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Triantaphyllopoulos KA. Long Non-Coding RNAs and Their "Discrete" Contribution to IBD and Johne's Disease-What Stands out in the Current Picture? A Comprehensive Review. Int J Mol Sci 2023; 24:13566. [PMID: 37686376 PMCID: PMC10487966 DOI: 10.3390/ijms241713566] [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: 07/25/2023] [Revised: 08/23/2023] [Accepted: 08/27/2023] [Indexed: 09/10/2023] Open
Abstract
Non-coding RNAs (ncRNA) have paved the way to new perspectives on the regulation of gene expression, not only in biology and medicine, but also in associated fields and technologies, ensuring advances in diagnostic means and therapeutic modalities. Critical in this multistep approach are the associations of long non-coding RNA (lncRNA) with diseases and their causal genes in their networks of interactions, gene enrichment and expression analysis, associated pathways, the monitoring of the involved genes and their functional roles during disease progression from one stage to another. Studies have shown that Johne's Disease (JD), caused by Mycobacterium avium subspecies partuberculosis (MAP), shares common lncRNAs, clinical findings, and other molecular entities with Crohn's Disease (CD). This has been a subject of vigorous investigation owing to the zoonotic nature of this condition, although results are still inconclusive. In this review, on one hand, the current knowledge of lncRNAs in cells is presented, focusing on the pathogenesis of gastrointestinal-related pathologies and MAP-related infections and, on the other hand, we attempt to dissect the associated genes and pathways involved. Furthermore, the recently characterized and novel lncRNAs share common pathologies with IBD and JD, including the expression, molecular networks, and dataset analysis results. These are also presented in an attempt to identify potential biomarkers pertinent to cattle and human disease phenotypes.
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Affiliation(s)
- Kostas A Triantaphyllopoulos
- Department of Biotechnology, School of Applied Biology and Biotechnology, Agricultural University of Athens, 75 Iera Odos St., 11855 Athens, Greece
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2
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Dou J, Thangaraj SV, Puttabyatappa M, Elangovan VR, Bakulski K, Padmanabhan V. Developmental programming: Adipose depot-specific regulation of non-coding RNAs and their relation to coding RNA expression in prenatal testosterone and prenatal bisphenol-A -treated female sheep. Mol Cell Endocrinol 2023; 564:111868. [PMID: 36708980 PMCID: PMC10069610 DOI: 10.1016/j.mce.2023.111868] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Revised: 01/19/2023] [Accepted: 01/22/2023] [Indexed: 01/27/2023]
Abstract
Inappropriate developmental exposure to steroids is linked to metabolic disorders. Prenatal testosterone excess or bisphenol A (BPA, an environmental estrogen mimic) leads to insulin resistance and adipocyte disruptions in female lambs. Adipocytes are key regulators of insulin sensitivity. Metabolic tissue-specific differences in insulin sensitivity coupled with adipose depot-specific changes in key mRNAs, were previously observed with prenatal steroid exposure. We hypothesized that depot-specific changes in the non-coding RNA (ncRNA) - regulators of gene expression would account for the direction of changes seen in mRNAs. Non-coding RNA (lncRNA, miRNA, snoRNA, snRNA) from various adipose depots of prenatal testosterone and BPA-treated animals were sequenced. Adipose depot-specific changes in the ncRNA that are consistent with the depot-specific mRNA expression in terms of directionality of changes and functional implications in insulin resistance, adipocyte differentiation and cardiac hypertrophy were found. Importantly, the adipose depot-specific ncRNA changes were model-specific and mutually exclusive, suggestive of different regulatory entry points in this regulation.
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Affiliation(s)
- John Dou
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, USA
| | | | | | | | - Kelly Bakulski
- Department of Epidemiology, University of Michigan, Ann Arbor, MI, USA.
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3
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Chen M, Lian D, Li Y, Zhao Y, Xu X, Liu Z, Zhang J, Zhang X, Wu S, Qi S, Deng S, Yu K, Lian Z. Global Long Noncoding RNA Expression Profiling of MSTN and FGF5 Double-Knockout Sheep Reveals the Key Gatekeepers of Skeletal Muscle Development. DNA Cell Biol 2023; 42:163-175. [PMID: 36917699 DOI: 10.1089/dna.2022.0574] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 03/16/2023] Open
Abstract
Improving livestock and poultry growth rates and increasing meat production are urgently needed worldwide. Previously, we produced a myostatin (MSTN) and fibroblast growth factor 5 (FGF5) double-knockout (MF-/-) sheep by CRISPR Cas9 system to improve meat production, and also wool production. Both MF-/- sheep and the F1 generation (MF+/-) sheep showed an obvious "double-muscle" phenotype. In this study, we identified the expression profiles of long noncoding RNAs (lncRNAs) in wild-type and MF+/- sheep, then screened out the key candidate lncRNAs that can regulate myogenic differentiation and skeletal muscle development. These key candidate lncRNAs can serve as critical gatekeepers for muscle contraction, calcium ion transport and skeletal muscle cell differentiation, apoptosis, autophagy, and skeletal muscle inflammation, further revealing that lncRNAs play crucial roles in regulating muscle phenotype in MF+/- sheep. In conclusion, our newly identified lncRNAs may emerge as novel molecules for muscle development or muscle disease and provide a new reference for MSTN-mediated regulation of skeletal muscle development.
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Affiliation(s)
- Mingming Chen
- Beijing Key Laboratory for Animal Genetic Improvement, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Di Lian
- State Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing, China
| | - Yan Li
- Laboratory Animal Center of the Academy of Military Medical Sciences, Beijing, China
| | - Yue Zhao
- Beijing Key Laboratory for Animal Genetic Improvement, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xueling Xu
- Beijing Key Laboratory for Animal Genetic Improvement, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Zhimei Liu
- Beijing Key Laboratory for Animal Genetic Improvement, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Jinlong Zhang
- Institute of Animal Husbandry and Veterinary Medicine, Tianjin Academy of Agricultural Sciences, Tianjin, China
| | - Xiaosheng Zhang
- Institute of Animal Husbandry and Veterinary Medicine, Tianjin Academy of Agricultural Sciences, Tianjin, China
| | - Sujun Wu
- Beijing Key Laboratory for Animal Genetic Improvement, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Shiyu Qi
- Beijing Key Laboratory for Animal Genetic Improvement, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Shoulong Deng
- NHC Key Laboratory of Human Disease Comparative Medicine, Institute of Laboratory Animal Sciences, Chinese Academy of Medical Sciences and Comparative Medicine Center, Peking Union Medical College, Beijing, China
| | - Kun Yu
- Beijing Key Laboratory for Animal Genetic Improvement, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Zhengxing Lian
- Beijing Key Laboratory for Animal Genetic Improvement, National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics and Breeding of the Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
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4
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Do DN, Suravajhala P. Editorial: Role of Non-Coding RNAs in Animals. Animals (Basel) 2023; 13:ani13050805. [PMID: 36899662 PMCID: PMC10000048 DOI: 10.3390/ani13050805] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/26/2022] [Revised: 01/10/2023] [Accepted: 02/21/2023] [Indexed: 02/25/2023] Open
Abstract
The importance of non-coding RNAs (ncRNAs), such as microRNAs (miRNA), long non-coding RNAs (lncRNA), and circular RNAs (circRNA), in gene regulation is increasingly being appreciated in many species [...].
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Affiliation(s)
- Duy Ngoc Do
- Faculty of Veterinary Medicine, Viet Nam National University of Agriculture, Hanoi 100000, Vietnam
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS B2N 5E3, Canada
- Correspondence: (D.N.D.); (P.S.)
| | - Prashanth Suravajhala
- Bioclues.org, Hyderabad 500072, India
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana 690525, India
- Correspondence: (D.N.D.); (P.S.)
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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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Zhang BB, Li MX, Wang HN, Liu C, Sun YY, Ma TH. An integrative analysis of lncRNAs and mRNAs highlights the potential roles of lncRNAs in the process of follicle selection in Taihang chickens. Theriogenology 2023; 195:122-130. [DOI: 10.1016/j.theriogenology.2022.10.024] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2022] [Revised: 10/17/2022] [Accepted: 10/20/2022] [Indexed: 11/07/2022]
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Čítek J, Brzáková M, Bauer J, Tichý L, Sztankóová Z, Vostrý L, Steyn Y. Genome-Wide Association Study for Body Conformation Traits and Fitness in Czech Holsteins. Animals (Basel) 2022; 12:ani12243522. [PMID: 36552441 PMCID: PMC10375906 DOI: 10.3390/ani12243522] [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: 09/27/2022] [Revised: 12/07/2022] [Accepted: 12/12/2022] [Indexed: 12/15/2022] Open
Abstract
The aim of this study was a genome-wide association study (GWAS) on conformation traits using 25,486 genotyped Czech Holsteins, with 35,227 common SNPs for each genotype. Linear trait records were collected between 1995 and 2020. The Interbull information from Multiple Across Country Evaluation (MACE) was included for bulls that mostly had daughter records in a foreign country. When using the Bonferroni correction, the number of SNPs that were either significant or approached the significance threshold was low-dairy capacity composite on BTA4, feet and legs composite BTA21, total score BTA10, stature BTA24, body depth BTA6, angularity BTA20, fore udder attachment BTA10. Without the Bonferroni correction, the total number of significant or near of significance SNPs was 32. The SNPs were localized on BTA1,2,4,5,6,7,8,18,22,25,26,28 for dairy capacity composite, BTA15,21 for feet and legs composite, BTA10 for total score, BTA24 stature, BTA6,23 body depth, BTA20 angularity, BTA2 rump angle, BTA9,10 rear legs rear view, BTA2,19 rear legs side view, BTA10 fore udder attachment, BTA2 udder depth, BTA10 rear udder height, BTA12 central alignment, BTA24 rear teat placement, BTA8,29 rear udder width. The results provide biological information for the improvement of body conformation and fitness in the Holstein population.
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Affiliation(s)
- Jindřich Čítek
- Department of Genetics and Agricultural Biotechnology, Faculty of Agriculture, University of South Bohemia in České Budějovice, Studentská 1668, 370 05 České Budějovice, Czech Republic
- Veterinary Research Institute, Hudcova 296, 621 00 Brno, Czech Republic
| | - Michaela Brzáková
- Institute of Animal Science, Přátelství 815, 104 00 Praha, Czech Republic
| | - Jiří Bauer
- Czech Moravian Breeders' Corporation, Benešovská 123, 252 09 Hradištko, Czech Republic
| | - Ladislav Tichý
- Institute of Animal Science, Přátelství 815, 104 00 Praha, Czech Republic
- Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, 165 00 Praha, Czech Republic
| | - Zuzana Sztankóová
- Institute of Animal Science, Přátelství 815, 104 00 Praha, Czech Republic
| | - Luboš Vostrý
- Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, 165 00 Praha, Czech Republic
| | - Yvette Steyn
- Department of Animal and Dairy Science, University of Georgia, 425 River Road, Athens, GA 30602, USA
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Bilbao-Arribas M, Jugo BM. Transcriptomic meta-analysis reveals unannotated long non-coding RNAs related to the immune response in sheep. Front Genet 2022; 13:1067350. [PMID: 36482891 PMCID: PMC9725098 DOI: 10.3389/fgene.2022.1067350] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/11/2022] [Accepted: 11/08/2022] [Indexed: 11/23/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are involved in several biological processes, including the immune system response to pathogens and vaccines. The annotation and functional characterization of lncRNAs is more advanced in humans than in livestock species. Here, we take advantage of the increasing number of high-throughput functional experiments deposited in public databases in order to uniformly analyse, profile unannotated lncRNAs and integrate 422 ovine RNA-seq samples from the ovine immune system. We identified 12302 unannotated lncRNA genes with support from independent CAGE-seq and histone modification ChIP-seq assays. Unannotated lncRNAs showed low expression levels and sequence conservation across other mammal species. There were differences in expression levels depending on the genomic location-based lncRNA classification. Differential expression analyses between unstimulated and samples stimulated with pathogen infection or vaccination resulted in hundreds of lncRNAs with changed expression. Gene co-expression analyses revealed immune gene-enriched clusters associated with immune system activation and related to interferon signalling, antiviral response or endoplasmic reticulum stress. Besides, differential co-expression networks were constructed in order to find condition-specific relationships between coding genes and lncRNAs. Overall, using a diverse set of immune system samples and bioinformatic approaches we identify several ovine lncRNAs associated with the response to an external stimulus. These findings help in the improvement of the ovine lncRNA catalogue and provide sheep-specific evidence for the implication in the general immune response for several lncRNAs.
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Oyelami FO, Usman T, Suravajhala P, Ali N, Do DN. Emerging Roles of Noncoding RNAs in Bovine Mastitis Diseases. Pathogens 2022; 11:pathogens11091009. [PMID: 36145441 PMCID: PMC9501195 DOI: 10.3390/pathogens11091009] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2022] [Revised: 08/26/2022] [Accepted: 08/26/2022] [Indexed: 11/16/2022] Open
Abstract
Non-coding RNAs (ncRNAs) are an abundant class of RNA with varying nucleotide lengths. They have been shown to have great potential in eutherians/human disease diagnosis and treatments and are now gaining more importance for the improvement of diseases in livestock. To date, thousands of ncRNAs have been discovered in the bovine genome and the continuous advancement in deep sequencing technologies and various bioinformatics tools has enabled the elucidation of their roles in bovine health. Among farm animals' diseases, mastitis, a common inflammatory disease in cattle, has caused devastating economic losses to dairy farmers over the last few decades. Here, we summarize the biology of bovine mastitis and comprehensively discuss the roles of ncRNAs in different types of mastitis infection. Based on our findings and relevant literature, we highlighted various evidence of ncRNA roles in mastitis. Different approaches (in vivo versus in vitro) for exploring ncRNA roles in mastitis are emphasized. More particularly, the potential applications of emerging genome editing technologies, as well as integrated omics platforms for ncRNA studies and implications for mastitis are presented.
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Affiliation(s)
- Favour Oluwapelumi Oyelami
- The John Curtin School of Medical Research, Australian National University, Canberra, ACT 2601, Australia
| | - Tahir Usman
- College of Veterinary Sciences & Animal Husbandry, Abdul Wali Khan University, Mardan 23200, KP, Pakistan
| | - Prashanth Suravajhala
- Amrita School of Biotechnology, Amrita Vishwa Vidyapeetham, Clappana 690525, Kerala, India
| | - Nawab Ali
- Department of Zoology, Abdul Wali Khan University, Mardan 23200, KP, Pakistan
| | - Duy N. Do
- Faculty of Veterinary Medicine, Viet Nam National University of Agriculture, Hanoi 100000, Vietnam
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS B2N 5E3, Canada
- Correspondence: ; Tel.: +1-9029578789
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Regulation of Non-Coding RNA in the Growth and Development of Skeletal Muscle in Domestic Chickens. Genes (Basel) 2022; 13:genes13061033. [PMID: 35741795 PMCID: PMC9222894 DOI: 10.3390/genes13061033] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2022] [Revised: 05/28/2022] [Accepted: 06/06/2022] [Indexed: 02/04/2023] Open
Abstract
Chicken is the most widely consumed meat product worldwide and is a high-quality source of protein for humans. The skeletal muscle, which accounts for the majority of chicken products and contains the most valuable components, is tightly correlated to meat product yield and quality. In domestic chickens, skeletal muscle growth is regulated by a complex network of molecules that includes some non-coding RNAs (ncRNAs). As a regulator of muscle growth and development, ncRNAs play a significant function in the development of skeletal muscle in domestic chickens. Recent advances in sequencing technology have contributed to the identification and characterization of more ncRNAs (mainly microRNAs (miRNAs), long non-coding RNAs (LncRNAs), and circular RNAs (CircRNAs)) involved in the development of domestic chicken skeletal muscle, where they are widely involved in proliferation, differentiation, fusion, and apoptosis of myoblasts and satellite cells, and the specification of muscle fiber type. In this review, we summarize the ncRNAs involved in the skeletal muscle growth and development of domestic chickens and discuss the potential limitations and challenges. It will provide a theoretical foundation for future comprehensive studies on ncRNA participation in the regulation of skeletal muscle growth and development in domestic chickens.
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Unravelling lncRNA mediated gene expression as potential mechanism for regulating secondary metabolism in Citrus limon. FOOD BIOSCI 2022. [DOI: 10.1016/j.fbio.2021.101448] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
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Mumtaz PT, Bhat B, Ibeagha-Awemu EM, Taban Q, Wang M, Dar MA, Bhat SA, Shabir N, Shah RA, Ganie NA, Velayutham D, Haq ZU, Ahmad SM. Mammary epithelial cell transcriptome reveals potential roles of lncRNAs in regulating milk synthesis pathways in Jersey and Kashmiri cattle. BMC Genomics 2022; 23:176. [PMID: 35246027 PMCID: PMC8896326 DOI: 10.1186/s12864-022-08406-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/09/2021] [Accepted: 02/15/2022] [Indexed: 11/10/2022] Open
Abstract
Background Long noncoding RNAs (lncRNAs) are now proven as essential regulatory elements, playing diverse roles in many biological processes including mammary gland development. However, little is known about their roles in the bovine lactation process. Results To identify and characterize the roles of lncRNAs in bovine lactation, high throughput RNA sequencing data from Jersey (high milk yield producer), and Kashmiri cattle (low milk yield producer) were utilized. Transcriptome data from three Kashmiri and three Jersey cattle throughout their lactation stages were utilized for differential expression analysis. At each stage (early, mid and late) three samples were taken from each breed. A total of 45 differentially expressed lncRNAs were identified between the three stages of lactation. The differentially expressed lncRNAs were found co-expressed with genes involved in the milk synthesis processes such as GPAM, LPL, and ABCG2 indicating their potential regulatory effects on milk quality genes. KEGG pathways analysis of potential cis and trans target genes of differentially expressed lncRNAs indicated that 27 and 48 pathways were significantly enriched between the three stages of lactation in Kashmiri and Jersey respectively, including mTOR signaling, PI3K-Akt signaling, and RAP1 signaling pathways. These pathways are known to play key roles in lactation biology and mammary gland development. Conclusions Expression profiles of lncRNAs across different lactation stages in Jersey and Kashmiri cattle provide a valuable resource for the study of the regulatory mechanisms involved in the lactation process as well as facilitate understanding of the role of lncRNAs in bovine lactation biology. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08406-x.
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Affiliation(s)
- Peerzada Tajamul Mumtaz
- Division of Animal Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry, Sher-e- Kashmir University of Agricultural Sciences and Technology - Kashmir, SKUAST-K, Shuhama, Jammu, 190006, India.,Department of Biochemistry, School of Life Sciences Jaipur National University, Jaipur, India
| | - Basharat Bhat
- Division of Animal Breeding and Genetics, Faculty of Veterinary Sciences and Animal Husbandry, SKUAST-K, Shuhama, Jammu, India
| | - Eveline M Ibeagha-Awemu
- Agriculture and Agri-Food Canada, Sherbrooke Research and Development Centre, Sherbrooke, Quebec, Canada
| | - Qamar Taban
- Division of Animal Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry, Sher-e- Kashmir University of Agricultural Sciences and Technology - Kashmir, SKUAST-K, Shuhama, Jammu, 190006, India
| | - Mengqi Wang
- Agriculture and Agri-Food Canada, Sherbrooke Research and Development Centre, Sherbrooke, Quebec, Canada
| | - Mashooq Ahmad Dar
- Division of Animal Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry, Sher-e- Kashmir University of Agricultural Sciences and Technology - Kashmir, SKUAST-K, Shuhama, Jammu, 190006, India
| | - Shakil Ahmad Bhat
- Division of Animal Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry, Sher-e- Kashmir University of Agricultural Sciences and Technology - Kashmir, SKUAST-K, Shuhama, Jammu, 190006, India
| | - Nadeem Shabir
- Division of Animal Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry, Sher-e- Kashmir University of Agricultural Sciences and Technology - Kashmir, SKUAST-K, Shuhama, Jammu, 190006, India
| | - Riaz Ahmad Shah
- Division of Animal Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry, Sher-e- Kashmir University of Agricultural Sciences and Technology - Kashmir, SKUAST-K, Shuhama, Jammu, 190006, India
| | - Nazir A Ganie
- Division of Animal Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry, Sher-e- Kashmir University of Agricultural Sciences and Technology - Kashmir, SKUAST-K, Shuhama, Jammu, 190006, India
| | | | - Zulfqar Ul Haq
- Division of Livestock Production and Management, SKUAST-K, Srinagar, India
| | - Syed Mudasir Ahmad
- Division of Animal Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry, Sher-e- Kashmir University of Agricultural Sciences and Technology - Kashmir, SKUAST-K, Shuhama, Jammu, 190006, India.
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Emerging Roles of Non-Coding RNAs in the Feed Efficiency of Livestock Species. Genes (Basel) 2022; 13:genes13020297. [PMID: 35205343 PMCID: PMC8872339 DOI: 10.3390/genes13020297] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Revised: 01/27/2022] [Accepted: 01/31/2022] [Indexed: 01/27/2023] Open
Abstract
A global population of already more than seven billion people has led to an increased demand for food and water, and especially the demand for meat. Moreover, the cost of feed used in animal production has also increased dramatically, which requires animal breeders to find alternatives to reduce feed consumption. Understanding the biology underlying feed efficiency (FE) allows for a better selection of feed-efficient animals. Non-coding RNAs (ncRNAs), especially micro RNAs (miRNAs) and long non-coding RNAs (lncRNAs), play important roles in the regulation of bio-logical processes and disease development. The functions of ncRNAs in the biology of FE have emerged as they participate in the regulation of many genes and pathways related to the major FE indicators, such as residual feed intake and feed conversion ratio. This review provides the state of the art studies related to the ncRNAs associated with FE in livestock species. The contribution of ncRNAs to FE in the liver, muscle, and adipose tissues were summarized. The research gap of the function of ncRNAs in key processes for improved FE, such as the nutrition, heat stress, and gut–brain axis, was examined. Finally, the potential uses of ncRNAs for the improvement of FE were discussed.
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Saadat N, Puttabyatappa M, Elangovan VR, Dou J, Ciarelli JN, Thompson RC, Bakulski KM, Padmanabhan V. Developmental Programming: Prenatal Testosterone Excess on Liver and Muscle Coding and Noncoding RNA in Female Sheep. Endocrinology 2022; 163:6413684. [PMID: 34718504 PMCID: PMC8667859 DOI: 10.1210/endocr/bqab225] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/10/2021] [Indexed: 11/19/2022]
Abstract
Prenatal testosterone (T)-treated female sheep manifest peripheral insulin resistance, ectopic lipid accumulation, and insulin signaling disruption in liver and muscle. This study investigated transcriptional changes and transcriptome signature of prenatal T excess-induced hepatic and muscle-specific metabolic disruptions. Genome-wide coding and noncoding (nc) RNA expression in liver and muscle from 21-month-old prenatal T-treated (T propionate 100 mg intramuscular twice weekly from days 30-90 of gestation; term: 147 days) and control females were compared. Prenatal T (1) induced differential expression of messenger RNAs (mRNAs) in liver (15 down, 17 up) and muscle (66 down, 176 up) (false discovery rate < 0.05, absolute log2 fold change > 0.5); (2) downregulated mitochondrial pathway genes in liver and muscle; (3) downregulated hepatic lipid catabolism and peroxisome proliferator-activated receptor (PPAR) signaling gene pathways; (4) modulated noncoding RNA (ncRNA) metabolic processes gene pathway in muscle; and (5) downregulated 5 uncharacterized long noncoding RNA (lncRNA) in the muscle but no ncRNA changes in the liver. Correlation analysis showed downregulation of lncRNAs LOC114112974 and LOC105607806 was associated with decreased TPK1, and LOC114113790 with increased ZNF470 expression. Orthogonal projections to latent structures discriminant analysis identified mRNAs HADHA and SLC25A45, and microRNAs MIR154A, MIR25, and MIR487B in the liver and ARIH1 and ITCH and miRNAs MIR369, MIR10A, and MIR10B in muscle as potential biomarkers of prenatal T excess. These findings suggest downregulation of mitochondria, lipid catabolism, and PPAR signaling genes in the liver and dysregulation of mitochondrial and ncRNA gene pathways in muscle are contributors of lipotoxic and insulin-resistant hepatic and muscle phenotype. Gestational T excess programming of metabolic dysfunctions involve tissue-specific ncRNA-modulated transcriptional changes.
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Affiliation(s)
- Nadia Saadat
- Department of Pediatrics, University of Michigan, Ann Arbor, Michigan 48019-5718, USA
| | - Muraly Puttabyatappa
- Department of Pediatrics, University of Michigan, Ann Arbor, Michigan 48019-5718, USA
| | | | - John Dou
- Department of Epidemiology, University of Michigan, Ann Arbor, Michigan 48019-5718, USA
| | - Joseph N Ciarelli
- Department of Pediatrics, University of Michigan, Ann Arbor, Michigan 48019-5718, USA
| | - Robert C Thompson
- Department of Psychiatry, University of Michigan, Ann Arbor, Michigan 48019-5718, USA
| | - Kelly M Bakulski
- Department of Epidemiology, University of Michigan, Ann Arbor, Michigan 48019-5718, USA
| | - Vasantha Padmanabhan
- Department of Pediatrics, University of Michigan, Ann Arbor, Michigan 48019-5718, USA
- Correspondence: Vasantha Padmanabhan, PhD, MS, Department of Pediatrics, University of Michigan, 7510 MSRB1, 1150 W Medical Center Dr, Ann Arbor, MI 48019-5718, USA.
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15
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Mumtaz PT, Taban Q, Bhat B, Ahmad SM, Dar MA, Kashoo ZA, Ganie NA, Shah RA. Expression of lncRNAs in response to bacterial infections of goat mammary epithelial cells reveals insights into mammary gland diseases. Microb Pathog 2021; 162:105367. [PMID: 34963641 DOI: 10.1016/j.micpath.2021.105367] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/25/2021] [Revised: 12/16/2021] [Accepted: 12/17/2021] [Indexed: 10/19/2022]
Abstract
Mastitis or inflammation of the mammary gland is a highly economic and deadly alarming disease for the dairy sector as well as policymakers caused by microbial infection. Transcriptomic and proteomic approaches have been widely employed to identify the underlying molecular mechanisms of bacterial infections in the mammary gland. Numerous differentially expressed mRNAs, miRNAs, and proteins together with their associated signaling pathways have been identified during bacterial infection, paving the way for analysis of their biological functions. Long noncoding RNAs (lncRNAs) are important regulators of multiple biological processes. However, little is known regarding their role in bacterial infection in mammary epithelial cells. Hence, RNA-sequencing was performed by infecting primary mammary epithelial cells (pMECs) with both gram-negative (E. coli) and gram-positive bacteria (S. aureus). Using stringent pipeline, a set of 1957 known and 1175 novel lncRNAs were identified, among which, 112 lncRNAs were found differentially expressed in bacteria challenged PMECs compared with the control. Additionally, potential targets of the lncRNAs were predicted in cis- and trans-configuration. KEGG analysis revealed that DE lncRNAs were associated with at least 15 immune-related pathways. Therefore, our study revealed that bacterial challenge triggers the expression of lncRNAs associated with immune response and defense mechanisms in goat mammary epithelial cells.
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Affiliation(s)
- Peerzada Tajamul Mumtaz
- Division of Animal Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry, Shuhama, SKUAST-K, India; Department of Biochemistry, School of Life Sciences Jaipur National University, India
| | - Qamar Taban
- Division of Animal Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry, Shuhama, SKUAST-K, India
| | - Basharat Bhat
- Division of Animal Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry, Shuhama, SKUAST-K, India
| | - Syed Mudasir Ahmad
- Division of Animal Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry, Shuhama, SKUAST-K, India.
| | - Mashooq Ahmad Dar
- Division of Animal Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry, Shuhama, SKUAST-K, India
| | - Zahid Amin Kashoo
- Division of Veterinary Microbiology, Faculty of Veterinary Sciences and Animal Husbandry, Shuhama, SKUAST-K, India
| | - Nazir A Ganie
- Division of Animal Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry, Shuhama, SKUAST-K, India
| | - Riaz Ahmad Shah
- Division of Animal Biotechnology, Faculty of Veterinary Sciences and Animal Husbandry, Shuhama, SKUAST-K, India
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16
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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: 0] [Impact Index Per Article: 0] [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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17
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Rahman MM, Hossain MT, Reza MS, Peng Y, Feng S, Wei Y. Identification of Potential Long Non-Coding RNA Candidates that Contribute to Triple-Negative Breast Cancer in Humans through Computational Approach. Int J Mol Sci 2021; 22:12359. [PMID: 34830241 PMCID: PMC8619140 DOI: 10.3390/ijms222212359] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2021] [Revised: 10/26/2021] [Accepted: 10/28/2021] [Indexed: 12/31/2022] Open
Abstract
Breast cancer (BC) is the most frequent malignancy identified in adult females, resulting in enormous financial losses worldwide. Owing to the heterogeneity as well as various molecular subtypes, the molecular pathways underlying carcinogenesis in various forms of BC are distinct. Therefore, the advancement of alternative therapy is required to combat the ailment. Recent analyses propose that long non-coding RNAs (lncRNAs) perform an essential function in controlling immune response, and therefore, may provide essential information about the disorder. However, their function in patients with triple-negative BC (TNBC) has not been explored in detail. Here, we analyzed the changes in the genomic expression of messenger RNA (mRNA) and lncRNA in standard control in response to cancer metastasis using publicly available single-cell RNA-Seq data. We identified a total of 197 potentially novel lncRNAs in TNBC patients of which 86 were differentially upregulated and 111 were differentially downregulated. In addition, among the 909 candidate lncRNA transcripts, 19 were significantly differentially expressed (DE) of which three were upregulated and 16 were downregulated. On the other hand, 1901 mRNA transcripts were significantly DE of which 1110 were upregulated and 791 were downregulated by TNBCs subtypes. The Gene Ontology (GO) analyses showed that some of the host genes were enriched in various biological, molecular, and cellular functions. The Kyoto encyclopedia of genes and genomes (KEGG) pathway analysis showed that some of the genes were involved in only one pathway of prostate cancer. The lncRNA-miRNA-gene network analysis showed that the lncRNAs TCONS_00076394 and TCONS_00051377 interacted with breast cancer-related micro RNAs (miRNAs) and the host genes of these lncRNAs were also functionally related to breast cancer. Thus, this study provides novel lncRNAs as potential biomarkers for the therapeutic intervention of this cancer subtype.
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MESH Headings
- Biomarkers, Tumor/genetics
- Biomarkers, Tumor/metabolism
- Computational Biology/methods
- Female
- Gene Expression Profiling
- Gene Expression Regulation, Neoplastic
- Gene Ontology
- Gene Regulatory Networks
- Humans
- Mammary Glands, Human/metabolism
- Mammary Glands, Human/pathology
- MicroRNAs/classification
- MicroRNAs/genetics
- MicroRNAs/metabolism
- Molecular Sequence Annotation
- RNA, Long Noncoding/classification
- RNA, Long Noncoding/genetics
- RNA, Long Noncoding/metabolism
- RNA, Messenger/classification
- RNA, Messenger/genetics
- RNA, Messenger/metabolism
- RNA, Neoplasm/classification
- RNA, Neoplasm/genetics
- RNA, Neoplasm/metabolism
- Triple Negative Breast Neoplasms/diagnosis
- Triple Negative Breast Neoplasms/genetics
- Triple Negative Breast Neoplasms/metabolism
- Triple Negative Breast Neoplasms/pathology
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Affiliation(s)
- Md. Motiar Rahman
- Department of Biochemistry and Molecular Biology, University of Rajshahi, Rajshahi 6205, Bangladesh
- Department of Chemistry, Binghamton University, State University of New York, Vestal, New York, NY 13902, USA
| | - Md. Tofazzal Hossain
- University of Chinese Academy of Sciences, No.19(A) Yuquan Road, Shijingshan District, Beijing 100049, China; (T.H.); (S.R.)
- Joint Engineering Research Center for Health Big Data Intelligent Analysis Technology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China;
- Department of Statistics, Bangabandhu Sheikh Mujibur Rahaman Science and Technology University, Gopalganj 8100, Bangladesh
| | - Md. Selim Reza
- University of Chinese Academy of Sciences, No.19(A) Yuquan Road, Shijingshan District, Beijing 100049, China; (T.H.); (S.R.)
- Joint Engineering Research Center for Health Big Data Intelligent Analysis Technology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China;
| | - Yin Peng
- Department of Pathology, The Shenzhen University School of Medicine, Shenzhen 518060, China;
| | - Shengzhong Feng
- Joint Engineering Research Center for Health Big Data Intelligent Analysis Technology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China;
| | - Yanjie Wei
- Joint Engineering Research Center for Health Big Data Intelligent Analysis Technology, Shenzhen Institutes of Advanced Technology, Chinese Academy of Sciences, Shenzhen 518055, China;
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18
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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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19
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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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20
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Murugesan KD, Gupta ID, Onteru SK, Dash A, Sukhija N, Sivalingam J, Mohanty AK. Profiling and integrated analysis of whole-transcriptome changes in uterine caruncles of pregnant and non-pregnant buffaloes. Genomics 2021; 113:2338-2349. [PMID: 34022349 DOI: 10.1016/j.ygeno.2021.05.018] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/06/2020] [Revised: 03/04/2021] [Accepted: 05/17/2021] [Indexed: 11/18/2022]
Abstract
Improved reproductive performance in buffaloes can be achieved by understanding the basic mechanism governing the embryonic attachment and feto-maternal communication. Considering this, trascriptomic profiling and integrative analysis of long intergenic non-coding RNAs were carried out in the uterine caruncles of pregnant and non-pregnant buffaloes. Transcriptome data of pregnant and non-pregnant uterine caruncles after quality control was used to perform the analysis. Total of 86 novel lincRNAs expressed in uterine caruncular tissues were identified and characterized. Differential expression analysis revealed that 447 mRNAs and 185 mRNAs were up- and down- regulated, respectively. The number of up- and down- regulated lincRNAs were 114 and 13, respectively. Of the identified 86 novel lincRNAs, six novel lincRNAs were up-regulated in the pregnant uterine caruncles. GO terms (biological process) and PANTHER pathways associated with reproduction and embryogenesis were over-represented in differentially expressed genes. Through miRNA interaction analysis, interactions of 16 differentially expressed lincRNAs with mi-RNAs involved in reproduction were identified. This study has provided a catalogue of differentially expressed genes and novel regions previously unknown to play a significant role in buffalo reproduction. The results from the current study extends the buffalo uterine lncRNAs database and provides candidate regulators for future molecular genetic studies on buffalo uterine physiology to improve the embryo implantation and successful completion of pregnancy.
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Affiliation(s)
- Kousalya Devi Murugesan
- Animal Genetics and Breeding Division, National Dairy Research Institute, Karnal 132001, Haryana, India.
| | - I D Gupta
- Animal Genetics and Breeding Division, National Dairy Research Institute, Karnal 132001, Haryana, India.
| | - Suneel Kumar Onteru
- Animal Biochemistry Division, National Dairy Research Institute, Karnal 132001, Haryana, India
| | - Aishwarya Dash
- Animal Genetics and Breeding Division, National Dairy Research Institute, Karnal 132001, Haryana, India
| | - Nidhi Sukhija
- Animal Genetics and Breeding Division, National Dairy Research Institute, Karnal 132001, Haryana, India
| | - Jayakumar Sivalingam
- Animal Genetics and Breeding Division, National Bureau of Animal Genetic Resources, Karnal 132001, Haryana, India.
| | - Ashok Kumar Mohanty
- Proteomics and Cell Biology Lab, Animal Biotechnology Center, National Dairy Research Institute, Karnal 132001, Haryana, India
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21
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Transcriptome profiling of Capsicum annuum using Illumina- and PacBio SMRT-based RNA-Seq for in-depth understanding of genes involved in trichome formation. Sci Rep 2021; 11:10164. [PMID: 33986344 PMCID: PMC8119447 DOI: 10.1038/s41598-021-89619-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/28/2020] [Accepted: 04/26/2021] [Indexed: 11/16/2022] Open
Abstract
Trichomes, specialized epidermal cells located in aerial parts of plants, play indispensable roles in resisting abiotic and biotic stresses. However, the regulatory genes essential for multicellular trichrome development in Capsicum annuum L. (pepper) remain unclear. In this study, the transcript profiles of peppers GZZY-23 (hairy) and PI246331 (hairless) were investigated to gain insights into the genes responsible for the formation of multicellular trichomes. A total of 40,079 genes, including 4743 novel genes and 13,568 differentially expressed genes (DEGs), were obtained. Functional enrichment analysis revealed that the most noticeable pathways were transcription factor activity, sequence-specific DNA binding, and plant hormone signal transduction, which might be critical for multicellular trichome formation in hairy plants. We screened 11 DEGs related to trichome development; 151 DEGs involved in plant hormone signal transduction; 312 DEGs belonging to the MYB, bHLH, HD-Zip, and zinc finger transcription factor families; and 1629 DEGs predicted as plant resistance genes (PRGs). Most of these DEGs were highly expressed in GZZY-23 or trichomes. Several homologs of trichome regulators, such as SlCycB2, SlCycB3, and H, were considerably upregulated in GZZY-23, especially in the trichomes. The transcriptomic data generated in this study provide a basis for future characterization of trichome formation in pepper.
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22
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Wang L, Xie Y, Chen W, Zhang Y, Zeng Y. The role of long noncoding RNAs in livestock adipose tissue deposition - A review. Anim Biosci 2021; 34:1089-1099. [PMID: 33902176 PMCID: PMC8255878 DOI: 10.5713/ab.21.0006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/07/2021] [Accepted: 03/29/2021] [Indexed: 11/27/2022] Open
Abstract
With the development of sequencing technology, numerous, long noncoding RNAs (lncRNAs) have been discovered and annotated. Increasing evidence has shown that lncRNAs play an essential role in regulating many biological and pathological processes, especially in cancer. However, there have been few studies on the roles of lncRNAs in livestock production. In animal products, meat quality and lean percentage are vital economic traits closely related to adipose tissue deposition. However, adipose tissue accumulation is also a pivotal contributor to obesity, diabetes, atherosclerosis, and many other diseases, as demonstrated by human studies. In livestock production, the mechanism by which lncRNAs regulate adipose tissue deposition is still unclear. In addition, the phenomenon that different animal species have different adipose tissue accumulation abilities is not well understood. In this review, we summarize the characteristics of lncRNAs and their four functional archetypes and review the current knowledge about lncRNA functions in adipose tissue deposition in livestock species. This review could provide theoretical significance to explore the functional mechanisms of lncRNAs in adipose tissue accumulation in animals.
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Affiliation(s)
- Lixue Wang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, Tai'an, Shandong 271018, China
| | - Yuhuai Xie
- Department of Immunology, School of Basic Medical Sciences, Fudan University, Shanghai, 200032, China
| | - Wei Chen
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, Tai'an, Shandong 271018, China
| | - Yu Zhang
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, Tai'an, Shandong 271018, China
| | - Yongqing Zeng
- Shandong Provincial Key Laboratory of Animal Biotechnology and Disease Control and Prevention, College of Animal Science and Technology, Shandong Agricultural University, Tai'an, Shandong 271018, China
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23
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Marete A, Ariel O, Ibeagha-Awemu E, Bissonnette N. Identification of Long Non-coding RNA Isolated From Naturally Infected Macrophages and Associated With Bovine Johne's Disease in Canadian Holstein Using a Combination of Neural Networks and Logistic Regression. Front Vet Sci 2021; 8:639053. [PMID: 33969037 PMCID: PMC8100051 DOI: 10.3389/fvets.2021.639053] [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: 12/08/2020] [Accepted: 02/15/2021] [Indexed: 01/15/2023] Open
Abstract
Mycobacterium avium ssp. paratuberculosis (MAP) causes chronic enteritis in most ruminants. The pathogen MAP causes Johne's disease (JD), a chronic, incurable, wasting disease. Weight loss, diarrhea, and a gradual drop in milk production characterize the disease's clinical phase, culminating in death. Several studies have characterized long non-coding RNA (lncRNA) in bovine tissues, and a previous study characterizes (lncRNA) in macrophages infected with MAP in vitro. In this study, we aim to characterize the lncRNA in macrophages from cows naturally infected with MAP. From 15 herds, feces and blood samples were collected for each cow older than 24 months, twice yearly over 3–5 years. Paired samples were analyzed by fecal PCR and blood ELISA. We used RNA-seq data to study lncRNA in macrophages from 33 JD(+) and 33 JD(–) dairy cows. We performed RNA-seq analysis using the “new Tuxedo” suite. We characterized lncRNA using logistic regression and multilayered neural networks and used DESeq2 for differential expression analysis and Panther and Reactome classification systems for gene ontology (GO) analysis. The study identified 13,301 lncRNA, 605 of which were novel lncRNA. We found seven genes close to differentially expressed lncRNA, including CCDC174, ERI1, FZD1, TWSG1, ZBTB38, ZNF814, and ZSCAN4. None of the genes associated with susceptibility to JD have been cited in the literature. LncRNA target genes were significantly enriched for biological process GO terms involved in immunity and nucleic acid regulation. These include the MyD88 pathway (TLR5), GO:0043312 (neutrophil degranulation), GO:0002446 (neutrophil-mediated immunity), and GO:0042119 (neutrophil activation). These results identified lncRNA with potential roles in host immunity and potential candidate genes and pathways through which lncRNA might function in response to MAP infection.
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Affiliation(s)
- Andrew Marete
- Agriculture and Agri-Food Canada, Sherbrooke Research and Development Centre, Sherbrooke, QC, Canada
| | - Olivier Ariel
- Agriculture and Agri-Food Canada, Sherbrooke Research and Development Centre, Sherbrooke, QC, Canada.,Faculty of Science, Sherbrooke University, Sherbrooke, QC, Canada
| | - Eveline Ibeagha-Awemu
- Agriculture and Agri-Food Canada, Sherbrooke Research and Development Centre, Sherbrooke, QC, Canada
| | - Nathalie Bissonnette
- Agriculture and Agri-Food Canada, Sherbrooke Research and Development Centre, Sherbrooke, QC, Canada
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24
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Zhang DY, Zhang XX, Li GZ, Li XL, Zhang YK, Zhao Y, Song QZ, Wang WM. Transcriptome analysis of long noncoding RNAs ribonucleic acids from the livers of Hu sheep with different residual feed intake. Animal 2020; 15:100098. [PMID: 33573993 DOI: 10.1016/j.animal.2020.100098] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/15/2020] [Revised: 09/23/2020] [Accepted: 09/24/2020] [Indexed: 11/24/2022] Open
Abstract
Long noncoding RNAs (LncRNAs), as key regulators, have vital functions in various biological activities. However, in sheep, little has been reported concerning the genetic mechanism of LncRNA regulation of feed efficiency. In the present study, we explored the genome-wide expression of LncRNAs and transcripts of uncertain coding potential (TUCPs) in the livers of sheep with extreme residual feed intake (RFI) using RNA sequencing. We identified 1 523 TUCPs and 1 996 LncRNAs, among which 10 LncRNAs and 16 TUCPs were identified as being differentially expressed between the High-RFI and Low-RFI groups. Co-expression and co-localization methods were used to search for LncRNA and TUCP target genes, which identified 970/1 538 and 23/27 genes, respectively. Ontology and pathways analysis revealed that the LncRNAs/TUCPs that were highly expressed in the Low-RFI group are mostly concentrated in energy metabolism pathways. For example, LNC_000890 and TUCP_000582 might regulate liver tissue metabolic efficiency. The LncRNAs/TUCPs that were highly expressed in the High-RFI group are mostly enriched in immune function pathways. For example, TUCP_000832 might regulate animal health, thereby affecting feed efficiency. Subsequently, a co-expression network was established by applying the expression information of both the differentially expressed LncRNAs and TUCPs and their target mRNAs. The network indicated that differentially expressed genes targeted by the upregulated LncRNAs and TUCPs were mainly related to energy metabolism, while those genes targeted by the downregulated LncRNAs and TUCPs were mainly related to immune response. These results provide the basis for further study of LncRNA/TUCP-mediated regulation of feed efficiency.
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Affiliation(s)
- D Y Zhang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - X X Zhang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China; Engineering Laboratory of Sheep Breeding and Reproduction Biotechnology in Gansu Province, Minqin Zhongtian Sheep Industry Co. Ltd, Minqin, Gansu 733300, China
| | - G Z Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - X L Li
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Y K Zhang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Y Zhao
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - Q Z Song
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China
| | - W M Wang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, Gansu 730070, China.
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Wu X, Zhou X, Xiong L, Pei J, Yao X, Liang C, Bao P, Chu M, Guo X, Yan P. Transcriptome Analysis Reveals the Potential Role of Long Non-coding RNAs in Mammary Gland of Yak During Lactation and Dry Period. Front Cell Dev Biol 2020; 8:579708. [PMID: 33324637 PMCID: PMC7723986 DOI: 10.3389/fcell.2020.579708] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2020] [Accepted: 11/09/2020] [Indexed: 12/26/2022] Open
Abstract
The mammary gland is a remarkably dynamic organ of milk synthesis and secretion, and it experiences drastic structural and metabolic changes during the transition from dry periods to lactation, which involves the expression and regulation of numerous genes and regulatory factors. Long non-coding RNA (lncRNA) has considered as a novel type of regulatory factors involved in a variety of biological processes. However, their role in the lactation cycle of yak is still poorly understood. To reveal the involved mechanism, Ribo-zero RNA sequencing was employed to profile the lncRNA transcriptome in mammary tissue samples from yak at two physiological stages, namely lactation (LP) and dry period (DP). Notably, 1,599 lncRNA transcripts were identified through four rigorous steps and filtered through protein-coding ability. A total of 59 lncRNAs showed significantly different expression between two stages. Accordingly, the results of qRT-PCR were consistent with that of the transcriptome data. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses indicated that target genes of differentially expressed lncRNAs (DELs) were involved in pathways related to lactation, such as ECM-receptor interaction, PI3K-Akt signaling pathway, biosynthesis of amino acids and focal adhesion etc. Finally, we constructed a lncRNA-gene regulatory network containing some well known candidate genes for milk yield and quality traits. This is the first study to demonstrate a global profile of lncRNA expression in the mammary gland of yak. These results contribute to a valuable resource for future genetic and molecular studies on improving milk yield and quality, and help us to gain a better understanding of the molecular mechanisms underlying lactogenesis and mammary gland development of yak.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Xian Guo
- Key Lab of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Ping Yan
- Key Lab of Yak Breeding Engineering, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
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26
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Liao X, Wang J, Zhu S, Xie Q, Wang L, Yu H, Ye Z, Yang C. Transcriptomic and functional analyses uncover the regulatory role of lncRNA000170 in tomato multicellular trichome formation. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2020; 104:18-29. [PMID: 32603492 DOI: 10.1111/tpj.14902] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/26/2019] [Revised: 06/13/2020] [Accepted: 06/17/2020] [Indexed: 05/24/2023]
Abstract
Trichomes are universal specific structures originating from nearly all terrestrial plants. Although quantities of long non-coding RNAs (lncRNAs) have been identified in many plant species, the role of lncRNAs in trichome formation still remains unknown. Here, we identified a total of 1303 lncRNAs in the young stems of woolly mutant LA3560 (Wo) and its non-woolly segregants (WT). Out of these lncRNAs, 86 lncRNAs were obviously upregulated in Wo and 110 lncRNAs were downregulated. We determined that seven lncRNAs were highly expressed in stem trichomes compared to trichome-free stems and several other tissues of LA3560 by a quantitative reverse transcriptase-polymerase chain reaction, including lncRNA000746, lncRNA000170, lncRNA000277, lncRNA000774, lncRNA000756, lncRNA000100, and lncRNA000898. Transgenic experiments revealed that overexpression of lncRNA000170 inhibited type I trichome formation on the lower stems of the adult transgenic plants. We further determined that lncRNA000170 was transcribed from the complementary strand of Solyc10g006360, for which expression can be induced by lncRNA000170 in its overexpression lines and woolly mutants. Solyc10g006360 overexpression also caused type I trichome decrease. In addition, several trichome regulators, such as Wo, H, SlCycB2, and SlCycB3, were markedly downregulated in lncRNA000170 overexpression lines. These findings demonstrate that lncRNA000170 may be involved in the regulatory pathway mediated by these trichome regulators.
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Affiliation(s)
- Xiaoli Liao
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, 430070, China
| | - Junqiang Wang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, 430070, China
| | - Shunhua Zhu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, 430070, China
| | - Qingmin Xie
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, 430070, China
| | - Lin Wang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, 430070, China
| | - Huiyang Yu
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, 430070, China
| | - Zhibiao Ye
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, 430070, China
| | - Changxian Yang
- Key Laboratory of Horticultural Plant Biology (Ministry of Education), Huazhong Agricultural University, Wuhan, 430070, China
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27
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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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28
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Tang R, Wang J, Zhou M, Lan Y, Jiang L, Price M, Yue B, Li D, Fan Z. Comprehensive analysis of lncRNA and mRNA expression changes in Tibetan chicken lung tissue between three developmental stages. Anim Genet 2020; 51:731-740. [DOI: 10.1111/age.12990] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/11/2019] [Revised: 06/04/2020] [Accepted: 07/06/2020] [Indexed: 12/22/2022]
Affiliation(s)
- Ruixiang Tang
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education) College of Life Sciences Sichuan University Chengdu 610064 China
| | - Jiao Wang
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education) College of Life Sciences Sichuan University Chengdu 610064 China
| | - Min Zhou
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education) College of Life Sciences Sichuan University Chengdu 610064 China
| | - Yue Lan
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife College of Life Sciences Sichuan University Chengdu 610064 China
| | - Lan Jiang
- Sichuan Key Laboratory of Conservation Biology on Endangered Wildlife College of Life Sciences Sichuan University Chengdu 610064 China
| | - Megan Price
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education) College of Life Sciences Sichuan University Chengdu 610064 China
| | - Bisong Yue
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education) College of Life Sciences Sichuan University Chengdu 610064 China
| | - Diyan Li
- Sichuan Agricultural University Chengdu 611130 China
| | - Zhenxin Fan
- Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education) College of Life Sciences Sichuan University Chengdu 610064 China
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29
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Li X, Li C, Xu Y, Yao R, Li H, Ni W, Quan R, Zhang M, Liu L, Yu S, Ullah Y, Hu R, Li Y, Guo T, Wang X, Hu S. Analysis of pituitary transcriptomics indicates that lncRNAs are involved in the regulation of sheep estrus. Funct Integr Genomics 2020; 20:563-573. [PMID: 32114660 DOI: 10.1007/s10142-020-00735-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/29/2019] [Revised: 11/17/2019] [Accepted: 02/06/2020] [Indexed: 12/13/2022]
Abstract
Seasonal estrus is a key factor limiting animal fertility, and understanding the molecular mechanisms that regulate animal estrus is important for improving animal fertility. The pituitary gland, which is the most important endocrine gland in mammals, plays an important role in regulating the physiological processes such as growth, development, and reproduction of animals. Here, we used RNA-seq technology to study the expression profile of lncRNAs in the anterior pituitary of sheep during estrus and anestrus. In this study, we identified a total of 995 lncRNAs, of which 335 lncRNAs were differentially expressed in two states (including 38 up-regulated and 297 down-regulated lncRNAs). RT-qPCR verified the expression levels of several lncRNAs. Target predictive analysis revealed that these lncRNAs can act in cis or trans and regulate the expression of genes involved in the regulation of sheep estrus. Target gene enrichment analysis of differentially expressed lncRNAs indicates that these lncRNAs can regulate sheep estrus by regulating hormone metabolism and energy metabolism. Through our research, we provide the expression profile of lncRNAs in the pituitary of sheep, which provides a valuable resource for further understanding of the genetic regulation of seasonal estrus in sheep from the perspective of lncRNAs.
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Affiliation(s)
- Xiaoyue Li
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, China
| | - Cunyuan Li
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, China.,College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang, China
| | - Yueren Xu
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, China
| | - Rui Yao
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, China
| | - Huixiang Li
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, China
| | - Wei Ni
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, China.
| | - Renzhe Quan
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, China
| | - Mengdan Zhang
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, China
| | - Li Liu
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, China
| | - Shuting Yu
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, China
| | - Yaseen Ullah
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, China
| | - Ruirui Hu
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, China
| | - Yaxin Li
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, China
| | - Tao Guo
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, China
| | - Xiaokui Wang
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, China
| | - Shengwei Hu
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang, China.
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30
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Choi JY, Won K, Son S, Shin D, Oh JD. Comparison of characteristics of long noncoding RNA in Hanwoo according to sex. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2020; 33:696-703. [PMID: 32054215 PMCID: PMC7206396 DOI: 10.5713/ajas.18.0533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/16/2018] [Accepted: 10/14/2019] [Indexed: 11/27/2022]
Abstract
Objective Cattle were some of the first animals domesticated by humans for the production of milk, meat, etc. Long noncoding RNA (lncRNA) is defined as longer than 200 bp in non-protein coding transcripts. lncRNA is known to function in regulating gene expression and is currently being studied in a variety of livestock including cattle. The purpose of this study is to analyze the characteristics of lncRNA according to sex in Hanwoo cattle. Methods This study was conducted using the skeletal muscles of 9 Hanwoo cattle include bulls, steers and cows. RNA was extracted from skeletal muscle of Hanwoo. Sequencing was conducted using Illumina HiSeq2000 and mapped to the Bovine Taurus genome. The expression levels of lncRNAs were measured by DEGseq and quantitative trait loci (QTL) data base was used to identify QTLs associated with lncRNA. The python script was used to match the nearby genes Results In this study, the expression patterns of transcripts of bulls, steers and cows were identified. And we identified significantly differentially expressed lncRNAs in bulls, steers and cows. In addition, characteristics of lncRNA which express differentially in muscles according to the sex of Hanwoo were identified. As a result, we found differentially expressed lncRNAs according to sex were related to shear force and body weight. Conclusion This study was classified and characterized lncRNA which differentially expressed by sex in Hanwoo cattle. We believe that the characterization of lncRNA by sex of Hanwoo will be helpful for future studies of the physiological mechanisms of Hanwoo cattle.
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Affiliation(s)
- Jae-Young Choi
- Subtropical Livestock Research Institute, National Institute of Animal Science, RDA, Jeju 63242, Korea
| | - KyeongHye Won
- Department of Animal Biotechnology, College of Agricultural and Life Sciences, Chonbuk National University, Jeonju 54896, Korea
| | - Seungwoo Son
- Department of Animal Biotechnology, College of Agricultural and Life Sciences, Chonbuk National University, Jeonju 54896, Korea
| | - Donghyun Shin
- The Animal Molecular Genetics & Breeding Center, Chonbuk National University, Jeonju, 54896, Korea
| | - Jae-Don Oh
- Department of Animal Biotechnology, College of Agricultural and Life Sciences, Chonbuk National University, Jeonju 54896, Korea
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31
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Groß C, Derks M, Megens HJ, Bosse M, Groenen MAM, Reinders M, de Ridder D. pCADD: SNV prioritisation in Sus scrofa. Genet Sel Evol 2020; 52:4. [PMID: 32033531 PMCID: PMC7006094 DOI: 10.1186/s12711-020-0528-9] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Accepted: 01/28/2020] [Indexed: 01/22/2023] Open
Abstract
BACKGROUND In animal breeding, identification of causative genetic variants is of major importance and high economical value. Usually, the number of candidate variants exceeds the number of variants that can be validated. One way of prioritizing probable candidates is by evaluating their potential to have a deleterious effect, e.g. by predicting their consequence. Due to experimental difficulties to evaluate variants that do not cause an amino-acid substitution, other prioritization methods are needed. For human genomes, the prediction of deleterious genomic variants has taken a step forward with the introduction of the combined annotation dependent depletion (CADD) method. In theory, this approach can be applied to any species. Here, we present pCADD (p for pig), a model to score single nucleotide variants (SNVs) in pig genomes. RESULTS To evaluate whether pCADD captures sites with biological meaning, we used transcripts from miRNAs and introns, sequences from genes that are specific for a particular tissue, and the different sites of codons, to test how well pCADD scores differentiate between functional and non-functional elements. Furthermore, we conducted an assessment of examples of non-coding and coding SNVs, which are causal for changes in phenotypes. Our results show that pCADD scores discriminate between functional and non-functional sequences and prioritize functional SNVs, and that pCADD is able to score the different positions in a codon relative to their redundancy. Taken together, these results indicate that based on pCADD scores, regions with biological relevance can be identified and distinguished according to their rate of adaptation. CONCLUSIONS We present the ability of pCADD to prioritize SNVs in the pig genome with respect to their putative deleteriousness, in accordance to the biological significance of the region in which they are located. We created scores for all possible SNVs, coding and non-coding, for all autosomes and the X chromosome of the pig reference sequence Sscrofa11.1, proposing a toolbox to prioritize variants and evaluate sequences to highlight new sites of interest to explain biological functions that are relevant to animal breeding.
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Affiliation(s)
- Christian Groß
- Delft Bioinformatics Lab, University of Technology Delft, 2600GA, Delft, The Netherlands. .,Bioinformatics Group, Wageningen University & Research, 6708 PB, Wageningen, The Netherlands.
| | - Martijn Derks
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen, The Netherlands
| | - Hendrik-Jan Megens
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen, The Netherlands
| | - Mirte Bosse
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen, The Netherlands
| | - Martien A M Groenen
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen, The Netherlands
| | - Marcel Reinders
- Delft Bioinformatics Lab, University of Technology Delft, 2600GA, Delft, The Netherlands
| | - Dick de Ridder
- Bioinformatics Group, Wageningen University & Research, 6708 PB, Wageningen, The Netherlands
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Li X, Li C, Wureli H, Ni W, Zhang M, Li H, Xu Y, Rizabek K, Bolatkhan M, Askar D, Gulzhan K, Hou X, Hu S. Screening and evaluating of long non-coding RNAs in prenatal and postnatal pituitary gland of sheep. Genomics 2019; 112:934-942. [PMID: 31200027 DOI: 10.1016/j.ygeno.2019.06.009] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2018] [Revised: 06/07/2019] [Accepted: 06/10/2019] [Indexed: 12/18/2022]
Abstract
Long non-coding RNAs are transcribed into RNA molecules that are >200 nucleotides in length. However, the expression and function analysis of lncRNAs in the sheep pituitary gland are still lacking. In this study, we identified 1755 lncRNAs (545 annotated lncRNAs and 1210 novel lncRNAs) from RNA-seq data in the pituitary gland of embryonic and adult sheep. A total of 235 lncRNAs were differentially expressed between embryonic and adult group. We verified the presence of some lncRNAs using RT-PCR and DNA sequencing, and identified some differentially expressed lncRNAs using qPCR. We also investigated the role of cis-acting lncRNAs on target genes. GO and KEGG enrichment analysis revealed that the target genes of lncRNAs were involved in the regulation of hormones secretion and some signaling pathways in the sheep pituitary gland. Our study provides comprehensive expression profiles of lncRNAs and valuable resource for understanding their function in the pituitary gland.
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Affiliation(s)
- Xiaoyue Li
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Cunyuan Li
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang 832003, China; College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Hazi Wureli
- College of Animal Science and Technology, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Wei Ni
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang 832003, China.
| | - Mengdan Zhang
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Huixiang Li
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Yueren Xu
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Kadyken Rizabek
- Department of Food Engineering, Kazakh National Agrarian University, Almaty Province 050010, Kazakhstan
| | - Makhatov Bolatkhan
- Department of Technology and Biological Resources, Kazakh National Agrarian University, Almaty Province 050010, Kazakhstan
| | - Dzhunysov Askar
- Department of Technology and Biological Resources, Kazakh National Agrarian University, Almaty Province 050010, Kazakhstan
| | - Kulmanova Gulzhan
- Department of Technology and Biological Resources, Kazakh National Agrarian University, Almaty Province 050010, Kazakhstan
| | - Xiaoxu Hou
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang 832003, China
| | - Shengwei Hu
- College of Life Sciences, Shihezi University, Shihezi, Xinjiang 832003, China.
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Wang H, Wang X, Li X, Wang Q, Qing S, Zhang Y, Gao MQ. A novel long non-coding RNA regulates the immune response in MAC-T cells and contributes to bovine mastitis. FEBS J 2019; 286:1780-1795. [PMID: 30771271 DOI: 10.1111/febs.14783] [Citation(s) in RCA: 32] [Impact Index Per Article: 6.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2018] [Revised: 12/21/2018] [Accepted: 02/13/2019] [Indexed: 12/13/2022]
Abstract
The long non-coding RNAs (lncRNAs) are known to transcriptionally regulate a wide spectrum of diseases. Here, we screened for potentially functional lncRNAs in a mammary epithelial cell model of bovine mastitis by RNA-Seq technology and identified a class of previously undetected mastitis-related lncRNAs. A novel lncRNA was widely expressed in a variety of bovine tissues with diverse relative abundance and had a relatively low expression in mammary tissue. Given its predicted target gene is TUBA1C, we name it lncRNA-TUB. We found a higher expression of lncRNA-TUB in mammary epithelial cells that received a proinflammatory stimulus compared to normal cells. Knockout of lncRNA-TUB by the CRISPR/Cas9 system revealed that it plays crucial roles in the morphological shape, proliferation, migration and β-casein secretion of mammary epithelial cells. In addition, lncRNA-TUB mediates Escherichia coli-induced inflammatory factor secretion and Staphylococcus aureus adhesion to epithelial cells. Our results suggest that the lncRNAs identified here function in bovine mastitis, and that lncRNA-TUB affects the basic biological characteristics and functions of bovine mammary epithelial cells in inflammatory conditions, providing valuable insights into the mechanisms of bovine mastitis.
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Affiliation(s)
- Hao Wang
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Xixi Wang
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Xueru Li
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Qianwen Wang
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Suzhu Qing
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
| | - Yong Zhang
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
- Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A&F University, Yangling, China
| | - Ming-Qing Gao
- College of Veterinary Medicine, Northwest A&F University, Yangling, China
- Key Laboratory of Animal Biotechnology, Ministry of Agriculture, Northwest A&F University, Yangling, China
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Identification and Expression Analysis of Long Noncoding RNAs in Fat-Tail of Sheep Breeds. G3-GENES GENOMES GENETICS 2019; 9:1263-1276. [PMID: 30787031 PMCID: PMC6469412 DOI: 10.1534/g3.118.201014] [Citation(s) in RCA: 26] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
Emerging evidence suggests that long non-coding RNAs (lncRNAs) participate in the regulation of a diverse range of biological processes. However, most studies have been focused on a few established model organisms and little is known about lncRNAs in fat-tail development in sheep. Here, the first profile of lncRNA in sheep fat-tail along with their possible roles in fat deposition were investigated, based on a comparative transcriptome analysis between fat-tailed (Lori-Bakhtiari) and thin-tailed (Zel) Iranian sheep breeds. Among all identified lncRNAs candidates, 358 and 66 transcripts were considered novel intergenic (lincRNAs) and novel intronic (ilncRNAs) corresponding to 302 and 58 gene loci, respectively. Our results indicated that a low percentage of the novel lncRNAs were conserved. Also, synteny analysis identified 168 novel lincRNAs with the same syntenic region in human, bovine and chicken. Only seven lncRNAs were identified as differentially expressed genes between fat and thin tailed breeds. Q-RT-PCR results were consistent with the RNA-Seq data and validated the findings. Target prediction analysis revealed that the novel lncRNAs may act in cis or trans and regulate the expression of genes that are involved in the lipid metabolism. A gene regulatory network including lncRNA-mRNA interactions were constructed and three significant modules were found, with genes relevant to lipid metabolism, insulin and calcium signaling pathway. Moreover, integrated analysis with AnimalQTLdb database further suggested six lincRNAs and one ilncRNAs as candidates of sheep fat-tail development. Our results highlighted the putative contributions of lncRNAs in regulating expression of genes associated with fat-tail development in sheep.
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Lin S, Zhang Z, Xie T, Hu B, Ruan Z, Zhang L, Li C, Li C, Luo W, Nie Q, Zhang X. Identification of a novel antisense RNA that regulates growth hormone receptor expression in chickens. RNA Biol 2019; 16:626-638. [PMID: 30764709 PMCID: PMC6546403 DOI: 10.1080/15476286.2019.1572440] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/28/2022] Open
Abstract
Natural antisense transcripts (NATs) are widely present in mammalian genomes and act as pivotal regulator molecules of gene expression. However, studies on NATs in the chicken are relatively rare. We identified a novel antisense transcript in the chicken, designated GHR-AS-EST, transcribed from the growth hormone receptor (GHR) locus, which encodes a well-known regulatory molecule of muscle development and fat deposition. GHR-AS-EST is predominantly expressed in the chicken liver and muscle tissues. GHR-AS-EST sequence conservation among vertebrates is weak. GHR-AS-EST forms an RNA-RNA duplex with GHBP to increase its stability, and regulates the expression of GHR sense transcripts at both the mRNA and protein levels. Further, GHR-AS-EST promotes cell proliferation by stimulating the expression of signaling factors in the JAK2/STAT pathway, and contributes to fat deposition via downregulating the expression of signaling factors in the JAK2/SOCS pathway in LMH hepatocellular carcinoma cells. We expect that the discovery of a NAT for a regulatory gene associated with cell proliferation and lipolysis will further our understanding of the molecular regulation of both muscle development and fat deposition.
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Affiliation(s)
- Shudai Lin
- a Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture , College of Animal Science of South China Agricultural University , Guangzhou , P.R. China.,b Animal Genomics and Improvement Laboratory, Agricultural Research Service , United States Department of Agriculture , Beltsville , MD , USA.,c Animal Biosciences and Biotechnology Laboratory, Agricultural Research Service , United States Department of Agriculture , Beltsville , MD , USA
| | - Zihao Zhang
- a Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture , College of Animal Science of South China Agricultural University , Guangzhou , P.R. China
| | - Tingting Xie
- a Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture , College of Animal Science of South China Agricultural University , Guangzhou , P.R. China
| | - Bowen Hu
- a Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture , College of Animal Science of South China Agricultural University , Guangzhou , P.R. China
| | - Zhuohao Ruan
- a Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture , College of Animal Science of South China Agricultural University , Guangzhou , P.R. China
| | - Li Zhang
- d Agricultural College , Guangdong Ocean University , Zhanjiang , P.R. China
| | - Congjun Li
- b Animal Genomics and Improvement Laboratory, Agricultural Research Service , United States Department of Agriculture , Beltsville , MD , USA
| | - Charles Li
- c Animal Biosciences and Biotechnology Laboratory, Agricultural Research Service , United States Department of Agriculture , Beltsville , MD , USA
| | - Wen Luo
- a Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture , College of Animal Science of South China Agricultural University , Guangzhou , P.R. China
| | - Qinghua Nie
- a Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture , College of Animal Science of South China Agricultural University , Guangzhou , P.R. China
| | - Xiquan Zhang
- a Guangdong Provincial Key Lab of Agro-Animal Genomics and Molecular Breeding and Key Lab of Chicken Genetics, Breeding and Reproduction, Ministry of Agriculture , College of Animal Science of South China Agricultural University , Guangzhou , P.R. China
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Gupta P, Peter S, Jung M, Lewin A, Hemmrich-Stanisak G, Franke A, von Kleist M, Schütte C, Einspanier R, Sharbati S, Bruegge JZ. Analysis of long non-coding RNA and mRNA expression in bovine macrophages brings up novel aspects of Mycobacterium avium subspecies paratuberculosis infections. Sci Rep 2019; 9:1571. [PMID: 30733564 PMCID: PMC6367368 DOI: 10.1038/s41598-018-38141-x] [Citation(s) in RCA: 21] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 12/18/2018] [Indexed: 12/12/2022] Open
Abstract
Paratuberculosis is a major disease in cattle that severely affects animal welfare and causes huge economic losses worldwide. Development of alternative diagnostic methods is of urgent need to control the disease. Recent studies suggest that long non-coding RNAs (lncRNAs) play a crucial role in regulating immune function and may confer valuable information about the disease. However, their role has not yet been investigated in cattle with respect to infection towards Paratuberculosis. Therefore, we investigated the alteration in genomic expression profiles of mRNA and lncRNA in bovine macrophages in response to Paratuberculosis infection using RNA-Seq. We identified 397 potentially novel lncRNA candidates in macrophages of which 38 were differentially regulated by the infection. A total of 820 coding genes were also significantly altered by the infection. Co-expression analysis of lncRNAs and their neighbouring coding genes suggest regulatory functions of lncRNAs in pathways related to immune response. For example, this included protein coding genes such as TNIP3, TNFAIP3 and NF-κB2 that play a role in NF-κB2 signalling, a pathway associated with immune response. This study advances our understanding of lncRNA roles during Paratuberculosis infection.
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Affiliation(s)
- Pooja Gupta
- Department of Mathematics and Informatics, Freie Universität Berlin, Berlin, Germany. .,Department of Mathematics for Life and Materials Sciences, Zuse Institute Berlin, Berlin, Germany.
| | - Sarah Peter
- Institute for the Reproduction of Farm Animals Schönow Inc, Bernau, Germany
| | - Markus Jung
- Institute for the Reproduction of Farm Animals Schönow Inc, Bernau, Germany
| | - Astrid Lewin
- Robert Koch-Institute, Department Infectious Diseases, Berlin, Germany
| | | | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Max von Kleist
- Department of Mathematics and Informatics, Freie Universität Berlin, Berlin, Germany
| | - Christof Schütte
- Department of Mathematics and Informatics, Freie Universität Berlin, Berlin, Germany.,Department of Mathematics for Life and Materials Sciences, Zuse Institute Berlin, Berlin, Germany
| | - Ralf Einspanier
- Institute of Veterinary Biochemistry, Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - Soroush Sharbati
- Institute of Veterinary Biochemistry, Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
| | - Jennifer Zur Bruegge
- Institute of Veterinary Biochemistry, Department of Veterinary Medicine, Freie Universität Berlin, Berlin, Germany
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37
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Liu G, Zheng J, Zhuang L, Lv Y, Zhu G, Pi L, Wang J, Chen C, Li Z, Liu J, Chen L, Cai G, Zhang X. A Prognostic 5-lncRNA Expression Signature for Head and Neck Squamous Cell Carcinoma. Sci Rep 2018; 8:15250. [PMID: 30323196 PMCID: PMC6189101 DOI: 10.1038/s41598-018-33642-1] [Citation(s) in RCA: 33] [Impact Index Per Article: 5.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2018] [Accepted: 10/02/2018] [Indexed: 12/12/2022] Open
Abstract
Head and neck squamous cell carcinoma (HNSCC) is a common malignant cancer that accounts for 5-10% of all cancers. This study aimed to identify essential genes associated with the prognosis of HNSCC and construct a powerful prognostic model for the risk assessment of HNSCC. RNAseq expression profile data for the patients with HNSCC were obtained from the TCGA database (GEO). A total of 500 samples with full clinical following-up were randomly divided into a training set and a validation set. The training set was used to screen for differentially expressed lncRNAs. Single-factor survival analysis was performed to obtain lncRNAs that associated with prognosis. A robust likelihood-based survival model was constructed to identify the lncRNAs that are essential for the prognosis of HNSCC. A co-expression network between genes and lncRNAs was also constructed to identify lncRNAs co-expressed with genes to serve as the final signature lncRNAs for prognosis. Finally, the prognostic effect of the signature lncRNAs was tested by multi-factor survival analysis and a scoring model for the prognosis of HNSCC was constructed. Moreover, the results of the validation set and the relative expression levels of the signature lncRNAs in the tumour and the adjacent tissue were consistent with the results of the training set. The 5 lncRNAs were distributed among 3 expression modules. Further KEGG pathway enrichment analysis showed that these 3 co-expressed modules participate in different pathways, and many of these pathways are associated with the development and progression of disease. Therefore, we proposed that the 5 validated lncRNAs can be used to predict the prognosis of HNSCC patients and can be applied in postoperative treatment and follow-up.
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Affiliation(s)
- Guancheng Liu
- Department of Otolaryngology Head and Neck Surgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Jinyang Zheng
- Department of Pathology, First Affiliated Hospital of Quanzhou, Fujian Medical University, 248 Dong Street, Quanzhou, 362000, Fujian, China
| | - Liming Zhuang
- Department of Otolaryngology Head and Neck Surgery, First Affiliated Hospital of Quanzhou, Fujian Medical University, 248 Dong Street, Quanzhou, 362000, Fujian, China
| | - Yunxia Lv
- Department of Thyroid Surgery, The Second Affiliated Hospital to Nanchang University, Nanchang, 330006, Jiangxi, China
| | - Gangcai Zhu
- Department of Otolaryngology Head and Neck Surgery, The second Xiangya Hospital, Central South University, Changsha, 410010, Hunan, China
| | - Leiming Pi
- Department of Otolaryngology Head and Neck Surgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Junchen Wang
- Department of Otolaryngology Head and Neck Surgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Changhan Chen
- Department of Otolaryngology Head and Neck Surgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Zhexuan Li
- Department of Otolaryngology Head and Neck Surgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China
| | - Jiangyi Liu
- Quanzhou Disease Prevention and Control Center, 248 Dong Street, Quanzhou, 362000, Fujian, China
| | - Liangjuan Chen
- Department of Otolaryngology Head and Neck Surgery, First Affiliated Hospital of Quanzhou, Fujian Medical University, 248 Dong Street, Quanzhou, 362000, Fujian, China
| | - Gengming Cai
- Department of Otolaryngology Head and Neck Surgery, First Affiliated Hospital of Quanzhou, Fujian Medical University, 248 Dong Street, Quanzhou, 362000, Fujian, China.
| | - Xin Zhang
- Department of Otolaryngology Head and Neck Surgery, Xiangya Hospital, Central South University, Changsha, 410008, Hunan, China.
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Liang G, Yang Y, Li H, Yu H, Li X, Tang Z, Li K. LncRNAnet: a comprehensive Sus scrofa
lncRNA database. Anim Genet 2018; 49:632-635. [DOI: 10.1111/age.12720] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/28/2018] [Indexed: 12/15/2022]
Affiliation(s)
- G. Liang
- College of Life Science; Foshan University; 1 Xianhu University Road Nanhai, Foshan Guangdong 528231 China
| | - Y. Yang
- College of Life Science; Foshan University; 1 Xianhu University Road Nanhai, Foshan Guangdong 528231 China
- Department of Pig Genomic Design and Breeding; Agricultural Genome Institute at Shenzhen; Chinese Academy of Agricultural Sciences; Shenzhen 518124 China
- Shenzhen Key Laboratory of Phenotype Analysis and Utilization of Agricultural Genome; Agricultural Genome Institute at Shenzhen; Chinese Academy of Agricultural Sciences; Shenzhen 518124 China
| | - H. Li
- College of Life Science; Foshan University; 1 Xianhu University Road Nanhai, Foshan Guangdong 528231 China
| | - H. Yu
- College of Life Science; Foshan University; 1 Xianhu University Road Nanhai, Foshan Guangdong 528231 China
| | - X. Li
- College of Life Science; Foshan University; 1 Xianhu University Road Nanhai, Foshan Guangdong 528231 China
- Department of Pig Genomic Design and Breeding; Agricultural Genome Institute at Shenzhen; Chinese Academy of Agricultural Sciences; Shenzhen 518124 China
- Shenzhen Key Laboratory of Phenotype Analysis and Utilization of Agricultural Genome; Agricultural Genome Institute at Shenzhen; Chinese Academy of Agricultural Sciences; Shenzhen 518124 China
| | - Z. Tang
- Department of Pig Genomic Design and Breeding; Agricultural Genome Institute at Shenzhen; Chinese Academy of Agricultural Sciences; Shenzhen 518124 China
- Shenzhen Key Laboratory of Phenotype Analysis and Utilization of Agricultural Genome; Agricultural Genome Institute at Shenzhen; Chinese Academy of Agricultural Sciences; Shenzhen 518124 China
| | - K. Li
- College of Life Science; Foshan University; 1 Xianhu University Road Nanhai, Foshan Guangdong 528231 China
- Department of Pig Genomic Design and Breeding; Agricultural Genome Institute at Shenzhen; Chinese Academy of Agricultural Sciences; Shenzhen 518124 China
- Shenzhen Key Laboratory of Phenotype Analysis and Utilization of Agricultural Genome; Agricultural Genome Institute at Shenzhen; Chinese Academy of Agricultural Sciences; Shenzhen 518124 China
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39
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Kern C, Wang Y, Chitwood J, Korf I, Delany M, Cheng H, Medrano JF, Van Eenennaam AL, Ernst C, Ross P, Zhou H. Genome-wide identification of tissue-specific long non-coding RNA in three farm animal species. BMC Genomics 2018; 19:684. [PMID: 30227846 PMCID: PMC6145346 DOI: 10.1186/s12864-018-5037-7] [Citation(s) in RCA: 74] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2017] [Accepted: 08/27/2018] [Indexed: 03/08/2023] Open
Abstract
Background Numerous long non-coding RNAs (lncRNAs) have been identified and their roles in gene regulation in humans, mice, and other model organisms studied; however, far less research has been focused on lncRNAs in farm animal species. While previous studies in chickens, cattle, and pigs identified lncRNAs in specific developmental stages or differentially expressed under specific conditions in a limited number of tissues, more comprehensive identification of lncRNAs in these species is needed. The goal of the FAANG Consortium (Functional Annotation of Animal Genomes) is to functionally annotate animal genomes, including the annotation of lncRNAs. As one of the FAANG pilot projects, lncRNAs were identified across eight tissues in two adult male biological replicates from chickens, cattle, and pigs. Results Comprehensive lncRNA annotations for the chicken, cattle, and pig genomes were generated by utilizing RNA-seq from eight tissue types from two biological replicates per species at the adult developmental stage. A total of 9393 lncRNAs in chickens, 7235 lncRNAs in cattle, and 14,429 lncRNAs in pigs were identified. Including novel isoforms and lncRNAs from novel loci, 5288 novel lncRNAs were identified in chickens, 3732 in cattle, and 4870 in pigs. These transcripts match previously known patterns of lncRNAs, such as generally lower expression levels than mRNAs and higher tissue specificity. An analysis of lncRNA conservation across species identified a set of conserved lncRNAs with potential functions associated with chromatin structure and gene regulation. Tissue-specific lncRNAs were identified. Genes proximal to tissue-specific lncRNAs were enriched for GO terms associated with the tissue of origin, such as leukocyte activation in spleen. Conclusions LncRNAs were identified in three important farm animal species using eight tissues from adult individuals. About half of the identified lncRNAs were not previously reported in the NCBI annotations for these species. While lncRNAs are less conserved than protein-coding genes, a set of positionally conserved lncRNAs were identified among chickens, cattle, and pigs with potential functions related to chromatin structure and gene regulation. Tissue-specific lncRNAs have potential regulatory functions on genes enriched for tissue-specific GO terms. Future work will include epigenetic data from ChIP-seq experiments to further refine these annotations. Electronic supplementary material The online version of this article (10.1186/s12864-018-5037-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Colin Kern
- Department of Animal Science, University of California, Davis, Davis, CA, USA
| | - Ying Wang
- Department of Animal Science, University of California, Davis, Davis, CA, USA
| | - James Chitwood
- Department of Animal Science, University of California, Davis, Davis, CA, USA
| | - Ian Korf
- Genome Center, University of California, Davis, Davis, CA, USA
| | - Mary Delany
- Department of Animal Science, University of California, Davis, Davis, CA, USA
| | - Hans Cheng
- USDA-ARS, Avian Disease and Oncology Laboratory, East Lansing, MI, USA
| | - Juan F Medrano
- Department of Animal Science, University of California, Davis, Davis, CA, USA
| | | | - Catherine Ernst
- Department of Animal Science, Michigan State University, East Lansing, MI, USA
| | - Pablo Ross
- Department of Animal Science, University of California, Davis, Davis, CA, USA.
| | - Huaijun Zhou
- Department of Animal Science, University of California, Davis, Davis, CA, USA.
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40
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Bush SJ, Muriuki C, McCulloch MEB, Farquhar IL, Clark EL, Hume DA. Cross-species inference of long non-coding RNAs greatly expands the ruminant transcriptome. Genet Sel Evol 2018; 50:20. [PMID: 29690875 PMCID: PMC5926538 DOI: 10.1186/s12711-018-0391-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2018] [Accepted: 04/13/2018] [Indexed: 02/06/2023] Open
Abstract
Background mRNA-like long non-coding RNAs (lncRNAs) are a significant component of mammalian transcriptomes, although most are expressed only at low levels, with high tissue-specificity and/or at specific developmental stages. Thus, in many cases lncRNA detection by RNA-sequencing (RNA-seq) is compromised by stochastic sampling. To account for this and create a catalogue of ruminant lncRNAs, we compared de novo assembled lncRNAs derived from large RNA-seq datasets in transcriptional atlas projects for sheep and goats with previous lncRNAs assembled in cattle and human. We then combined the novel lncRNAs with the sheep transcriptional atlas to identify co-regulated sets of protein-coding and non-coding loci. Results Few lncRNAs could be reproducibly assembled from a single dataset, even with deep sequencing of the same tissues from multiple animals. Furthermore, there was little sequence overlap between lncRNAs that were assembled from pooled RNA-seq data. We combined positional conservation (synteny) with cross-species mapping of candidate lncRNAs to identify a consensus set of ruminant lncRNAs and then used the RNA-seq data to demonstrate detectable and reproducible expression in each species. In sheep, 20 to 30% of lncRNAs were located close to protein-coding genes with which they are strongly co-expressed, which is consistent with the evolutionary origin of some ncRNAs in enhancer sequences. Nevertheless, most of the lncRNAs are not co-expressed with neighbouring protein-coding genes. Conclusions Alongside substantially expanding the ruminant lncRNA repertoire, the outcomes of our analysis demonstrate that stochastic sampling can be partly overcome by combining RNA-seq datasets from related species. This has practical implications for the future discovery of lncRNAs in other species. Electronic supplementary material The online version of this article (10.1186/s12711-018-0391-0) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Stephen J Bush
- The Roslin Institute, University of Edinburgh, Easter Bush Campus, Edinburgh, Midlothian, EH25 9RG, UK. .,Nuffield Department of Clinical Medicine, John Radcliffe Hospital, University of Oxford, Headington, Oxford, OX3 9DU, UK.
| | - Charity Muriuki
- The Roslin Institute, University of Edinburgh, Easter Bush Campus, Edinburgh, Midlothian, EH25 9RG, UK
| | - Mary E B McCulloch
- The Roslin Institute, University of Edinburgh, Easter Bush Campus, Edinburgh, Midlothian, EH25 9RG, UK
| | - Iseabail L Farquhar
- Centre for Synthetic and Systems Biology, CH Waddington Building, Max Borne Crescent, King's Buildings, University of Edinburgh, Edinburgh, EH9 3BF, UK
| | - Emily L Clark
- The Roslin Institute, University of Edinburgh, Easter Bush Campus, Edinburgh, Midlothian, EH25 9RG, UK
| | - David A Hume
- The Roslin Institute, University of Edinburgh, Easter Bush Campus, Edinburgh, Midlothian, EH25 9RG, UK. .,Translational Research Institute, Mater Research-University of Queensland, 37 Kent Street, Woolloongabba, QLD, 4102, Australia.
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41
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Weikard R, Hadlich F, Hammon HM, Frieten D, Gerbert C, Koch C, Dusel G, Kuehn C. Long noncoding RNAs are associated with metabolic and cellular processes in the jejunum mucosa of pre-weaning calves in response to different diets. Oncotarget 2018; 9:21052-21069. [PMID: 29765519 PMCID: PMC5940403 DOI: 10.18632/oncotarget.24898] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2017] [Accepted: 02/25/2018] [Indexed: 01/05/2023] Open
Abstract
Long noncoding RNAs (lncRNAs) emerged as important regulatory component of mechanisms involved in gene expression, chromatin modification and epigenetic processes, but they are rarely annotated in the bovine genome. Our study monitored the jejunum transcriptome of German Holstein calves fed two different milk diets using transcriptome sequencing (RNA-seq). To identify potential lncRNAs within the pool of unknown transcripts, four bioinformatic lncRNA prediction tools were applied. The intersection of the alignment-free lncRNA prediction tools (CNCI, PLEK and FEELnc) predicted 1,812 lncRNA transcripts concordantly comprising a catalogue of 1,042 putative lncRNA loci expressed in the calves’ intestinal mucosa. Nine lncRNA loci were differentially expressed (DE lncRNAs) between both calf groups. To elucidate their biological function, we applied a systems biology approach that combines weighted gene co-expression network analysis with functional enrichment and biological pathway analysis. Four DE lncRNAs were found to be strongly correlated with a gene network module (GNM) enriched for genes from canonical pathways of remodeling of epithelial adherens junction, tight junction and integrin signaling. Another DE lncRNA was strongly correlated with a GNM enriched for genes associated with energy metabolism and maintaining of cellular homeostasis with a focus on mitochondrial processes. Our data suggest that these DE lncRNAs may play potential regulatory roles in modulating biological processes associated with energy metabolism pathways and cellular signaling processes affecting the barrier function of intestinal epithelial cells of calves in response to different feeding regimens in the pre-weaning period.
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Affiliation(s)
- Rosemarie Weikard
- Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Frieder Hadlich
- Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Harald M Hammon
- Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | | | - Caroline Gerbert
- Educational and Research Centre for Animal Husbandry, Hofgut Neumühle, Münchweiler, Germany
| | - Christian Koch
- Educational and Research Centre for Animal Husbandry, Hofgut Neumühle, Münchweiler, Germany
| | - Georg Dusel
- University of Applied Sciences, Bingen, Germany
| | - Christa Kuehn
- Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany.,Faculty of Agricultural and Environmental Sciences, University Rostock, Rostock, Germany
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Amills M, Capote J, Tosser-Klopp G. Goat domestication and breeding: a jigsaw of historical, biological and molecular data with missing pieces. Anim Genet 2017; 48:631-644. [PMID: 28872195 DOI: 10.1111/age.12598] [Citation(s) in RCA: 44] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/14/2017] [Indexed: 12/23/2022]
Abstract
Domestic goats (Capra hircus) are spread across the five continents with a census of 1 billion individuals. The worldwide population of goats descends from a limited number of bezoars (Capra aegagrus) domesticated 10 000 YBP (years before the present) in the Fertile Crescent. The extraordinary adaptability and hardiness of goats favoured their rapid spread over the Old World, reaching the Iberian Peninsula and Southern Africa 7000 YBP and 2000 YBP respectively. Molecular studies have revealed one major mitochondrial haplogroup A and five less frequent haplogroups B, C, D, F and G. Moreover, the analysis of autosomal and Y-chromosome markers has evidenced an appreciable geographic differentiation. The implementation of new molecular technologies, such as whole-genome sequencing and genome-wide genotyping, allows for the exploration of caprine diversity at an unprecedented scale, thus providing new insights into the evolutionary history of goats. In spite of a number of pitfalls, the characterization of the functional elements of the goat genome is expected to play a key role in understanding the genetic determination of economically relevant traits. Genomic selection and genome editing also hold great potential, particularly for improving traits that cannot be modified easily by traditional selection.
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Affiliation(s)
- M Amills
- Department of Animal Genetics, Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona, Bellaterra, 08193, Spain
| | - J Capote
- Instituto Canario de Investigaciones Agrarias, La Laguna, 38108, Tenerife, Spain
| | - G Tosser-Klopp
- INRA-GenPhySE-Génétique, Physiologie et Systèmes d'Elevage-UMR1388, 24 Chemin de Borde Rouge-Auzeville CS 52627, 31326, Castanet Tolosan Cedex, France
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