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Cracco RC, Alexandre PA, Polizel GHG, Fernandes AC, de Almeida Santana MH. Evaluation of Muscle Long Non-Coding RNA Profile during Rearing and Finishing Phase of Bulls Subjected to Different Prenatal Nutritional Strategies. Animals (Basel) 2024; 14:652. [PMID: 38396620 PMCID: PMC10886332 DOI: 10.3390/ani14040652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/29/2023] [Revised: 02/07/2024] [Accepted: 02/16/2024] [Indexed: 02/25/2024] Open
Abstract
Maternal nutrition has the ability of influence critical processes in fetal life, including muscle development. Also, in this period, epigenetic sensitivity to external stimuli is higher and produces long-lasting effects. Thus, the aim of this study was to investigate epigenetic mechanisms, including the identification and characterization of long non-coding RNA (lncRNA) from animals that had undergone different strategies of prenatal supplementation. A group of Nellore cows (n = 126) were separated into three nutritional plans: NP (control)-Not Programmed, without protein-energy supplementation; PP-Partially Programmed, protein-energy supplementation in the final third of pregnancy; and CP-Complete Programming, protein-energy supplementation during the full period of gestation. A total of 63 male offspring were used in this study, of which 15 (5 per treatment) had Longissimus thoracis muscle at 15 (biopsy) and 22 months (slaughter). Biopsy samples were subjected to RNA extraction and sequencing. Differential expression (DE) of remodeling factors and chromatin-modifying enzyme genes were performed. For the identification and characterization of lncRNA, a series of size filters and protein coding potential tests were performed. The lncRNAs identified had their differential expression and regulatory potential tested. Regarding DE of epigenetic mechanisms, no differentially expressed gene was found (p > 0.1). Identification of potential lncRNA was successful, identifying 1823 transcripts at 15 months and 1533 at 22 months. Among these, four were considered differentially expressed between treatments at 15 months and 6 were differentially expressed at 22 months. Yet, when testing regulatory potential, 13 lncRNAs were considered key regulators in the PP group, and 17 in the CP group. PP group lncRNAs possibly regulate fat-cell differentiation, in utero embryonic development, and transforming growth factor beta receptor, whereas lncRNA in the CP group regulates in utero embryonic development, fat-cell differentiation and vasculogenesis. Maternal nutrition had no effect on differential expression of epigenetic mechanisms; however, it seems to impair lncRNA regulation of epigenetics.
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Affiliation(s)
- Roberta Cavalcante Cracco
- Department of Animal Science, College of Animal Science and Food Engineering—USP, Av. Duque de Caxias Norte, 225, Pirassununga 13635-900, SP, Brazil; (R.C.C.); (G.H.G.P.)
| | - Pamela Almeida Alexandre
- Microbiomes for One Systems Health (MOSH), CSIRO Agriculture & Food, 306 Carmody Rd, St Lucia, QLD 4067, Australia;
| | - Guilherme Henrique Gebim Polizel
- Department of Animal Science, College of Animal Science and Food Engineering—USP, Av. Duque de Caxias Norte, 225, Pirassununga 13635-900, SP, Brazil; (R.C.C.); (G.H.G.P.)
| | - Arícia Christofaro Fernandes
- Department of Animal Science, College of Animal Science and Food Engineering—USP, Av. Duque de Caxias Norte, 225, Pirassununga 13635-900, SP, Brazil; (R.C.C.); (G.H.G.P.)
| | - Miguel Henrique de Almeida Santana
- Department of Animal Science, College of Animal Science and Food Engineering—USP, Av. Duque de Caxias Norte, 225, Pirassununga 13635-900, SP, Brazil; (R.C.C.); (G.H.G.P.)
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Natrajan MS, Hall JM, Weigand MR, Peng Y, Williams MM, Momin M, Damron FH, Dubey P, Tondella ML, Pawloski LC. Genome-based prediction of cross-protective, HLA-DR-presented epitopes as putative vaccine antigens for multiple Bordetella species. Microbiol Spectr 2024; 12:e0352723. [PMID: 38054724 PMCID: PMC10783135 DOI: 10.1128/spectrum.03527-23] [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: 10/12/2023] [Accepted: 11/07/2023] [Indexed: 12/07/2023] Open
Abstract
IMPORTANCE Pertussis, caused by Bordetella pertussis, can cause debilitating respiratory symptoms, so whole-cell pertussis vaccines (wPVs) were introduced in the 1940s. However, reactogenicity of wPV necessitated the development of acellular pertussis vaccines (aPVs) that were introduced in the 1990s. Since then, until the COVID-19 pandemic began, reported pertussis incidence was increasing, suggesting that aPVs do not induce long-lasting immunity and may not effectively prevent transmission. Additionally, aPVs do not provide protection against other Bordetella species that are observed during outbreaks. The significance of this work is in determining potential new vaccine antigens for multiple Bordetella species that are predicted to elicit long-term immune responses. Genome-based approaches have aided the development of novel vaccines; here, these methods identified Bordetella vaccine candidates that may be cross-protective and predicted to induce strong memory responses. These targets can lead to an improved vaccine with a strong safety profile while also strengthening the longevity of the immune response.
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Affiliation(s)
- Muktha S. Natrajan
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
- Laboratory Leadership Service, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Jesse M. Hall
- Department of Microbial Infection and Immunity, College of Medicine, The Ohio State University, Columbus, Ohio, USA
| | - Michael R. Weigand
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Yanhui Peng
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Margaret M. Williams
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Mohamed Momin
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Frederick Heath Damron
- Department of Microbiology, Immunology, and Cell Biology, West Virginia University, Morgantown, West Virginia, USA
| | - Purnima Dubey
- Department of Microbial Infection and Immunity, College of Medicine, The Ohio State University, Columbus, Ohio, USA
| | - Maria Lucia Tondella
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
| | - Lucia C. Pawloski
- Division of Bacterial Diseases, National Center for Immunization and Respiratory Diseases, Centers for Disease Control and Prevention, Atlanta, Georgia, USA
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3
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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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4
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Li J, Li N, Zhu L, Zhang Z, Li X, Wang J, Xun H, Zhao J, Wang X, Wang T, Wang H, Liu B, Li Y, Gong L. Mutation of a major CG methylase alters genome-wide lncRNA expression in rice. G3-GENES GENOMES GENETICS 2021; 11:6146525. [PMID: 33617633 PMCID: PMC8049413 DOI: 10.1093/g3journal/jkab049] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/15/2020] [Accepted: 02/08/2021] [Indexed: 11/14/2022]
Abstract
Plant long non-coding RNAs (lncRNAs) function in diverse biological processes, and lncRNA expression is under epigenetic regulation, including by cytosine DNA methylation. However, it remains unclear whether 5-methylcytosine (5mC) plays a similar role in different sequence contexts (CG, CHG, and CHH). In this study, we characterized and compared the profiles of genome-wide lncRNA profiles (including long intergenic non-coding RNAs [lincRNAs] and long noncoding natural antisense transcripts [lncNATs]) of a null mutant of the rice DNA methyltransferase 1, OsMET1-2 (designated OsMET1-2-/-) and its isogenic wild type (OsMET1-2+/+). The En/Spm transposable element (TE) family, which was heavily methylated in OsMET1-2+/+, was transcriptionally de-repressed in OsMET1-2-/- due to genome-wide erasure of CG methylation, and this led to abundant production of specific lncRNAs. In addition, RdDM-mediated CHH hypermethylation was increased in the 5'-upstream genomic regions of lncRNAs in OsMET1-2-/-. The positive correlation between the expression of lincRNAs and that of their proximal protein-coding genes was also analyzed. Our study shows that CG methylation negatively regulates the TE-related expression of lncRNA and demonstrates that CHH methylation is also involved in the regulation of lncRNA expression.
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Affiliation(s)
- Juzuo Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Ning Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Ling Zhu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Zhibin Zhang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Xiaochong Li
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Jinbin Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Hongwei Xun
- Jilin Provincial Key Laboratory of Agricultural Biotechnology, Jilin Academy of Agricultural Sciences, Changchun 130033, China
| | - Jing Zhao
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Xiaofei Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Tianya Wang
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Hongyan Wang
- Laboratory of Plant Epigenetics and Evolution, School of Life Science, Liaoning University, Shenyang 110036, China
| | - Bao Liu
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
| | - Yu Li
- Engineering Research Center of the Ministry of Education (MOE) for Edible and Medicinal Fungi, Jilin Agricultural University, Changchun, Jilin 130118, China
| | - Lei Gong
- Key Laboratory of Molecular Epigenetics of the Ministry of Education (MOE), Northeast Normal University, Changchun 130024, China
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5
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Yu L, Wei Y, Sun HX, Mahdi AK, Pinzon Arteaga CA, Sakurai M, Schmitz DA, Zheng C, Ballard ED, Li J, Tanaka N, Kohara A, Okamura D, Mutto AA, Gu Y, Ross PJ, Wu J. Derivation of Intermediate Pluripotent Stem Cells Amenable to Primordial Germ Cell Specification. Cell Stem Cell 2020; 28:550-567.e12. [PMID: 33271070 DOI: 10.1016/j.stem.2020.11.003] [Citation(s) in RCA: 101] [Impact Index Per Article: 25.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Revised: 07/17/2020] [Accepted: 11/06/2020] [Indexed: 02/07/2023]
Abstract
Dynamic pluripotent stem cell (PSC) states are in vitro adaptations of pluripotency continuum in vivo. Previous studies have generated a number of PSCs with distinct properties. To date, however, no known PSCs have demonstrated dual competency for chimera formation and direct responsiveness to primordial germ cell (PGC) specification, a unique functional feature of formative pluripotency. Here, by modulating fibroblast growth factor (FGF), transforming growth factor β (TGF-β), and WNT pathways, we derived PSCs from mice, horses, and humans (designated as XPSCs) that are permissive for direct PGC-like cell induction in vitro and are capable of contributing to intra- or inter-species chimeras in vivo. XPSCs represent a pluripotency state between naive and primed pluripotency and harbor molecular, cellular, and phenotypic features characteristic of formative pluripotency. XPSCs open new avenues for studying mammalian pluripotency and dissecting the molecular mechanisms governing PGC specification. Our method may be broadly applicable for the derivation of analogous stem cells from other mammalian species.
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Affiliation(s)
- Leqian Yu
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Yulei Wei
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; School of Biotechnology and Health Sciences, Wuyi University, Jiangmen 529020, China; International Healthcare Innovation Institute, Jiangmen 529040, China
| | - Hai-Xi Sun
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen 518083, China; China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Ahmed K Mahdi
- Department of Animal Science, University of California, Davis, Davis, CA 95616, USA
| | - Carlos A Pinzon Arteaga
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Masahiro Sakurai
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Daniel A Schmitz
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Canbin Zheng
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Department of Microsurgery, Orthopaedic Trauma and Hand Surgery, First Affiliated Hospital of Sun Yat-sen University, Guangzhou 510080, China
| | - Emily D Ballard
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA
| | - Jie Li
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen 518083, China; China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Noriko Tanaka
- Department of Advanced Bioscience, Graduate School of Agriculture, Kindai University, Nakamachi, Nara 631-8505, Japan
| | - Aoi Kohara
- Department of Advanced Bioscience, Graduate School of Agriculture, Kindai University, Nakamachi, Nara 631-8505, Japan
| | - Daiji Okamura
- Department of Advanced Bioscience, Graduate School of Agriculture, Kindai University, Nakamachi, Nara 631-8505, Japan
| | - Adrian A Mutto
- Instituto de Investigaciones Biotecnológicas IIB-INTECH Dr. Rodolfo Ugalde, UNSAM-CONICET, Buenos Aires 1650, Argentina
| | - Ying Gu
- Guangdong Provincial Key Laboratory of Genome Read and Write, BGI-Shenzhen, Shenzhen 518083, China; China National GeneBank, BGI-Shenzhen, Shenzhen 518120, China
| | - Pablo J Ross
- Department of Animal Science, University of California, Davis, Davis, CA 95616, USA
| | - Jun Wu
- Department of Molecular Biology, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA; Hamon Center for Regenerative Science and Medicine, University of Texas Southwestern Medical Center, Dallas, TX 75390, USA.
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6
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An integrative atlas of chicken long non-coding genes and their annotations across 25 tissues. Sci Rep 2020; 10:20457. [PMID: 33235280 PMCID: PMC7686352 DOI: 10.1038/s41598-020-77586-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 11/11/2020] [Indexed: 12/11/2022] Open
Abstract
Long non-coding RNAs (LNC) regulate numerous biological processes. In contrast to human, the identification of LNC in farm species, like chicken, is still lacunar. We propose a catalogue of 52,075 chicken genes enriched in LNC (http://www.fragencode.org/), built from the Ensembl reference extended using novel LNC modelled here from 364 RNA-seq and LNC from four public databases. The Ensembl reference grew from 4,643 to 30,084 LNC, of which 59% and 41% with expression ≥ 0.5 and ≥ 1 TPM respectively. Characterization of these LNC relatively to the closest protein coding genes (PCG) revealed that 79% of LNC are in intergenic regions, as in other species. Expression analysis across 25 tissues revealed an enrichment of co-expressed LNC:PCG pairs, suggesting co-regulation and/or co-function. As expected LNC were more tissue-specific than PCG (25% vs. 10%). Similarly to human, 16% of chicken LNC hosted one or more miRNA. We highlighted a new chicken LNC, hosting miR155, conserved in human, highly expressed in immune tissues like miR155, and correlated with immunity-related PCG in both species. Among LNC:PCG pairs tissue-specific in the same tissue, we revealed an enrichment of divergent pairs with the PCG coding transcription factors, as for example LHX5, HXD3 and TBX4, in both human and chicken.
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7
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Pechanec MY, Boyd TN, Baar K, Mienaltowski MJ. Adding exogenous biglycan or decorin improves tendon formation for equine peritenon and tendon proper cells in vitro. BMC Musculoskelet Disord 2020; 21:627. [PMID: 32967653 PMCID: PMC7513506 DOI: 10.1186/s12891-020-03650-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Accepted: 09/15/2020] [Indexed: 12/17/2022] Open
Abstract
Background Tendon injuries amount to one of the leading causes of career-ending injuries in horses due to the inability for tendon to completely repair and the high reinjury potential. As a result, novel therapeutics are necessary to improve repair with the goal of decreasing leg lameness and potential reinjury. Small leucine-rich repeat proteoglycans (SLRPs), a class of regulatory molecules responsible for collagen organization and maturation, may be one such therapeutic to improve tendon repair. Before SLRP supplementation can occur in vivo, proper evaluation of the effect of these molecules in vitro needs to be assessed. The objective of this study was to evaluate the effectiveness of purified bovine biglycan or decorin on tendon proper and peritenon cell populations in three-dimensional tendon constructs. Methods Equine tendon proper or peritenon cell seeded fibrin three-dimensional constructs were supplemented with biglycan or decorin at two concentrations (5 nM or 25 nM). The functionality and ultrastructural morphology of the constructs were assessed using biomechanics, collagen content analysis, transmission electron microscopy (TEM), and gene expression by real time – quantitative polymerase chain reaction (RT-qPCR). Results SLRP supplementation affected both tendon proper and peritenon cells-seeded constructs. With additional SLRPs, material and tensile properties of constructs strengthened, though ultrastructural analyses indicated production of similar-sized or smaller fibrils. Overall expression of tendon markers was bolstered more in peritenon cells supplemented with either SLRP, while supplementation of SLRPs to TP cell-derived constructs demonstrated fewer changes in tendon and extracellular matrix markers. Moreover, relative to non-supplemented tendon proper cell-seeded constructs, SLRP supplementation of the peritenon cells showed increases in mechanical strength, material properties, and collagen content. Conclusions The SLRP-supplemented peritenon cells produced constructs with greater mechanical and material properties than tendon proper seeded constructs, as well as increased expression of matrix assembly molecules. These findings provide evidence that SLRPs should be further investigated for their potential to improve tendon formation in engineered grafts or post-injury.
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Affiliation(s)
- Monica Y Pechanec
- Department of Animal Science, University of California Davis, 2251 Meyer Hall, One Shields Ave, Davis, CA, 95616, USA
| | - Tannah N Boyd
- Department of Animal Science, University of California Davis, 2251 Meyer Hall, One Shields Ave, Davis, CA, 95616, USA
| | - Keith Baar
- Department of Neurobiology, Physiology, and Behavior, University of California Davis, 195 Briggs Hall, One Shields Ave, Davis, CA, 95616, USA.,Department of Physiology and Membrane Biology, University of California Davis School of Medicine, 195 Briggs Hall, One Shields Ave, Davis, CA, 95616, USA
| | - Michael J Mienaltowski
- Department of Animal Science, University of California Davis, 2251 Meyer Hall, One Shields Ave, Davis, CA, 95616, USA.
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Dahlgren AR, Scott EY, Mansour T, Hales EN, Ross PJ, Kalbfleisch TS, MacLeod JN, Petersen JL, Bellone RR, Finno CJ. Comparison of Poly-A + Selection and rRNA Depletion in Detection of lncRNA in Two Equine Tissues Using RNA-seq. Noncoding RNA 2020; 6:E32. [PMID: 32825772 PMCID: PMC7549351 DOI: 10.3390/ncrna6030032] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2020] [Revised: 08/17/2020] [Accepted: 08/18/2020] [Indexed: 12/14/2022] Open
Abstract
Long non-coding RNAs (lncRNAs) are untranslated regulatory transcripts longer than 200 nucleotides that can play a role in transcriptional, post-translational, and epigenetic regulation. Traditionally, RNA-sequencing (RNA-seq) libraries have been created by isolating transcriptomic RNA via poly-A+ selection. In the past 10 years, methods to perform ribosomal RNA (rRNA) depletion of total RNA have been developed as an alternative, aiming for better coverage of whole transcriptomic RNA, both polyadenylated and non-polyadenylated transcripts. The purpose of this study was to determine which library preparation method is optimal for lncRNA investigations in the horse. Using liver and cerebral parietal lobe tissues from two healthy Thoroughbred mares, RNA-seq libraries were prepared using standard poly-A+ selection and rRNA-depletion methods. Averaging the two biologic replicates, poly-A+ selection yielded 327 and 773 more unique lncRNA transcripts for liver and parietal lobe, respectively. More lncRNA were found to be unique to poly-A+ selected libraries, and rRNA-depletion identified small nucleolar RNA (snoRNA) to have a higher relative expression than in the poly-A+ selected libraries. Overall, poly-A+ selection provides a more thorough identification of total lncRNA in equine tissues while rRNA-depletion may allow for easier detection of snoRNAs.
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Affiliation(s)
- Anna R. Dahlgren
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California Davis, Davis, CA 95616, USA; (A.R.D.); (T.M.); (E.N.H.); (R.R.B.)
| | - Erica Y. Scott
- Department of Animal Science, College of Agricultural and Environmental Sciences, University of California Davis, Davis, CA 95616, USA; (E.Y.S.); (P.J.R.)
| | - Tamer Mansour
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California Davis, Davis, CA 95616, USA; (A.R.D.); (T.M.); (E.N.H.); (R.R.B.)
| | - Erin N. Hales
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California Davis, Davis, CA 95616, USA; (A.R.D.); (T.M.); (E.N.H.); (R.R.B.)
| | - Pablo J. Ross
- Department of Animal Science, College of Agricultural and Environmental Sciences, University of California Davis, Davis, CA 95616, USA; (E.Y.S.); (P.J.R.)
| | - Theodore S. Kalbfleisch
- Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY 40546, USA; (T.S.K.); (J.N.M.)
| | - James N. MacLeod
- Gluck Equine Research Center, Department of Veterinary Science, University of Kentucky, Lexington, KY 40546, USA; (T.S.K.); (J.N.M.)
| | - Jessica L. Petersen
- Department of Animal Science, University of Nebraska Lincoln, Lincoln, NE 68583, USA;
| | - Rebecca R. Bellone
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California Davis, Davis, CA 95616, USA; (A.R.D.); (T.M.); (E.N.H.); (R.R.B.)
- Veterinary Genetics Laboratory, School of Veterinary Medicine, University of California Davis, Davis, CA 95616, USA
| | - Carrie J. Finno
- Department of Population Health and Reproduction, School of Veterinary Medicine, University of California Davis, Davis, CA 95616, USA; (A.R.D.); (T.M.); (E.N.H.); (R.R.B.)
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Shi T, Hu W, Hou H, Zhao Z, Shang M, Zhang L. Identification and Comparative Analysis of Long Non-Coding RNA in the Skeletal Muscle of Two Dezhou Donkey Strains. Genes (Basel) 2020; 11:E508. [PMID: 32375413 PMCID: PMC7288655 DOI: 10.3390/genes11050508] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2020] [Revised: 04/28/2020] [Accepted: 04/29/2020] [Indexed: 11/16/2022] Open
Abstract
Long non-coding RNA (lncRNA) has been extensively studied in many livestock. However, compared with other livestock breeds, there is less research regarding donkey lncRNA function. It has been reported that lncRNA plays an important role in the timing control of development, aging, and death of livestock. Therefore, the study of donkey skeletal muscle lncRNA is of great significance for exploring donkey meat production performance. In this study, RNA-Seq was used to perform high-throughput sequencing of skeletal muscle (longissimus dorsi and gluteus) of two Dezhou donkey strains (SanFen and WuTou). The differentially expressed lncRNAs were screened between different strains and tissues. Then candidate genes for conjoint analysis were screened based on Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) analysis. Finally, the accuracy of the sequencing data was verified by real-time quantitative polymerase chain reaction (RT-qPCR). Herein, we identified 3869 novel lncRNAs and 73 differentially expressed lncRNAs. Through the comparison between groups, the specific expression of lncRNAs were found in different strains and muscle tissues. Importantly, we constructed the lncRNA-miRNA-mRNA interaction network and found three important candidate lncRNAs (MSTRG.9787.1, MSTRG.3144.1, and MSTRG.9886.1) and four candidate genes (ACTN1, CDON, FMOD, and BMPR1B). Analysis of the KEGG pathway indicates that the TGF-β signaling pathway plays a pivotal role in the growth and development of skeletal muscle in Dezhou donkey strains.
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Affiliation(s)
| | | | | | | | | | - Li Zhang
- Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China; (T.S.); (W.H.); (H.H.); (Z.Z.); (M.S.)
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10
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He Z, Yan T, Yuan Y, Yang D, Yang G. miRNAs and lncRNAs in Echinococcus and Echinococcosis. Int J Mol Sci 2020; 21:ijms21030730. [PMID: 31979099 PMCID: PMC7037763 DOI: 10.3390/ijms21030730] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2019] [Revised: 01/16/2020] [Accepted: 01/19/2020] [Indexed: 01/04/2023] Open
Abstract
Echinococcosis are considered to be potentially lethal zoonotic diseases that cause serious damage to hosts. The metacestode of Echinococcus multilocularis and E. granulosus can result in causing the alveolar and cystic echinococcoses, respectively. Recent studies have shown that non-coding RNAs are widely expressed in Echinococcus spp. and hosts. In this review, the two main types of non-coding RNAs—long non-coding RNAs (lncRNAs) and microRNAs (miRNAs)—and the wide-scale involvement of these molecules in these parasites and their hosts were discussed. The expression pattern of miRNAs in Echinococcus spp. is species- and developmental stage-specific. Furthermore, common miRNAs were detected in three Echinococcus spp. and their intermediate hosts. Here, we primarily focus on recent insights from transcriptome studies, the expression patterns of miRNAs and lncRNAs, and miRNA-related databases and techniques that are used to investigate miRNAs in Echinococcus and echinococcosis. This review provides new avenues for screening therapeutic and diagnostic markers.
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Affiliation(s)
- Zhi He
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, Sichuan, China; (Z.H.); (T.Y.); (Y.Y.)
| | - Taiming Yan
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, Sichuan, China; (Z.H.); (T.Y.); (Y.Y.)
| | - Ya Yuan
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, Sichuan, China; (Z.H.); (T.Y.); (Y.Y.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
| | - Deying Yang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, Sichuan, China; (Z.H.); (T.Y.); (Y.Y.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 611130, Sichuan, China
- Correspondence: ; Tel.: +86-028-8278-3043
| | - Guangyou Yang
- College of Veterinary Medicine, Sichuan Agricultural University, Chengdu 611130, Sichuan, China;
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Pu Y, Zhang Y, Zhang T, Han J, Ma Y, Liu X. Identification of Novel lncRNAs Differentially Expressed in Placentas of Chinese Ningqiang Pony and Yili Horse Breeds. Animals (Basel) 2020; 10:E119. [PMID: 31940795 PMCID: PMC7022612 DOI: 10.3390/ani10010119] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2019] [Revised: 12/30/2019] [Accepted: 01/09/2020] [Indexed: 12/24/2022] Open
Abstract
As a nutrient sensor, the placenta plays a key role in regulating fetus growth and development. Long non-coding RNAs (lncRNAs) have been shown to regulate growth-related traits. However, the biological function of lncRNAs in horse placentas remains unclear. To compare the expression patterns of lncRNAs in the placentas of the Chinese Ningqiang (NQ) and Yili (YL) breeds, we performed a transcriptome analysis using RNA sequencing (RNA-seq) technology. NQ is a pony breed with an average adult height at the withers of less than 106 cm, whereas that of YL is around 148 cm. Based on 813 million high-quality reads and stringent quality control procedures, 3011 transcripts coding for 1464 placental lncRNAs were identified and mapped to the horse reference genome. We found 107 differentially expressed lncRNAs (DELs) between NQ and YL, including 68 up-regulated and 39 down-regulated DELs in YL. Six (TBX3, CACNA1F, EDN3, KAT5, ZNF281, TMED2, and TGFB1) out of the 233 genes targeted by DELs were identified as being involved in limb development, skeletal myoblast differentiation, and embryo development. Two DELs were predicted to target the TBX3 gene, which was found to be under strong selection and associated with small body size in the Chinese Debao pony breed. This finding suggests the potential functional significance of placental lncRNAs in regulating horse body size.
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Affiliation(s)
- Yabin Pu
- Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (Y.P.); (Y.Z.)
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China;
| | - Yanli Zhang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (Y.P.); (Y.Z.)
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China;
| | - Tian Zhang
- State Key Laboratory of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing 100700, China;
| | - Jianlin Han
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China;
- International Livestock Research Institute (ILRI), Nairobi 00100, Kenya
| | - Yuehui Ma
- Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (Y.P.); (Y.Z.)
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China;
| | - Xuexue Liu
- Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (Y.P.); (Y.Z.)
- CAAS-ILRI Joint Laboratory on Livestock and Forage Genetic Resources, Institute of Animal Science, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China;
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Young R, Lefevre L, Bush SJ, Joshi A, Singh SH, Jadhav SK, Dhanikachalam V, Lisowski ZM, Iamartino D, Summers KM, Williams JL, Archibald AL, Gokhale S, Kumar S, Hume DA. A Gene Expression Atlas of the Domestic Water Buffalo ( Bubalus bubalis). Front Genet 2019; 10:668. [PMID: 31428126 PMCID: PMC6689995 DOI: 10.3389/fgene.2019.00668] [Citation(s) in RCA: 22] [Impact Index Per Article: 4.4] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 06/26/2019] [Indexed: 12/19/2022] Open
Abstract
The domestic water buffalo (Bubalus bubalis) makes a major contribution to the global agricultural economy in the form of milk, meat, hides, and draught power. The global water buffalo population is predominantly found in Asia, and per head of population more people depend upon the buffalo than on any other livestock species. Despite its agricultural importance, there are comparatively fewer genomic and transcriptomic resources available for buffalo than for other livestock species. We have generated a large-scale gene expression atlas covering multiple tissue and cell types from all major organ systems collected from three breeds of riverine water buffalo (Mediterranean, Pandharpuri and Bhadawari) and used the network analysis tool Graphia Professional to identify clusters of genes with similar expression profiles. Alongside similar data, we and others have generated for ruminants as part of the Functional Annotation of Animal Genomes Consortium; this comprehensive transcriptome supports functional annotation and comparative analysis of the water buffalo genome.
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Affiliation(s)
- Rachel Young
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | - Lucas Lefevre
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | - Stephen J. Bush
- Nuffield Department of Clinical Medicine, University of Oxford, Oxford, United Kingdom
| | - Akshay Joshi
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | | | | | - Velu Dhanikachalam
- Central Research Station, BAIF Development Research Foundation, Pune, India
| | - Zofia M. Lisowski
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | | | - Kim M. Summers
- Mater Research Institute-University of Queensland, Translational Research Institute, Brisbane, QLD, Australia
| | - John L. Williams
- Davies Research Centre, School of Animal and Veterinary Sciences, University of Adelaide, Adelaide, SA, Australia
| | - Alan L. Archibald
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Edinburgh, United Kingdom
| | - Suresh Gokhale
- Central Research Station, BAIF Development Research Foundation, Pune, India
| | - Satish Kumar
- Centre for Cellular and Molecular Biology, Hyderabad, India
- School of Life Science, Central University of Haryana, Mahendergargh, India
| | - David A. Hume
- Mater Research Institute-University of Queensland, Translational Research Institute, Brisbane, QLD, Australia
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13
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Zhu H, Gifford RJ, Murcia PR. Distribution, Diversity, and Evolution of Endogenous Retroviruses in Perissodactyl Genomes. J Virol 2018; 92:e00927-18. [PMID: 30209175 PMCID: PMC6232481 DOI: 10.1128/jvi.00927-18] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2018] [Accepted: 09/01/2018] [Indexed: 01/01/2023] Open
Abstract
The evolution of mammalian genomes has been shaped by interactions with endogenous retroviruses (ERVs). In this study, we investigated the distribution and diversity of ERVs in the mammalian order Perissodactyla, with a view to understanding their impact on the evolution of modern equids (family Equidae). We characterize the major ERV lineages in the horse genome in terms of their genomic distribution, ancestral genome organization, and time of activity. Our results show that subsequent to their ancestral divergence from rhinoceroses and tapirs, equids acquired four novel ERV lineages. We show that two of these ERV lineages proliferated extensively in the lineage leading to modern horses, and one contains loci that are actively transcribed in specific tissues. In addition, we show that the white rhinoceros has resisted germ line colonization by retroviruses for more than 54 million years-longer than any other extant mammalian species. The map of equine ERVs that we provide here will be of great utility to future studies aiming to investigate the potential functional roles of equine ERVs and their impact on equine evolution.IMPORTANCE ERVs in the host genome are highly informative about the long-term interactions of retroviruses and hosts. They are also interesting because they have influenced the evolution of mammalian genomes in various ways. In this study, we derive a calibrated timeline describing the process through which ERV diversity has been generated in the equine germ line. We determined the distribution and diversity of perissodactyl ERV lineages and inferred their retrotranspositional activity during evolution, thereby gaining insight into the long-term coevolutionary history of retroviruses and mammals. Our study provides a platform for future investigations to identify equine ERV loci involved in physiological processes and/or pathological conditions.
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Affiliation(s)
- Henan Zhu
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
| | | | - Pablo Ramiro Murcia
- MRC-University of Glasgow Centre for Virus Research, Glasgow, United Kingdom
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14
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Giuffra E, Tuggle CK. Functional Annotation of Animal Genomes (FAANG): Current Achievements and Roadmap. Annu Rev Anim Biosci 2018; 7:65-88. [PMID: 30427726 DOI: 10.1146/annurev-animal-020518-114913] [Citation(s) in RCA: 99] [Impact Index Per Article: 16.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
Functional annotation of genomes is a prerequisite for contemporary basic and applied genomic research, yet farmed animal genomics is deficient in such annotation. To address this, the FAANG (Functional Annotation of Animal Genomes) Consortium is producing genome-wide data sets on RNA expression, DNA methylation, and chromatin modification, as well as chromatin accessibility and interactions. In addition to informing our understanding of genome function, including comparative approaches to elucidate constrained sequence or epigenetic elements, these annotation maps will improve the precision and sensitivity of genomic selection for animal improvement. A scientific community-driven effort has already created a coordinated data collection and analysis enterprise crucial for the success of this global effort. Although it is early in this continuing process, functional data have already been produced and application to genetic improvement reported. The functional annotation delivered by the FAANG initiative will add value and utility to the greatly improved genome sequences being established for domesticated animal species.
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Affiliation(s)
- Elisabetta Giuffra
- Génétique Animale et Biologie Intégrative (GABI), Institut National de la Recherche Agronomique (INRA), AgroParisTech, Université Paris Saclay, 78350 Jouy-en-Josas, France;
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15
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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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16
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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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