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Zheng W, Chen Y, Wang Y, Chen S, Xu XW. Genome-Wide Identification and Involvement in Response to Biotic and Abiotic Stresses of lncRNAs in Turbot ( Scophthalmus maximus). Int J Mol Sci 2023; 24:15870. [PMID: 37958851 PMCID: PMC10648414 DOI: 10.3390/ijms242115870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Revised: 10/25/2023] [Accepted: 10/27/2023] [Indexed: 11/15/2023] Open
Abstract
Long non-coding RNAs (lncRNAs) play crucial roles in a variety of biological processes, including stress response. However, the number, characteristics and stress-related expression of lncRNAs in turbot are still largely unknown. In this study, a total of 12,999 lncRNAs were identified at the genome-wide level of turbot for the first time using 24 RNA-seq datasets. Sequence characteristic analyses of transcripts showed that lncRNA transcripts were shorter in average length, lower in average GC content and in average expression level as compared to the coding genes. Expression pattern analyses of lncRNAs in 12 distinct tissues showed that lncRNAs, especially lincRNA, exhibited stronger tissue-specific expression than coding genes. Moreover, 612, 1351, 1060, 875, 420 and 1689 differentially expressed (DE) lncRNAs under Vibrio anguillarum, Enteromyxum scophthalmi, and Megalocytivirus infection and heat, oxygen, and salinity stress conditions were identified, respectively. Among them, 151 and 62 lncRNAs showed differential expression under various abiotic and biotic stresses, respectively, and 11 lncRNAs differentially expressed under both abiotic and biotic stresses were selected as comprehensive stress-responsive lncRNA candidates. Furthermore, expression pattern analysis and qPCR validation both verified the comprehensive stress-responsive functions of these 11 lncRNAs. In addition, 497 significantly co-expressed target genes (correlation coefficient (R) > 0.7 and q-value < 0.05) for these 11 comprehensive stress-responsive lncRNA candidates were identified. Finally, GO and KEGG enrichment analyses indicated that these target genes were enriched mainly in molecular function, such as cytokine activity and active transmembrane transporter activity, in biological processes, such as response to stimulus and immune response, and in pathways, such as protein families: signaling and cellular processes, transporters and metabolism. These findings not only provide valuable reference resources for further research on the molecular basis and function of lncRNAs in turbot but also help to accelerate the progress of molecularly selective breeding of stress-resistant turbot strains or varieties.
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Affiliation(s)
- Weiwei Zheng
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (W.Z.); (Y.C.); (Y.W.)
| | - Yadong Chen
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (W.Z.); (Y.C.); (Y.W.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao 266237, China
| | - Yaning Wang
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (W.Z.); (Y.C.); (Y.W.)
- College of Life Science, Qingdao University, Qingdao 266071, China
| | - Songlin Chen
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (W.Z.); (Y.C.); (Y.W.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao 266237, China
| | - Xi-wen Xu
- State Key Laboratory of Mariculture Biobreeding and Sustainable Goods, Yellow Sea Fisheries Research Institute, Chinese Academy of Fishery Sciences, Qingdao 266071, China; (W.Z.); (Y.C.); (Y.W.)
- Laboratory for Marine Fisheries Science and Food Production Processes, Laoshan Laboratory, Qingdao 266237, China
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2
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Lim B, Kim SC, Kim WI, Kim JM. Integrative time-serial networks for genome-wide lncRNA-mRNA interactions reveal interferon-inducible antiviral and T-cell receptor regulations against PRRSV infection. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2023; 147:104759. [PMID: 37315774 DOI: 10.1016/j.dci.2023.104759] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2022] [Accepted: 06/10/2023] [Indexed: 06/16/2023]
Abstract
Porcine reproductive and respiratory syndrome virus (PRRSV) infection severely affects the swine industry each year. Although the host mechanisms against PRRSV infection have been identified in key target tissues through whole transcriptome sequencing, specific molecular regulators have not been elucidated. Long non-coding RNA (lncRNA) expression is highly specific and could thus be used to effectively identify PRRSV-specific candidates. Here, we identified novel lncRNAs in lungs, bronchial lymph nodes, and tonsils after PRRSV infection and constructed phenotype-based integrative co-expression networks using time-series differentially expressed (DE) lncRNAs and mRNAs. After the analyses, a total of 309 lncRNA-mRNA interactions were identified. During early host innate signalling, interferon-inducible and interferon genes were positively regulated by specific lncRNA. Moreover, T-cell receptor genes in lung adaptive immune signalling were negatively regulated by specific lncRNA. Collectively, our findings provide insights into the genome-wide lncRNA-mRNA interactions and dynamic regulation of lncRNA-mediated mechanisms against PRRSV infection.
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Affiliation(s)
- Byeonghwi Lim
- Functional Genomics & Bioinformatics Laboratory, Department of Animal Science and Technology, Chung-Ang University, Anseong, Gyeonggi-do, 17546, Republic of Korea
| | - Seung-Chai Kim
- College of Veterinary Medicine, Jeonbuk National University, Iksan, Jeollabuk-do, 54596, Republic of Korea
| | - Won-Il Kim
- College of Veterinary Medicine, Jeonbuk National University, Iksan, Jeollabuk-do, 54596, Republic of Korea.
| | - Jun-Mo Kim
- Functional Genomics & Bioinformatics Laboratory, Department of Animal Science and Technology, Chung-Ang University, Anseong, Gyeonggi-do, 17546, Republic of Korea.
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3
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Chen C, Chang Y, Deng Y, Cui Q, Liu Y, Li H, Ren H, Zhu J, Liu Q, Peng Y. Comprehensive analysis of miRNAs, lncRNAs and mRNAs profiles in backfat tissue between Daweizi and Yorkshire pigs. Anim Biosci 2023; 36:404-416. [PMID: 36397714 PMCID: PMC9996253 DOI: 10.5713/ab.22.0165] [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: 04/24/2022] [Accepted: 09/11/2022] [Indexed: 11/14/2022] Open
Abstract
OBJECTIVE Daweizi (DWZ) is a famous indigenous pig breed in China and characterized by tender meat and high fat percentage. However, the expression profiles and functions of transcripts in DWZ pigs is still in infancy. The object of this study was to depict the transcript profiles in DWZ pigs and screen the potential pathway influence adipogenesis and fat deposition. METHODS Histological analysis of backfat tissue was firstly performed between DWZ and lean-type Yorkshire pigs, and then RNA sequencing technology was utilized to explore miRNAs, lncRNAs and mRNAs profiles in backfat tissue. 18 differentially expressed (DE) transcripts were randomly selected for quantitative real-time polymerase chain reaction (QPCR) to validate the reliability of the sequencing results. Finally, gene ontology (GO) and Kyoto encyclopedia of genes and genomes (KEGG) enrichment analysis were conducted to investigate the potential pathways influence adipocyte differentiation, adipogenesis and lipid metabolism, and a schematic model was further proposed. RESULTS A total of 1,625 differentially expressed transcripts were identified in DWZ pigs, including 27 upregulated and 45 downregulated miRNAs, 64 upregulated and 119 downregulated lncRNA, 814 upregulated and 556 downregulated mRNAs. QPCR analysis exhibited strong consistency with the sequencing data. GO and KEGG analysis elucidated that the differentially expressed transcripts were mainly associated with cell growth and death, signal transduction, peroxisome proliferator-activated receptors (PPAR), AMP-activated protein kinase (AMPK), PI3K-Akt, adipocytokine and foxo signaling pathways, all of which are strongly involved in cell development, lipid metabolism and adipogenesis. Further analysis indicated that the BGIR9823_87926/miR-194a-5p/AQP7 network may be effective in the process of adipocyte differentiation or adipogenesis. CONCLUSION Our study provides comprehensive insights into the regulatory network of backfat deposition and lipid metabolism in pigs from the point of view of miRNAs, lncRNAs and mRNAs.
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Affiliation(s)
- Chen Chen
- Hunan Institute of Animal and Veterinary Science, Changsha 410131, China
| | - Yitong Chang
- College of Animal Science and Technology, Hunan Agricultural University, Changsha, 410128, China
| | - Yuan Deng
- Hunan Institute of Animal and Veterinary Science, Changsha 410131, China
| | - Qingming Cui
- Hunan Institute of Animal and Veterinary Science, Changsha 410131, China
| | - Yingying Liu
- Hunan Institute of Animal and Veterinary Science, Changsha 410131, China
| | - Huali Li
- Hunan Institute of Animal and Veterinary Science, Changsha 410131, China
| | - Huibo Ren
- Hunan Institute of Animal and Veterinary Science, Changsha 410131, China
| | - Ji Zhu
- Hunan Institute of Animal and Veterinary Science, Changsha 410131, China
| | - Qi Liu
- Hunan Tianfu Ecological Agricultural Limited Company, Changsha, 410144, China
| | - Yinglin Peng
- Hunan Institute of Animal and Veterinary Science, Changsha 410131, China.,College of Animal Science and Technology, Hunan Agricultural University, Changsha, 410128, China
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Transcriptomics and Lipid Metabolomics Analysis of Subcutaneous, Visceral, and Abdominal Adipose Tissues of Beef Cattle. Genes (Basel) 2022; 14:genes14010037. [PMID: 36672778 PMCID: PMC9858949 DOI: 10.3390/genes14010037] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/23/2022] [Revised: 12/13/2022] [Accepted: 12/20/2022] [Indexed: 12/25/2022] Open
Abstract
Fat deposition traits are influenced by genetics and environment, which affect meat quality, growth rate, and energy metabolism of domestic animals. However, at present, the molecular mechanism of fat deposition is not entirely understood in beef cattle. Therefore, the current study conducted transcriptomics and lipid metabolomics analysis of subcutaneous, visceral, and abdominal adipose tissue (SAT, VAT, and AAT) of Huaxi cattle to investigate the differences among these adipose tissues and systematically explore how candidate genes interact with metabolites to affect fat deposition. These results demonstrated that compared with SAT, the gene expression patterns and metabolite contents of VAT and AAT were more consistent. Particularly, SCD expression, monounsaturated fatty acid (MUFA) and triglyceride (TG) content were higher in SAT, whereas PCK1 expression and the contents of saturated fatty acid (SFA), diacylglycerol (DG), and lysoglycerophosphocholine (LPC) were higher in VAT. Notably, in contrast to PCK1, 10 candidates including SCD, ELOVL6, ACACA, and FABP7 were identified to affect fat deposition through positively regulating MUFA and TG, and negatively regulating SFA, DG, and LPC. These findings uncovered novel gene resources and offered a theoretical basis for future investigation of fat deposition in beef cattle.
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Yang W, Liu Z, Zhao Q, Du H, Yu J, Wang H, Liu X, Liu H, Jing X, Yang H, Shi G, Zhou L, Liu J. Population Genetic Structure and Selection Signature Analysis of Beijing Black Pig. Front Genet 2022; 13:860669. [PMID: 35401688 PMCID: PMC8987279 DOI: 10.3389/fgene.2022.860669] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2022] [Accepted: 03/08/2022] [Indexed: 12/04/2022] Open
Abstract
Beijing Black pig is an excellent cultivated black pig breed in China, with desirable body shape, tender meat quality and robust disease resistance. To explore the level of admixture and selection signatures of Beijing Black pigs, a total number of 90 individuals covering nine pig breeds were used in our study, including Beijing Black pig, Large White, Landrace, Duroc, Lantang pig, Luchuan pig, Mashen pig, Huainan pig and Min pig. These animals were resequenced with 18.19 folds mapped read depth on average. Generally, we found that Beijing Black pig was genetically closer to commercial pig breeds by population genetic structure and genetic diversity analysis, and was also affected by Chinese domestic breeds Huainan pig and Min pig. These results are consistent with the cross-breeding history of Beijing Black pig. Selection signal detections were performed on three pig breeds, Beijing Black pig, Duroc and Large White, using three complementary methods (FST, θπ, and XP-EHH). In total, 1,167 significant selected regions and 392 candidate genes were identified. Functional annotations were enriched to pathways related to immune processes and meat and lipid metabolism. Finally, potential candidate genes, influencing meat quality (GPHA2, EHD1, HNF1A, C12orf43, GLTP, TRPV4, MVK, and MMAB), reproduction (PPP2R5B and MAP9), and disease resistance (OASL, ANKRD13A, and GIT2), were further detected by gene annotation analysis. Our results advanced the understanding of the genetic mechanism behind artificial selection of Beijing Black pigs, and provided theoretical basis for the subsequent breeding and genetic research of this breed.
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Affiliation(s)
- Wenjing Yang
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Zhen Liu
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Qiqi Zhao
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Heng Du
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Jian Yu
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Hongwei Wang
- Beijing Heiliu Stockbreeding Technology Co.,Ltd, Beijing, China
| | - Xiance Liu
- Beijing Heiliu Stockbreeding Technology Co.,Ltd, Beijing, China
| | - Hai Liu
- Beijing Heiliu Stockbreeding Technology Co.,Ltd, Beijing, China
| | - Xitao Jing
- Beijing Heiliu Stockbreeding Technology Co.,Ltd, Beijing, China
| | - Hongping Yang
- Beijing Heiliu Stockbreeding Technology Co.,Ltd, Beijing, China
| | - Guohua Shi
- Beijing Heiliu Stockbreeding Technology Co.,Ltd, Beijing, China
| | - Lei Zhou
- College of Animal Science and Technology, China Agricultural University, Beijing, China
- *Correspondence: Lei Zhou, ; Jianfeng Liu,
| | - Jianfeng Liu
- College of Animal Science and Technology, China Agricultural University, Beijing, China
- *Correspondence: Lei Zhou, ; Jianfeng Liu,
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6
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Vahedi SM, Salek Ardestani S, Karimi K, Banabazi MH. Weighted single-step GWAS for body mass index and scans for recent signatures of selection in Yorkshire pigs. J Hered 2022; 113:325-335. [DOI: 10.1093/jhered/esac004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2022] [Accepted: 01/24/2022] [Indexed: 11/14/2022] Open
Abstract
Abstract
Controlling extra fat deposition is economically favorable in modern swine industry. Understanding the genetic architecture of fat deposition traits such as body mass index (BMI) can help in improving genomic selection for such traits. We utilized a weighted single-step genome-wide association study (WssGWAS) to detect genetic regions and candidate genes associated with BMI in a Yorkshire pig population. Three extended haplotype homozygosity (EHH)-related statistics were also incorporated within a de-correlated composite of multiple signals (DCMS) framework to detect recent selection signatures signals. Overall, the full pedigree consisted of 7,016 pigs, of which 5,561 had BMI records and 598 pigs were genotyped with an 80 K single nucleotide polymorphism (SNP) array. Results showed that the most significant windows (top 15) explained 9.35% of BMI genetic variance. Several genes were detected in regions previously associated with pig fat deposition traits and treated as potential candidate genes for BMI in Yorkshire pigs: FTMT, SRFBP1, KHDRBS3, FOXG1, SOD3, LRRC32, TSKU, ACER3, B3GNT6, CCDC201, ADCY1, RAMP3, TBRG4, CCM2. Signature of selection analysis revealed multiple candidate genes previously associated with various economic traits. However, BMI genetic variance explained by regions under selection pressure was minimal (1.31%). In conclusion, candidate genes associated with Yorkshire pigs’ BMI trait were identified using WssGWAS. Gene enrichment analysis indicated that the identified candidate genes were enriched in the insulin secretion pathway. We anticipate that these results further advance our understanding of the genetic architecture of BMI in Yorkshire pigs and provide information for genomic selection for fat deposition in this breed.
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Affiliation(s)
- Seyed Milad Vahedi
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | | | - Karim Karimi
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, Canada
| | - Mohammad Hossein Banabazi
- Department of Biotechnology, Animal Science Research Institute of Iran, Agricultural Research, Education & Extension Organization, Karaj, Iran
- Department of animal breeding and genetics (HGEN), Centre for Veterinary Medicine and Animal Science (VHC), Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
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7
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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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8
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Yang CX, Liang H, Wu ZW, Huo LJ, Du ZQ. Identification of lncRNAs involved in maternal-to-zygotic transition of in vitro-produced porcine embryos by single-cell RNA-seq. Reprod Domest Anim 2021; 57:111-122. [PMID: 34725864 DOI: 10.1111/rda.14034] [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: 08/28/2021] [Accepted: 10/18/2021] [Indexed: 11/30/2022]
Abstract
Long non-coding RNAs (lncRNAs) function through multiple tiers of molecular circuits and are vital to gamete maturation and early embryo development. However, in pig early embryos, identification and expression dynamics of lncRNAs remain less studied. Here, we systematically analysed the expression dynamics of lncRNAs based on our previously published single-cell RNA-seq data from pig mature oocytes (GSE160334), and single blastomeres biopsied from pig in vitro fertilized (IVF) and early parthenogenetically activated (PA) embryos (1- to 8-cell stages; GSE164812). With the progression of embryo development, the total number of expressed lncRNAs gradually decreased and showed great variation at each developmental stage for both IVF and PA groups. Consecutive stage pairwise comparison of MII oocytes, 1-cell zygotes, 2-cell, 4-cell and 8-cell IVF embryos identified 151, 245, 1119 and 188 differentially expressed (DE) lncRNAs, including 119, 80, 867, 77 up-regulated and 32, 165, 252, 111 down-regulated, while 289, 437, 895 and 495 DE lncRNAs (141, 89, 768, 97 up-regulated and 148, 348, 127, 398 down-regulated) were identified in PA embryos at the same stages. The DE lncRNAs identified within IVF embryos were much different from that identified within PA embryos, showing embryo type-specific manner. Further cross-comparison between PA and IVF embryos identified 184, 656, 2502 and 266 DE lncRNAs for the 1- to 8-cell embryo stages, respectively. Further GO and KEGG enrichment analysis of DE mRNAs targeted by DELs indicated that different signalling pathways were involved in maternal-only and bi-parental embryo development. Collectively, comparative profiling of lncRNA expression dynamics between pig IVF and PA embryos provides a valuable resource, to investigate further regulatory mechanisms of lncRNAs associated with ZGA and maternal RNA decay during early embryo development.
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Affiliation(s)
- Cai-Xia Yang
- College of Animal Science, Yangtze University, Jingzhou, Hubei, China
| | - Hao Liang
- College of Animal Science, Yangtze University, Jingzhou, Hubei, China
| | - Zi-Wei Wu
- College of Animal Science, Yangtze University, Jingzhou, Hubei, China
| | - Li-Jun Huo
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction, Education Ministry of China, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
| | - Zhi-Qiang Du
- College of Animal Science, Yangtze University, Jingzhou, Hubei, China
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9
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Weldenegodguad M, Pokharel K, Niiranen L, Soppela P, Ammosov I, Honkatukia M, Lindeberg H, Peippo J, Reilas T, Mazzullo N, Mäkelä KA, Nyman T, Tervahauta A, Herzig KH, Stammler F, Kantanen J. Adipose gene expression profiles reveal insights into the adaptation of northern Eurasian semi-domestic reindeer (Rangifer tarandus). Commun Biol 2021; 4:1170. [PMID: 34620965 PMCID: PMC8497613 DOI: 10.1038/s42003-021-02703-z] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 09/21/2021] [Indexed: 02/08/2023] Open
Abstract
Reindeer (Rangifer tarandus) are semi-domesticated animals adapted to the challenging conditions of northern Eurasia. Adipose tissues play a crucial role in northern animals by altering gene expression in their tissues to regulate energy homoeostasis and thermogenic activity. Here, we perform transcriptome profiling by RNA sequencing of adipose tissues from three different anatomical depots: metacarpal (bone marrow), perirenal, and prescapular fat in Finnish and Even reindeer (in Sakha) during spring and winter. A total of 16,212 genes are expressed in our data. Gene expression profiles in metacarpal tissue are distinct from perirenal and prescapular adipose tissues. Notably, metacarpal adipose tissue appears to have a significant role in the regulation of the energy metabolism of reindeer in spring when their nutritional condition is poor after winter. During spring, genes associated with the immune system are upregulated in the perirenal and prescapular adipose tissue. Blood and tissue parameters reflecting general physiological and metabolic status show less seasonal variation in Even reindeer than in Finnish reindeer. This study identifies candidate genes potentially involved in immune response, fat deposition, and energy metabolism and provides new information on the mechanisms by which reindeer adapt to harsh arctic conditions.
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Affiliation(s)
- Melak Weldenegodguad
- grid.22642.300000 0004 4668 6757Natural Resources Institute Finland (Luke), Jokioinen, Finland ,grid.9668.10000 0001 0726 2490Department of Environmental and Biological Sciences, University of Eastern Finland, Kuopio, Finland
| | - Kisun Pokharel
- grid.22642.300000 0004 4668 6757Natural Resources Institute Finland (Luke), Jokioinen, Finland
| | - Laura Niiranen
- grid.10858.340000 0001 0941 4873Research Unit of Biomedicine, Faculty of Medicine, University of Oulu, Oulu, Finland
| | - Päivi Soppela
- grid.37430.330000 0001 0744 995XArctic Centre, University of Lapland, Rovaniemi, Finland
| | - Innokentyi Ammosov
- grid.495192.2Laboratory of Reindeer Husbandry and Traditional Industries, Yakut Scientific Research Institute of Agriculture, Yakutsk, The Sakha Republic (Yakutia) Russia
| | | | - Heli Lindeberg
- grid.22642.300000 0004 4668 6757Natural Resources Institute Finland (Luke), Maaninka, Finland
| | - Jaana Peippo
- grid.22642.300000 0004 4668 6757Natural Resources Institute Finland (Luke), Jokioinen, Finland ,NordGen—Nordic Genetic Resource Center, Ås, Norway
| | - Tiina Reilas
- grid.22642.300000 0004 4668 6757Natural Resources Institute Finland (Luke), Jokioinen, Finland
| | - Nuccio Mazzullo
- grid.37430.330000 0001 0744 995XArctic Centre, University of Lapland, Rovaniemi, Finland
| | - Kari A. Mäkelä
- grid.10858.340000 0001 0941 4873Research Unit of Biomedicine, Faculty of Medicine, University of Oulu, Oulu, Finland
| | - Tommi Nyman
- grid.454322.60000 0004 4910 9859Department of Ecosystems in the Barents Region, Norwegian Institute of Bioeconomy Research, Svanvik, Norway
| | - Arja Tervahauta
- grid.9668.10000 0001 0726 2490Department of Environmental and Biological Sciences, University of Eastern Finland, Kuopio, Finland
| | - Karl-Heinz Herzig
- grid.10858.340000 0001 0941 4873Research Unit of Biomedicine, Faculty of Medicine, University of Oulu, Oulu, Finland ,grid.10858.340000 0001 0941 4873Medical Research Center, Faculty of Medicine, University of Oulu, Oulu, Finland ,grid.412326.00000 0004 4685 4917Oulu University Hospital, Oulu, Finland ,grid.22254.330000 0001 2205 0971Institute of Pediatrics, Poznań University of Medical Sciences, Poznań, Poland
| | - Florian Stammler
- grid.37430.330000 0001 0744 995XArctic Centre, University of Lapland, Rovaniemi, Finland
| | - Juha Kantanen
- grid.22642.300000 0004 4668 6757Natural Resources Institute Finland (Luke), Jokioinen, Finland
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10
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Li X, Zou C, Li M, Fang C, Li K, Liu Z, Li C. Transcriptome Analysis of In Vitro Fertilization and Parthenogenesis Activation during Early Embryonic Development in Pigs. Genes (Basel) 2021; 12:genes12101461. [PMID: 34680856 PMCID: PMC8535918 DOI: 10.3390/genes12101461] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/07/2021] [Revised: 09/14/2021] [Accepted: 09/15/2021] [Indexed: 11/16/2022] Open
Abstract
Parthenogenesis activation (PA), as an important artificial breeding method, can stably preserve the dominant genotype of a species. However, the delayed development of PA embryos is still overly severe and largely leads to pre-implantation failure in pigs. The mechanisms underlying the deficiencies of PA embryos have not been completely understood. For further understanding of the molecular mechanism behind PA embryo failure, we performed transcriptome analysis among pig oocytes (meiosis II, MII) and early embryos at three developmental stages (zygote, morula, and blastocyst) in vitro fertilization (IVF) and PA group. Totally, 11,110 differentially expressed genes (DEGs), 4694 differentially expressed lincRNAs (DELs) were identified, and most DEGs enriched the regulation of apoptotic processes. Through cis- and trans-manner functional prediction, we found that hub lincRNAs were mostly involved in abnormal parthenogenesis embryonic development. In addition, twenty DE imprinted genes showed that some paternally imprinted genes in IVF displayed higher expression than that in PA. Notably, we identified that three DELs of imprinted genes (MEST, PLAGL1, and DIRAS3) were up regulated in IVF, and there was no significant change in PA group. Disordered expression of key genes for embryonic development might play key roles in abnormal parthenogenesis embryonic development. Our study indicates that embryos derived from different production techniques have varied in vitro development to the blastocyst stage, and they also affect the transcription level of corresponding genes, such as imprinted genes. This work will help future research on these genes and molecular-assisted breeding for pig parthenotes.
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Affiliation(s)
- Xin Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China; (X.L.); (C.Z.); (M.L.); (C.F.)
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Cheng Zou
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China; (X.L.); (C.Z.); (M.L.); (C.F.)
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Mengxun Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China; (X.L.); (C.Z.); (M.L.); (C.F.)
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Chengchi Fang
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China; (X.L.); (C.Z.); (M.L.); (C.F.)
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
| | - Kui Li
- Agricultural Genome Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518124, China;
- State Key Laboratory of Animal Nutrition, Key Laboratory of Animal Genetics Breeding and Reproduction of Ministry of Agriculture and Rural Affairs of China, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Zhiguo Liu
- State Key Laboratory of Animal Nutrition, Key Laboratory of Animal Genetics Breeding and Reproduction of Ministry of Agriculture and Rural Affairs of China, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
- Correspondence: (Z.L.); (C.L.)
| | - Changchun Li
- Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education and Key Laboratory of Swine Genetics and Breeding of the Ministry of Agriculture, Huazhong Agricultural University, Wuhan 430070, China; (X.L.); (C.Z.); (M.L.); (C.F.)
- The Cooperative Innovation Center for Sustainable Pig Production, Wuhan 430070, China
- Correspondence: (Z.L.); (C.L.)
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11
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Xiong L, Pei J, Kalwar Q, Wu X, Yan P, Guo X. Fat deposition in yak during different phenological seasons. Livest Sci 2021. [DOI: 10.1016/j.livsci.2021.104671] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
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12
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Peng WX, He PX, Liu LJ, Zhu T, Zhong YQ, Xiang L, Peng K, Yang JJ, Xiang GD. LncRNA GAS5 activates the HIF1A/VEGF pathway by binding to TAF15 to promote wound healing in diabetic foot ulcers. J Transl Med 2021; 101:1071-1083. [PMID: 33875793 DOI: 10.1038/s41374-021-00598-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 7.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2020] [Revised: 03/01/2021] [Accepted: 03/05/2021] [Indexed: 12/14/2022] Open
Abstract
A diabetic foot ulcer (DFU) is one of the most devastating complications of diabetes. It has been reported that lncRNA GAS5 plays a vital role in wound healing in DFUs. However, the specific mechanism remains unclear. In this research, we aimed to investigate the role of GAS5 in wound healing in DFUs as well as the underlying mechanism. qPCR or western blotting was performed to measure the expression levels of GAS5, HIF1A, VEGF and TAF15. CCK-8 or EdU assays, flow cytometry, wound healing assays and tube formation assays were carried out to assess the proliferation, apoptosis, wound healing and in vitro angiogenesis of HUVECs, respectively. RNA pull-down and RIP assays were performed to verify the interaction between GAS5 and TAF15. ChIP and luciferase assays were conducted to verify the binding of TAF15 to the HIF1A promoter. In the DFU mouse model, H&E and Masson staining were used to determine epidermal and dermal thickness and collagen formation. GAS5 and HIF1A were downregulated in the skin tissues of DFU patients, and GAS5 overexpression promoted cell proliferation, wound healing and tubule formation in HG-treated HUVECs. In addition, GAS5 facilitated HIF1A expression by interacting with TAF15. Rescue assays demonstrated that the suppression of HIF1A/VEGF pathway activation partially reversed the functional roles of GAS5 in HUVECs. Furthermore, GAS5 accelerated wound healing by activating the HIF1A/VEGF pathway in mice with DFUs. GAS5 activates the HIF1A/VEGF pathway by binding to TAF15, resulting in accelerated wound healing in DFUs. Our findings may provide a theoretical basis for the clinical treatment of DFUs.
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Affiliation(s)
- Wei-Xia Peng
- The First School of Clinical Medicine, Southern Medical University, Guangzhou, Guangdong, PR China
- Department of Endocrine, Yiyang Central Hospital, Yiyang, Hunan, PR China
| | - Pei-Xiang He
- Department of Endocrine, Yiyang Central Hospital, Yiyang, Hunan, PR China
| | - Li-Jun Liu
- Department of Endocrine, Yiyang Central Hospital, Yiyang, Hunan, PR China
| | - Ting Zhu
- Department of Endocrine, Yiyang Central Hospital, Yiyang, Hunan, PR China
| | - Ya-Qin Zhong
- Department of Endocrine, Yiyang Central Hospital, Yiyang, Hunan, PR China
| | - Lin Xiang
- Department of Endocrine, Central Theater General Hospital of PLA, Wuhan, Hubei, PR China
| | - Ke Peng
- Department of Endocrine, Yiyang Central Hospital, Yiyang, Hunan, PR China
| | - Jing-Jin Yang
- Department of Endocrine, Huaihua First People's Hospital, Huaihua, Hunan, PR China
| | - Guang-Da Xiang
- The First School of Clinical Medicine, Southern Medical University, Guangzhou, Guangdong, PR China.
- Department of Endocrine, Central Theater General Hospital of PLA, Wuhan, Hubei, PR China.
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13
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Yang XM, Liang Y, Zhong ZJ, Tao X, Yang YK, Zhang P, Wang Y, Lei YF, Chen XH, Zeng K, Gong JJ, Ying SC, Zhang JL, Pang JH, Lv XB, Gu YR, He ZP. Comparison of long non-coding RNAs in adipose and muscle tissues between seven indigenous Chinese and the Yorkshire pig breeds. Anim Genet 2021; 52:645-655. [PMID: 34324723 DOI: 10.1111/age.13123] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 07/02/2021] [Indexed: 12/01/2022]
Abstract
lncRNAs play crucial roles in fat metabolism in animals. Previously, we have compared the mRNA transcriptome profiles between seven fat-type Chinese pig breeds and one lean-type Western breed (Yorkshire, YY). The associations between differentially expressed (DE) genes and phenotypical traits were investigated. In the present study, to further explore the underlying regulatory mechanisms, lncRNAs were sequenced and compared between YY and Chinese indigenous breeds. The results showed 9114 and 7538 DE lncRNAs between at least one Chinese breed and the YY breed in the adipose and muscle tissue respectively. KEGG enrichment analysis revealed that the target genes of these DE lncRNAs mainly influenced the glucolipid metabolism, which is an important process affecting meat quality. Correlation analyses between the DE lncRNA and DE mRNA genes related to meat quality and growth traits were performed. The results showed that LTCONS_00073280 was associated with intramuscular fat content. Four lncRNAs (LTCONS_00101781, LTCONS_00037879, LTCONS_00088260 and LTCONS-00128343) might mediate backfat thickness. Overall, this study provides candidate lncRNAs that potentially affect meat quality, which might be useful for molecular breeding of pig breeds in future.
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Affiliation(s)
- X-M Yang
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, Sichuan, 610000, China
| | - Y Liang
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, Sichuan, 610000, China
| | - Z-J Zhong
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, Sichuan, 610000, China
| | - X Tao
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, Sichuan, 610000, China
| | - Y-K Yang
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, Sichuan, 610000, China
| | - P Zhang
- Chengdu Agricultural Technology Vocational College, Chengdu, Sichuan, 610000, China
| | - Y Wang
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, Sichuan, 610000, China
| | - Y-F Lei
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, Sichuan, 610000, China
| | - X-H Chen
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, Sichuan, 610000, China
| | - K Zeng
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, Sichuan, 610000, China
| | - J-J Gong
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, Sichuan, 610000, China
| | - S-C Ying
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, Sichuan, 610000, China
| | - J-L Zhang
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, Sichuan, 610000, China
| | - J-H Pang
- Chengdu Biotechservice Institute, Chengdu, Sichuan, 610000, China
| | - X-B Lv
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, Sichuan, 610000, China
| | - Y-R Gu
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, Sichuan, 610000, China
| | - Z-P He
- Animal Breeding and Genetics Key Laboratory of Sichuan Province, Sichuan Animal Science Academy, Chengdu, Sichuan, 610000, China
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14
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Negi A, George Kokkat J, Jasrotia RS, Madhavan S, Jaiswal S, Angadi UB, Iquebal MA, Kalathil Palliyarakkal M, Palaniyandi U, Rai A, Kumar D. Drought responsiveness in black pepper (Piper nigrum L.): Genes associated and development of a web-genomic resource. PHYSIOLOGIA PLANTARUM 2021; 172:669-683. [PMID: 33305409 DOI: 10.1111/ppl.13308] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/02/2020] [Revised: 11/03/2020] [Accepted: 12/07/2020] [Indexed: 06/12/2023]
Abstract
Black pepper (Piper nigrum L.; 2n = 52; Piperaceae), the king of spices, is a perennial, trailing woody flowering vine and has global importance with widespread dietary, medicinal, and preservative uses. It is an economically important germplasm cultivated for its fruit and the major cash crop in >30 tropical countries. Crop production is mainly affected by drought stress. The present study deals with the candidate gene identification from drought-affected black pepper leaf transcriptome generated by Illumina Hiseq2000. It also aims to mine putative molecular markers (namely SSRs, SNPs, and InDels) and generate primers for them. The identification of transcription factors and pathways involved in drought tolerance is also reported here. De novo transcriptome assembly was performed with trinity assembler. In total, 4914 differential expressed genes, 2110 transcriptional factors, 786 domains and 1137 families, 20,124 putative SSR markers, and 259,236 variants were identified. At2g30105 (unidentified gene containing leucine-rich repeats and ubiquitin-like domain), serine threonine protein kinase, Mitogen-activated protein kinase, Nucleotide Binding Site-Leucine Rich Repeat, Myeloblastosis-related proteins, basic helix-loop-helix are all found upregulated and are reported to be associated with plant tolerance against drought condition. All these information are catalogued in the Black Pepper Drought Transcriptome Database (BPDRTDb), freely accessible for academic use at http://webtom.cabgrid.res.in/bpdrtdb/. This database is a good foundation for the genetic improvement of pepper plants, breeding programmes, and mapping population of this crop. Putative markers can also be a reliable genomic resource to develop drought-tolerant variety for better black pepper productivity.
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Affiliation(s)
- Ankita Negi
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Johnson George Kokkat
- Division of Crop Improvement & Biotechnology, ICAR-Indian Institute of Spices Research, Kozhikode, India
| | - Rahul S Jasrotia
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Soumya Madhavan
- Division of Crop Improvement & Biotechnology, ICAR-Indian Institute of Spices Research, Kozhikode, India
| | - Sarika Jaiswal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Ulavappa Basavanneppa Angadi
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Mir Asif Iquebal
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | | | - Umadevi Palaniyandi
- Division of Crop Improvement & Biotechnology, ICAR-Indian Institute of Spices Research, Kozhikode, India
- RBGRC, ICAR-IARI Regional Centre, India
| | - Anil Rai
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
| | - Dinesh Kumar
- Centre for Agricultural Bioinformatics, ICAR-Indian Agricultural Statistics Research Institute, New Delhi, India
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15
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Fu X, Zhao B, Tian K, Wu Y, Suo L, Ba G, Ciren D, De J, Awang C, Gun S, Yang B. Integrated analysis of lncRNA and mRNA reveals novel insights into cashmere fineness in Tibetan cashmere goats. PeerJ 2020; 8:e10217. [PMID: 33240606 PMCID: PMC7659624 DOI: 10.7717/peerj.10217] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2020] [Accepted: 09/29/2020] [Indexed: 12/15/2022] Open
Abstract
Tibetan cashmere goats are famous for producing the finest, softest and lightest cashmere fiber in China. The growth and development of skin are closely related to fineness and are the key factors affecting the quality of cashmere. To investigate the specific role of long noncoding RNAs (lncRNAs) and messenger RNAs (mRNAs) in regulating cashmere fineness of Tibetan Cashmere goats in the anagen phase, we conducted high-throughput RNA sequencing of fine-type and coarse-type skin tissues. We identified 2,059 lncRNA candidates (1,589 lncRNAs annotated, 470 lncRNAs novel), and 80 differentially expressed (DE) lncRNAs and their potential targets were predicted. We also identified 384 DE messenger RNAs (mRNAs) out of 29,119 mRNAs. Several key genes in KRT26, KRT28, KRT39, IFT88, JAK3, NOTCH2 and NOTCH3 and a series of lncRNAs, including ENSCHIT00000009853, MSTRG.16794.17, MSTRG.17532.2, were shown to be potentially important for regulating cashmere fineness. GO and KEGG enrichment analyses of DE mRNAs and DE lncRNAs targets significantly enriched in positive regulation of the canonical Wnt signaling pathway, regulation of protein processing and metabolism processes. The mRNA-mRNA and lncRNA-mRNA regulatory networks further revealed potential transcripts involved in cashmere fineness. We further validated the expression patterns of DE mRNAs and DE lncRNAs by quantitative real-time PCR (qRT-PCR), and the results were consistent with the sequencing data. This study will shed new light on selective cashmere goat breeding, and these lncRNAs and mRNAs that were found to be enriched in Capra hircus RNA database.
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Affiliation(s)
- Xuefeng Fu
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China.,Key Laboratory of Genetics Breeding and Reproduction of Xinjiang Wool-sheep & Cashmere-goat, Institute of Animal Science, Xinjiang Academy of Animal Sciences, Urumqi, China.,Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Bingru Zhao
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Kechuan Tian
- Key Laboratory of Genetics Breeding and Reproduction of Xinjiang Wool-sheep & Cashmere-goat, Institute of Animal Science, Xinjiang Academy of Animal Sciences, Urumqi, China
| | - Yujiang Wu
- Institute of Animal Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| | - Langda Suo
- Institute of Animal Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| | - Gui Ba
- Institute of Animal Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| | - Deji Ciren
- Institute of Animal Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| | - Ji De
- Institute of Animal Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| | - Cuoji Awang
- Institute of Animal Science, Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, China
| | - Shuangbao Gun
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China
| | - Bohui Yang
- College of Animal Science and Technology, Gansu Agricultural University, Lanzhou, China.,Lanzhou Institute of Husbandry and Pharmaceutical Sciences of Chinese Academy of Agricultural Sciences, Lanzhou, China
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16
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Abstract
Less than 2% of mammalian genomes code for proteins, but 'the majority of its bases can be found in primary transcripts' - a phenomenon termed the pervasive transcription, which was first reported in 2007. Even though most of the transcripts do not code for proteins, they play a variety of biological functions, with regulation of gene expression appearing as the most common one. Those transcripts are divided into two groups based on their length: small non-coding RNAs, which are maximally 200 bp long, and long non-coding RNAs (lncRNAs), which are longer than 200 nucleotides. The advances in next-generation sequencing methods provided a new possibility of investigating the full set of RNA molecules in the cell. In this review, we summarized the current state of knowledge on lncRNAs in three major livestock species - Sus scrofa, Bos taurus and Gallus gallus, based on the literature and the content of biological databases. In the NONCODE database, the largest number of identified lncRNA transcripts is available for pigs, but cattle have the largest number of lncRNA genes. Poultry is represented by less than a half of records. Genomic annotation of lncRNAs showed that the majority of them are assigned to introns (pig, poultry) or intergenic (cattle). The comparison with well-annotated human and mouse genomes indicates that such annotation is a result of lack of proper lncRNA annotation data. Since lncRNAs play an important role in genomic studies, their characterization in farm animals' genomes is critical in bridging the gap between genotype and phenotype.
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17
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The Interaction of lncRNA XLOC-2222497, AKR1C1, and Progesterone in Porcine Endometrium and Pregnancy. Int J Mol Sci 2020; 21:ijms21093232. [PMID: 32370225 DOI: 10.3390/ijms21093232] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/05/2020] [Revised: 04/26/2020] [Accepted: 04/28/2020] [Indexed: 12/17/2022] Open
Abstract
The endometrium is an important tissue for pregnancy and plays an important role in reproduction. In this study, high-throughput transcriptome sequencing was performed in endometrium samples of Meishan and Yorkshire pigs on days 18 and 32 of pregnancy. Aldo-keto reductase family 1 member C1 (AKR1C1) was found to be a differentially expressed gene, and was identified by quantitative real-time PCR (qRT-PCR) and Western blot. Immunohistochemistry results revealed the cellular localization of the AKR1C1 protein in the endometrium. Luciferase activity assay demonstrated that the AKR1C1 core promoter region was located in the region from -706 to -564, containing two nuclear factor erythroid 2-related factor 2 (NRF2) binding sites (antioxidant response elements, AREs). XLOC-2222497 was identified as a nuclear long non-coding RNA (lncRNA) highly expressed in the endometrium. XLOC-2222497 overexpression and knockdown have an effect on the expression of AKR1C1. Endocrinologic measurement showed the difference in progesterone levels between Meishan and Yorkshire pigs. Progesterone treatment upregulated AKR1C1 and XLOC-2222497 expression in porcine endometrial epithelial cells. In conclusion, transcriptome analysis revealed differentially expressed transcripts during the early pregnancy process. Further experiments demonstrated the interaction of XLOC-2222497/AKR1C1/progesterone in the endometrium and provided new potential targets for pregnancy maintenance and its control.
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