal Science, Faculty of Animal Science and Food Engineering, University of Sao Paulo, Pirassununga, Sao Paulo 13635-900, Brazil;
| | - José Bento S. Ferraz
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of Sao Paulo, Pirassununga, Sao Paulo 13635-900, Brazil; (R.B.B.); (G.R.); (J.B.S.F.); (H.F.)
| | - Heidge Fukumasu
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of Sao Paulo, Pirassununga, Sao Paulo 13635-900, Brazil; (R.B.B.); (G.R.); (J.B.S.F.); (H.F.)
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25
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Chen Q, Shen J, Hanif Q, Chen N, Huang Y, Dang R, Lan X, Chen H, Lei C. Whole genome analyses revealed genomic difference between European taurine and East Asian taurine. J Anim Breed Genet 2020; 138:56-68. [PMID: 32770713 DOI: 10.1111/jbg.12501] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/03/2020] [Revised: 06/29/2020] [Accepted: 07/10/2020] [Indexed: 12/19/2022]
Abstract
European taurine and East Asian taurine are two main clades in Bos taurus, but their genomic differences are not clearly elucidated. Here, we sequenced 16 Mongolian cattle genomes and compared them to the 92 genomes of 10 representative breeds worldwide. We found the highest LD level in Mishima cattle and the fastest LD decay in European taurine. Phylogenetic analysis revealed that Mongolian, Hanwoo and Mishima cattle were clustered into East Asian taurine. From selective sweep, gene annotation, functional enrichment and differential expression analysis, we identified selective signals including genes and/or pathways related to rapid growth and large body size in European taurine, and superior meat quality in East Asian taurine. Our findings will help us understand the evolutionary history and formation process of the breeds and provide theoretical materials regarding the genetic mechanism underlying breed characteristics and molecular breeding programmes of the taurine clades in the future.
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Affiliation(s)
- Qiuming Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Jiafei Shen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Quratulain Hanif
- National Institute for Biotechnology and Genetic Engineering, Pakistan Institute of Engineering and Applied Sciences, Faisalabad, Pakistan.,Pakistan Institute of Engineering and Applied Sciences, Nilore, Islamabad, Pakistan
| | - Ningbo Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Yongzhen Huang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Ruihua Dang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Xianyong Lan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Hong Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Chuzhao Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
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26
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Jia G, Wang Y, Yu Y, Li Z, Wang X. Long non‑coding RNA NR2F1‑AS1 facilitates the osteosarcoma cell malignant phenotype via the miR‑485‑5p/miR‑218‑5p/BIRC5 axis. Oncol Rep 2020; 44:1583-1595. [PMID: 32945459 PMCID: PMC7448419 DOI: 10.3892/or.2020.7698] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Accepted: 06/17/2020] [Indexed: 12/18/2022] Open
Abstract
Long non-coding RNA (lncRNA) NR2F1 antisense RNA 1 (NR2F1-AS1) has been reported to be an oncogene in several cancer types, including osteosarcoma (OS). However, the underlying fundamental molecular mechanism of NR2F1-AS1 in OS remains largely unknown, which the present study aimed to elucidate. The present study demonstrated that NR2F1-AS1 expression is markedly increased in OS, and NR2F1-AS1 was shown to exert oncogenic functions in OS. Further molecular mechanistic studies revealed that microRNA (miR)-485-5p and miR-218-5p were direct targets of NR2F1-AS1. More importantly, miR-485-5p and miR-218-5p exhibited low expression levels and were negatively correlated with NR2F1-AS1 expression in OS tissues. It was then identified that baculoviral inhibitor of apoptosis repeat-containing 5 (BIRC5) was a direct target of miR-485-5p and miR-218-5p in OS cells. Furthermore, a series of experiments suggested that NR2F1-AS1 affects the proliferation, migration, invasion and apoptosis of OS cells by regulating BIRC5. Finally, it was revealed that silencing of NR2F1-AS1 repressed the OS cell malignant phenotype by binding with miR-485-5p and miR-218-5p, and then downregulating BIRC5 expression, which suggests that the NR2F1-AS1/miR-485-5p/miR-218-5p/BIRC5 axis could be a potential target for treating OS.
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Affiliation(s)
- Guanghui Jia
- Department of Foot and Ankle Surgery, Zhengzhou Orthopedics Hospital, Zhengzhou, Henan 450052, P.R. China
| | - Yalei Wang
- Department of Foot and Ankle Surgery, Zhengzhou Orthopedics Hospital, Zhengzhou, Henan 450052, P.R. China
| | - Yali Yu
- Department of Laboratory, Zhengzhou Orthopedics Hospital, Zhengzhou, Henan 450052, P.R. China
| | - Zijun Li
- Department of Laboratory, Zhengzhou Orthopedics Hospital, Zhengzhou, Henan 450052, P.R. China
| | - Xiangyu Wang
- Department of Foot and Ankle Surgery, Zhengzhou Orthopedics Hospital, Zhengzhou, Henan 450052, P.R. China
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27
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Indication of Premelanosome Protein (PMEL) Expression Outside of Pigmented Bovine Skin Suggests Functions Beyond Eumelanogenesis. Genes (Basel) 2020; 11:genes11070788. [PMID: 32668786 PMCID: PMC7397160 DOI: 10.3390/genes11070788] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/13/2020] [Revised: 06/25/2020] [Accepted: 07/07/2020] [Indexed: 01/23/2023] Open
Abstract
The premelanosome protein (PMEL) is important for fibril formation within melanosomes during vertebrate melanogenesis. Fibrils form a matrix for pigment deposition within pigmented tissues such as skin and hair. PMEL mutations are known to modulate eumelanic pigmentation in vertebrates. However, in bovines, PMEL mutations were also found to alter pheomelanic pigmentation resulting in coat color dilution. Furthermore, epistatic effects of a mutated PMEL allele were detected in the phenotypic expression of the bovine hair defect "rat-tail syndrome" (RTS) characterized by charcoal coat color and hair deformation. Reports about PMEL gene expression in non-pigmented tissues raised the hypothesis that there may be unknown functions of the PMEL protein beyond eumelanin deposition to PMEL fibrils. In our study, we analysed the PMEL protein expression in pigmented skin and non-pigmented bovine tissues (non-pigmented skin, thyroid gland, rumen, liver, kidney, and adrenal gland cortex). We found that a processed form of the bovine PMEL protein is expressed in pigmented as well as in non-pigmented tissues, which is in line with gene expression data from targeted RT-PCR and whole transcriptome RNAseq analysis. The PMEL protein is located in membranes and within the cytosol of epithelial cells. Based on our data from bovine tissues, we concluded that at least in cattle PMEL potentially has additional, yet unexplored functions, which might contribute to effects of PMEL mutations on pheomelanin coat color dilution and charcoal coat color in RTS animals. However, indication of PMEL protein in unpigmented cells and tissues will require further confirmation in the future, because there have been no confirmed reports before, which had detected bovine PMEL protein with specific antibodies either in pigmented or unpigmented tissue.
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28
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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:E3292. [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] [Grants] [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
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29
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Ehsani R, Drabløs F. Enhanced identification of significant regulators of gene expression. BMC Bioinformatics 2020; 21:134. [PMID: 32252623 PMCID: PMC7132893 DOI: 10.1186/s12859-020-3468-z] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/12/2019] [Accepted: 03/24/2020] [Indexed: 12/29/2022] Open
Abstract
Background Diseases like cancer will lead to changes in gene expression, and it is relevant to identify key regulatory genes that can be linked directly to these changes. This can be done by computing a Regulatory Impact Factor (RIF) score for relevant regulators. However, this computation is based on estimating correlated patterns of gene expression, often Pearson correlation, and an assumption about a set of specific regulators, normally transcription factors. This study explores alternative measures of correlation, using the Fisher and Sobolev metrics, and an extended set of regulators, including epigenetic regulators and long non-coding RNAs (lncRNAs). Data on prostate cancer have been used to explore the effect of these modifications. Results A tool for computation of RIF scores with alternative correlation measures and extended sets of regulators was developed and tested on gene expression data for prostate cancer. The study showed that the Fisher and Sobolev metrics lead to improved identification of well-documented regulators of gene expression in prostate cancer, and the sets of identified key regulators showed improved overlap with previously defined gene sets of relevance to cancer. The extended set of regulators lead to identification of several interesting candidates for further studies, including lncRNAs. Several key processes were identified as important, including spindle assembly and the epithelial-mesenchymal transition (EMT). Conclusions The study has shown that using alternative metrics of correlation can improve the performance of tools based on correlation of gene expression in genomic data. The Fisher and Sobolev metrics should be considered also in other correlation-based applications.
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Affiliation(s)
- Rezvan Ehsani
- Department of Mathematics, University of Zabol, Zabol, Iran. .,Department of Bioinformatics, University of Zabol, Zabol, Iran.
| | - Finn Drabløs
- Department of Cancer Research and Molecular Medicine, NTNU - Norwegian University of Science and Technology, NO-7491, Trondheim, Norway.
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30
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Yan XM, Zhang Z, Meng Y, Li HB, Gao L, Luo D, Jiang H, Gao Y, Yuan B, Zhang JB. Genome-wide identification and analysis of circular RNAs differentially expressed in the longissimus dorsi between Kazakh cattle and Xinjiang brown cattle. PeerJ 2020; 8:e8646. [PMID: 32211228 PMCID: PMC7081781 DOI: 10.7717/peerj.8646] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2019] [Accepted: 01/27/2020] [Indexed: 12/18/2022] Open
Abstract
Xinjiang brown cattle have better meat quality than Kazakh cattle. Circular RNAs (circRNAs) are a type of RNA that can participate in the regulation of gene transcription. Whether circRNAs are differentially expressed in the longissimus dorsi between these two types of cattle and whether differentially expressed circRNAs regulate muscle formation and differentiation are still unknown. In this study, we established two RNA-seq libraries, each of which consisted of three samples. A total of 5,177 circRNAs were identified in longissimus dorsi samples from Kazakh cattle and Xinjiang brown cattle using the Illumina platform, 46 of which were differentially expressed. Fifty-five Gene Ontology terms were significantly enriched, and 12 Kyoto Encyclopedia of Genes and Genomes pathways were identified for the differentially expressed genes. Muscle biological processes were associated with the origin genes of the differentially expressed circRNAs. In addition, we randomly selected six overexpressed circRNAs and compared their levels in longissimus dorsi tissue from Kazakh cattle and Xinjiang brown cattle using RT-qPCR. Furthermore, we predicted 66 interactions among 65 circRNAs and 14 miRNAs using miRanda and established a coexpression network. A few microRNAs known for their involvement in myoblast regulation, such as miR-133b and miR-664a, were identified in this network. Notably, bta_circ_03789_1 and bta_circ_05453_1 are potential miRNA sponges that may regulate insulin-like growth factor 1 receptor expression. These findings provide an important reference for prospective investigations of the role of circRNA in longissimus muscle growth and development. This study provides a theoretical basis for targeting circRNAs to improve beef quality and taste.
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Affiliation(s)
- Xiang-Min Yan
- Department of Laboratory Animals, Jilin University, Changchun, Jilin, China.,Institute of Animal Husbandry, Xinjiang Academy of Animal Husbandry, Ürümqi, Xinjiang, China
| | - Zhe Zhang
- Department of Laboratory Animals, Jilin University, Changchun, Jilin, China
| | - Yu Meng
- Department of Laboratory Animals, Jilin University, Changchun, Jilin, China
| | - Hong-Bo Li
- Institute of Animal Husbandry, Xinjiang Academy of Animal Husbandry, Ürümqi, Xinjiang, China
| | - Liang Gao
- Yili Vocational and Technical College, Yili, Xinjiang, China
| | - Dan Luo
- Department of Laboratory Animals, Jilin University, Changchun, Jilin, China
| | - Hao Jiang
- Department of Laboratory Animals, Jilin University, Changchun, Jilin, China
| | - Yan Gao
- Department of Laboratory Animals, Jilin University, Changchun, Jilin, China
| | - Bao Yuan
- Department of Laboratory Animals, Jilin University, Changchun, Jilin, China
| | - Jia-Bao Zhang
- Department of Laboratory Animals, Jilin University, Changchun, Jilin, China
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