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Bush SJ, Goriely A. Can the male germline offer insight into mammalian brain size expansion? Andrology 2024. [PMID: 39291969 DOI: 10.1111/andr.13766] [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: 07/01/2024] [Revised: 08/26/2024] [Accepted: 09/09/2024] [Indexed: 09/19/2024]
Abstract
Recent advances in single-cell transcriptomic data have greatly expanded our understanding of both spermatogenesis and the molecular mechanisms of male infertility. However, this growing wealth of data could also shed light on a seemingly unrelated biological problem: the genetic basis of mammalian brain size expansion throughout evolution. It is now increasingly recognized that the testis and brain share many cellular and molecular similarities including pivotal roles for the RAS/MAPK and PI3K/AKT/mTOR pathways, mutations in which are known to have a pronounced impact on cell proliferation. Most notably, in the stem cell lineages of both organs, new mutations have been shown to increase cellular output over time. These include 'selfish' mutations in spermatogonial stem cells, which disproportionately increase the proportion of mutant sperm, and-to draw a parallel-human-specific mutations in neural stem cells which, by increasing the number of neurons, have been implicated in neocortical expansion. Here we speculate that the origin for many 'expansion'-associated mutations is the male germline and that as such, a deeper understanding of the mechanisms controlling testicular turnover may yield fresh insight into the biology and evolution of the brain.
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Affiliation(s)
- Stephen J Bush
- School of Automation Science and Engineering, Xi'an Jiaotong University, Xi'an, China
| | - Anne Goriely
- MRC Weatherall Institute of Molecular Medicine, Radcliffe Department of Medicine, University of Oxford, Oxford, UK
- NIHR Oxford Biomedical Research Centre, Oxford, UK
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2
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Ben Braiek M, Szymczak S, André C, Bardou P, Fidelle F, Granado-Tajada I, Plisson-Petit F, Sarry J, Woloszyn F, Moreno-Romieux C, Fabre S. A single base pair duplication in the SLC33A1 gene is associated with fetal losses and neonatal lethality in Manech Tête Rousse dairy sheep. Anim Genet 2024; 55:644-657. [PMID: 38922751 DOI: 10.1111/age.13459] [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: 03/06/2024] [Revised: 06/07/2024] [Accepted: 06/08/2024] [Indexed: 06/28/2024]
Abstract
We recently discovered that the Manech Tête Rousse (MTR) deficient homozygous haplotype 2 (MTRDHH2) probably carries a recessive lethal mutation in sheep. In this study, we fine-mapped this region through whole-genome sequencing of five MTRDHH2 heterozygous carriers and 95 non-carriers from various ovine breeds. We identified a single base pair duplication within the SLC33A1 gene, leading to a frameshift mutation and a premature stop codon (p.Arg246Alafs*3). SLC33A1 encodes a transmembrane transporter of acetyl-coenzyme A that is crucial for cellular metabolism. To investigate the lethality of this mutation in homozygous MTR sheep, we performed at-risk matings using artificial insemination (AI) between heterozygous SLC33A1 variant carriers (SLC33A1_dupG). Pregnancy was confirmed 15 days post-AI using a blood test measuring interferon Tau-stimulated MX1 gene expression. Ultrasonography between 45 and 60 days post-AI revealed a 12% reduction in AI success compared with safe matings, indicating embryonic/fetal loss. This was supported by the MX1 differential expression test suggesting fetal losses between 15 and 60 days of gestation. We also observed a 34.7% pre-weaning mortality rate in 49 lambs born from at-risk matings. Homozygous SLC33A1_dupG lambs accounted for 47% of this mortality, with deaths occurring mostly within the first 5 days without visible clinical signs. Therefore, appropriate management of SLC33A1_dupG with an allele frequency of 0.04 in the MTR selection scheme would help increase overall fertility and lamb survival.
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Affiliation(s)
- Maxime Ben Braiek
- GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet-Tolosan, France
| | - Soline Szymczak
- GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet-Tolosan, France
| | | | | | | | - Itsasne Granado-Tajada
- Department of Animal Production, NEIKER-BRTA Basque Institute of Agricultural Research and Development, Arkaute, Spain
| | | | - Julien Sarry
- GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet-Tolosan, France
| | - Florent Woloszyn
- GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet-Tolosan, France
| | | | - Stéphane Fabre
- GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet-Tolosan, France
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3
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Varela-Martínez E, Luigi-Sierra MG, Guan D, López-Béjar M, Casas E, Olvera-Maneu S, Gardela J, Palomo MJ, Osuagwuh UI, Ohaneje UL, Mármol-Sánchez E, Amills M. The landscape of long noncoding RNA expression in the goat brain. J Dairy Sci 2024; 107:4075-4091. [PMID: 38278299 DOI: 10.3168/jds.2023-23966] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2023] [Accepted: 12/22/2023] [Indexed: 01/28/2024]
Abstract
The brain regulates multiple metabolic processes, such as food intake, energy expenditure, insulin secretion, hepatic glucose production, and glucose and fatty acid metabolism in adipose tissue, which are fundamental for the maintenance of energy and glucose homeostasis during lactation and pregnancy. In addition, brain expression has a fundamental impact on the development of maternal behavior. Although brain functions are partly regulated by long noncoding RNAs (lncRNAs), their expression profiles have not been characterized in depth in any ruminant species. We have sequenced the transcriptome of 12 brain tissues from 3 goats that were 1 mo pregnant and 4 nonpregnant goats to investigate their lncRNA expression patterns. Between 4,363 (adenohypophysis) and 4,604 (olfactory bulb) lncRNAs were expressed in brain tissues, leading us to establish a set of 794 already annotated lncRNAs and 5,098 novel lncRNA candidates. The detected lncRNAs shared features with those of other mammals, and tissue-specific lncRNAs were enriched in brain development-related terms. Differential expression analyses between goats that were 1 mo pregnant and nonpregnant goats showed that the lncRNA expression profiles of certain brain regions experience substantial changes associated with early pregnancy (238 lncRNAs are differentially expressed in the olfactory bulb), but others do not. Enrichment analysis showed that differentially expressed lncRNAs from the olfactory bulb are co-expressed with genes previously linked to behavioral changes related to pregnancy. These findings provide a first characterization of the landscape of lncRNA expression in the goat brain and provides valuable clues to understand the molecular events triggered by early pregnancy in the central nervous system.
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Affiliation(s)
- Endika Varela-Martínez
- Department of Genetics, Physical Anthropology and Animal Physiology, Faculty of Science and Technology, University of the Basque Country (UPV/EHU), B. Sarriena, Leioa 48940, Spain; Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - María Gracia Luigi-Sierra
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - Dailu Guan
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - Manel López-Béjar
- Department of Animal Health and Anatomy, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - Encarna Casas
- Department of Animal Health and Anatomy, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - Sergi Olvera-Maneu
- Department of Animal Health and Anatomy, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain; Department of Veterinary Medicine, University of Nicosia School of Veterinary Medicine, 2414 Nicosia, Cyprus
| | - Jaume Gardela
- Department of Animal Health and Anatomy, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - Maria Jesús Palomo
- Department of Animal Medicine and Surgery, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - Uchebuchi Ike Osuagwuh
- Department of Animal Medicine and Surgery, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - Uchechi Linda Ohaneje
- Department of Animal Medicine and Surgery, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - Emilio Mármol-Sánchez
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - Marcel Amills
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona, Bellaterra 08193, Spain; Department de Ciència Animal I dels Aliments, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain.
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4
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Wang Y, Huang Y, Zhen Y, Wang J, Wang L, Chen N, Wu F, Zhang L, Shen Y, Bi C, Li S, Pool K, Blache D, Maloney SK, Liu D, Yang Z, Li C, Yu X, Zhang Z, Chen Y, Xue C, Gu Y, Huang W, Yan L, Wei W, Wang Y, Zhang J, Zhang Y, Sun Y, Wang S, Zhao X, Luo C, Wang H, Ding L, Yang QY, Zhou P, Wang M. De novo transcriptome assembly database for 100 tissues from each of seven species of domestic herbivore. Sci Data 2024; 11:488. [PMID: 38734729 PMCID: PMC11088706 DOI: 10.1038/s41597-024-03338-5] [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: 12/13/2023] [Accepted: 05/02/2024] [Indexed: 05/13/2024] Open
Abstract
Domesticated herbivores are an important agricultural resource that play a critical role in global food security, particularly as they can adapt to varied environments, including marginal lands. An understanding of the molecular basis of their biology would contribute to better management and sustainable production. Thus, we conducted transcriptome sequencing of 100 to 105 tissues from two females of each of seven species of herbivore (cattle, sheep, goats, sika deer, horses, donkeys, and rabbits) including two breeds of sheep. The quality of raw and trimmed reads was assessed in terms of base quality, GC content, duplication sequence rate, overrepresented k-mers, and quality score distribution with FastQC. The high-quality filtered RNA-seq raw reads were deposited in a public database which provides approximately 54 billion high-quality paired-end sequencing reads in total, with an average mapping rate of ~93.92%. Transcriptome databases represent valuable resources that can be used to study patterns of gene expression, and pathways that are related to key biological processes, including important economic traits in herbivores.
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Affiliation(s)
- Yifan Wang
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural Reclamation Sciences, Shihezi, 832000, P. R. China
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, P. R. China
- College of Life Science, Guizhou University, Guiyang, 550025, P. R. China
| | - Yiming Huang
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural Reclamation Sciences, Shihezi, 832000, P. R. China
- Hubei Key Laboratory of Agricultural Bioinformatics and Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, P. R. China
| | - Yongkang Zhen
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, P. R. China
| | - Jiasheng Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, P. R. China
| | - Limin Wang
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural Reclamation Sciences, Shihezi, 832000, P. R. China
| | - Ning Chen
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural Reclamation Sciences, Shihezi, 832000, P. R. China
| | - Feifan Wu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, P. R. China
| | - Linna Zhang
- Hubei Key Laboratory of Agricultural Bioinformatics and Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, P. R. China
| | - Yizhao Shen
- College of Animal Science and Technology, Hebei Agricultural University, Baoding, 071033, P. R. China
| | - Congliang Bi
- College of Life Science, Linyi University, Linyi, 276005, P. R. China
| | - Song Li
- College of Life Science, Guizhou University, Guiyang, 550025, P. R. China
| | - Kelsey Pool
- UWA Institute of Agriculture, The University of Western Australia, Perth, WA, 6009, Australia
| | - Dominique Blache
- UWA Institute of Agriculture, The University of Western Australia, Perth, WA, 6009, Australia
| | - Shane K Maloney
- UWA Institute of Agriculture, The University of Western Australia, Perth, WA, 6009, Australia
| | - Dongxu Liu
- Hubei Key Laboratory of Agricultural Bioinformatics and Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, P. R. China
| | - Zhiquan Yang
- Hubei Key Laboratory of Agricultural Bioinformatics and Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, P. R. China
| | - Chuang Li
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, P. R. China
| | - Xiang Yu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, P. R. China
| | - Zhenbin Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, P. R. China
| | - Yifei Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, P. R. China
| | - Chun Xue
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, P. R. China
| | - Yalan Gu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, P. R. China
| | - Weidong Huang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, P. R. China
| | - Lu Yan
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, P. R. China
| | - Wenjun Wei
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, P. R. China
| | - Yusu Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, P. R. China
| | - Jinying Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, P. R. China
| | - Yifan Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, P. R. China
| | - Yiquan Sun
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, P. R. China
| | - Shengbo Wang
- Hubei Key Laboratory of Agricultural Bioinformatics and Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, P. R. China
| | - Xinle Zhao
- Hubei Key Laboratory of Agricultural Bioinformatics and Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, P. R. China
| | - Chengfang Luo
- Hubei Key Laboratory of Agricultural Bioinformatics and Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, P. R. China
| | - Haodong Wang
- Hubei Key Laboratory of Agricultural Bioinformatics and Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, P. R. China
| | - Luoyang Ding
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, P. R. China.
- UWA Institute of Agriculture, The University of Western Australia, Perth, WA, 6009, Australia.
| | - Qing-Yong Yang
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural Reclamation Sciences, Shihezi, 832000, P. R. China.
- Hubei Key Laboratory of Agricultural Bioinformatics and Hubei Engineering Technology Research Center of Agricultural Big Data, College of Informatics, Huazhong Agricultural University, Wuhan, 430070, P. R. China.
| | - Ping Zhou
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural Reclamation Sciences, Shihezi, 832000, P. R. China.
| | - Mengzhi Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, P. R. China.
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5
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Ben Braiek M, Moreno-Romieux C, André C, Astruc JM, Bardou P, Bordes A, Debat F, Fidelle F, Granado-Tajada I, Hozé C, Plisson-Petit F, Rivemale F, Sarry J, Tadi N, Woloszyn F, Fabre S. Searching for homozygous haplotype deficiency in Manech Tête Rousse dairy sheep revealed a nonsense variant in the MMUT gene affecting newborn lamb viability. Genet Sel Evol 2024; 56:16. [PMID: 38424485 PMCID: PMC10905913 DOI: 10.1186/s12711-024-00886-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2023] [Accepted: 02/19/2024] [Indexed: 03/02/2024] Open
Abstract
BACKGROUND Recessive deleterious variants are known to segregate in livestock populations, as in humans, and some may be lethal in the homozygous state. RESULTS We used phased 50 k single nucleotide polymorphism (SNP) genotypes and pedigree data to scan the genome of 6845 Manech Tête Rousse dairy sheep to search for deficiency in homozygous haplotypes (DHH). Five Manech Tête Rousse deficient homozygous haplotypes (MTRDHH1 to 5) were identified, with a homozygous deficiency ranging from 84 to 100%. These haplotypes are located on Ovis aries chromosome (OAR)1 (MTRDHH2 and 3), OAR10 (MTRDHH4), OAR13 (MTRDHH5), and OAR20 (MTRDHH1), and have carrier frequencies ranging from 7.8 to 16.6%. When comparing at-risk matings between DHH carriers to safe matings between non-carriers, two DHH (MTRDHH1 and 2) were linked with decreased insemination success and/or increased stillbirth incidence. We investigated the MTRDHH1 haplotype, which substantially increased stillbirth rate, and identified a single nucleotide variant (SNV) inducing a premature stop codon (p.Gln409*) in the methylmalonyl-CoA mutase (MMUT) gene by using a whole-genome sequencing approach. We generated homozygous lambs for the MMUT mutation by at-risk mating between heterozygous carriers, and most of them died within the first 24 h after birth without any obvious clinical symptoms. Reverse transcriptase-qPCR and western blotting on post-mortem liver and kidney biological samples showed a decreased expression of MMUT mRNA in the liver and absence of a full-length MMUT protein in the mutant homozygous lambs. CONCLUSIONS We identified five homozygous deficient haplotypes that are likely to harbor five independent deleterious recessive variants in sheep. One of these was detected in the MMUT gene, which is associated with lamb lethality in the homozygous state. A specific management of these haplotypes/variants in the MTR dairy sheep selection program would help enhance the overall fertility and lamb survival.
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Affiliation(s)
- Maxime Ben Braiek
- GenPhySE, Université de Toulouse, INRAE, ENVT, 31326, Castanet-Tolosan, France
| | | | | | - Jean-Michel Astruc
- Institut de l'Elevage, 24 Chemin de Borde-Rouge, 31321, Castanet-Tolosan, France
| | | | - Arnaud Bordes
- GenPhySE, Université de Toulouse, INRAE, ENVT, 31326, Castanet-Tolosan, France
| | - Frédéric Debat
- GenPhySE, Université de Toulouse, INRAE, ENVT, 31326, Castanet-Tolosan, France
| | | | - Itsasne Granado-Tajada
- Department of Animal Production, NEIKER-BRTA Basque Institute of Agricultural Research and Development, Agrifood Campus of Arkaute s/n, 01080, Arkaute, Spain
| | - Chris Hozé
- Eliance, 149 Rue de Bercy, 75595, Paris, France
- GABI, Université Paris-Saclay, INRAE, AgroParisTech, 78350, Jouy-en-Josas, France
| | | | - François Rivemale
- GenPhySE, Université de Toulouse, INRAE, ENVT, 31326, Castanet-Tolosan, France
| | - Julien Sarry
- GenPhySE, Université de Toulouse, INRAE, ENVT, 31326, Castanet-Tolosan, France
| | - Némuel Tadi
- GenPhySE, Université de Toulouse, INRAE, ENVT, 31326, Castanet-Tolosan, France
| | - Florent Woloszyn
- GenPhySE, Université de Toulouse, INRAE, ENVT, 31326, Castanet-Tolosan, France
| | - Stéphane Fabre
- GenPhySE, Université de Toulouse, INRAE, ENVT, 31326, Castanet-Tolosan, France.
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6
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Vasoya D, Connelley T, Tzelos T, Todd H, Ballingall KT. Large scale transcriptional analysis of MHC class I haplotype diversity in sheep. HLA 2024; 103:e15356. [PMID: 38304958 DOI: 10.1111/tan.15356] [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: 10/25/2023] [Revised: 12/15/2023] [Accepted: 01/09/2024] [Indexed: 02/03/2024]
Abstract
Domestic sheep (Ovis aries) have been an important component of livestock agricultural production for thousands of years. Preserving genetic diversity within livestock populations maintains a capacity to respond to changing environments and rapidly evolving pathogens. MHC genetic diversity can influence immune functionality at individual and population levels. Here, we focus on defining functional MHC class I haplotype diversity in a large cohort of Scottish Blackface sheep pre-selected for high levels of MHC class II DRB1 diversity. Using high-throughput amplicon sequencing with three independent sets of barcoded primers we identified 134 MHC class I transcripts within 38 haplotypes. Haplotypes were identified with between two and six MHC class I genes, plus variable numbers of conserved sequences with very low read frequencies. One or two highly transcribed transcripts dominate each haplotype indicative of two highly polymorphic, classical MHC class I genes. Additional clusters of medium, low, and very low expressed transcripts are described, indicative of lower transcribed classical, non-classical and genes whose function remains to be determined.
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Affiliation(s)
- Deepali Vasoya
- Division of Infection and Immunity, The Roslin Institute, The University of Edinburgh, Scotland, UK
| | - Timothy Connelley
- Division of Infection and Immunity, The Roslin Institute, The University of Edinburgh, Scotland, UK
| | - Thomas Tzelos
- Division of Infection and Immunity, The Roslin Institute, The University of Edinburgh, Scotland, UK
- Moredun Research Institute, Pentlands Science Park, Scotland, UK
| | - Helen Todd
- Moredun Research Institute, Pentlands Science Park, Scotland, UK
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7
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Chapuis AF, Alfituri OA, Hope JC, Stevens J, Moore J, Mclean K, Androscuk D, Dry I. Expression and functional characterization of bovine receptor activator of NF-κB ligand (RANKL). Vet Immunol Immunopathol 2024; 268:110705. [PMID: 38157760 DOI: 10.1016/j.vetimm.2023.110705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 12/15/2023] [Accepted: 12/16/2023] [Indexed: 01/03/2024]
Abstract
Receptor activator of nuclear factor Kappa-B Ligand (RANKL) is a member of the tumor necrosis factor ligand (TNF) family involved in immune responses and immunomodulation. Expressed in various cells types around the body, RANKL plays a crucial role in bone remodeling and development of the thymus, lymph nodes and mammary glands. Research in other species demonstrates that RANKL is required for the development of microfold cells (M cells) in the gut, however limited information specific to cattle is available. Cloning and expression of bovine RANKL (BoRANKL) was carried out and bioactivity of the protein was demonstrated in the induction of osteoclast differentiation from both bovine and ovine bone marrow cells. The effects of BoRANKL on particle uptake in bovine enteroids was also assessed. The production of cross-reactive bovine RANKL protein will enable further investigations into cell differentiation using the available ruminant organoid systems, and their role in investigating host-pathogen interactions in cattle and sheep.
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Affiliation(s)
- Ambre F Chapuis
- Moredun Research Institute, Pentlands Science Park, Penicuik EH26 0PZ, UK; The Roslin Institute, University of Edinburgh, Easter Bush, EH25 9RG, UK
| | - Omar A Alfituri
- The Roslin Institute, University of Edinburgh, Easter Bush, EH25 9RG, UK
| | - Jayne C Hope
- The Roslin Institute, University of Edinburgh, Easter Bush, EH25 9RG, UK
| | - Jo Stevens
- The Roslin Institute, University of Edinburgh, Easter Bush, EH25 9RG, UK
| | - Jo Moore
- Moredun Research Institute, Pentlands Science Park, Penicuik EH26 0PZ, UK
| | - Kevin Mclean
- Moredun Research Institute, Pentlands Science Park, Penicuik EH26 0PZ, UK
| | - Dorota Androscuk
- Moredun Research Institute, Pentlands Science Park, Penicuik EH26 0PZ, UK
| | - Inga Dry
- The Roslin Institute, University of Edinburgh, Easter Bush, EH25 9RG, UK.
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8
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Rudd Garces G, Letko A, Häfliger IM, Müller J, Herden C, Nesseler A, Wagner H, Schmidt MJ, Drögemüller C, Lühken G. MFSD2A frameshift variant in Kerry Hill sheep with microcephaly. Anim Genet 2024; 55:152-157. [PMID: 37921236 DOI: 10.1111/age.13374] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/21/2023] [Revised: 10/15/2023] [Accepted: 10/17/2023] [Indexed: 11/04/2023]
Abstract
Microcephaly is a rare neurodevelopmental disorder characterized by reduced skull circumference and brain volume that occurs sporadically in farm animals. We investigated an early-onset neurodegenerative disorder observed in seven lambs of purebred Kerry Hill sheep. Clinical signs included inability to stand or severe ataxia, convulsions, and early death. Diagnostic imaging and brain necropsy confirmed microcephaly. The pedigree of the lambs suggested monogenic autosomal recessive inheritance. We sequenced the genome of one affected lamb, and comparison with 115 control genomes revealed a single private protein-changing variant. This frameshift variant, MFSD2A: c.285dupA, p.(Asp96fs*9), represents a 1-bp duplication predicted to truncate 80% of the open reading frame. MFSD2A is a transmembrane protein that is essential for maintaining blood-brain barrier homeostasis and plays a key role in regulating brain lipogenesis. Human MFSD2A pathogenic variants are associated with a neurodevelopmental disorder with progressive microcephaly, spasticity, and brain imaging abnormalities (NEDMISBA, OMIM 616486). Here we present evidence for the occurrence of a recessively inherited form of microcephaly in sheep due to a loss-of-function variant in MFSD2A (OMIA 002371-9940). To the best of our knowledge, this is the first report of a spontaneous MFSD2A variant in domestic animals.
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Affiliation(s)
- Gabriela Rudd Garces
- Institute of Animal Breeding and Genetics, Justus Liebig University Giessen, Giessen, Germany
| | - Anna Letko
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Irene M Häfliger
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Jana Müller
- Institute for Veterinary Pathology, Justus Liebig University Giessen, Giessen, Germany
| | - Christiane Herden
- Institute for Veterinary Pathology, Justus Liebig University Giessen, Giessen, Germany
- Center for Mind, Brain and Behavior, Justus Liebig University Giessen, Giessen, Germany
| | | | - Henrik Wagner
- Veterinary Clinic for Reproduction and Neonatology, Justus Liebig University, Giessen, Germany
| | - Martin J Schmidt
- Clinic for Small Animals, Neurosurgery, Neuroradiology and Clinical Neurology, Justus Liebig University Giessen, Giessen, Germany
| | - Cord Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Gesine Lühken
- Institute of Animal Breeding and Genetics, Justus Liebig University Giessen, Giessen, Germany
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9
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Robic A, Hadlich F, Costa Monteiro Moreira G, Louise Clark E, Plastow G, Charlier C, Kühn C. Innovative construction of the first reliable catalogue of bovine circular RNAs. RNA Biol 2024; 21:52-74. [PMID: 38989833 PMCID: PMC11244336 DOI: 10.1080/15476286.2024.2375090] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 06/26/2024] [Indexed: 07/12/2024] Open
Abstract
The aim of this study was to compare the circular transcriptome of divergent tissues in order to understand: i) the presence of circular RNAs (circRNAs) that are not exonic circRNAs, i.e. originated from backsplicing involving known exons and, ii) the origin of artificial circRNA (artif_circRNA), i.e. circRNA not generated in-vivo. CircRNA identification is mostly an in-silico process, and the analysis of data from the BovReg project (https://www.bovreg.eu/) provided an opportunity to explore new ways to identify reliable circRNAs. By considering 117 tissue samples, we characterized 23,926 exonic circRNAs, 337 circRNAs from 273 introns (191 ciRNAs, 146 intron circles), 108 circRNAs from small non-coding genes and nearly 36.6K circRNAs classified as other_circRNAs. Furthermore, for 63 of those samples we analysed in parallel data from total-RNAseq (ribosomal RNAs depleted prior to library preparation) with paired mRNAseq (library prepared with poly(A)-selected RNAs). The high number of circRNAs detected in mRNAseq, and the significant number of novel circRNAs, mainly other_circRNAs, led us to consider all circRNAs detected in mRNAseq as artificial. This study provided evidence of 189 false entries in the list of exonic circRNAs: 103 artif_circRNAs identified by total RNAseq/mRNAseq comparison using two circRNA tools, 26 probable artif_circRNAs, and 65 identified by deep annotation analysis. Extensive benchmarking was performed (including analyses with CIRI2 and CIRCexplorer-2) and confirmed 94% of the 23,737 reliable exonic circRNAs. Moreover, this study demonstrates the effectiveness of a panel of highly expressed exonic circRNAs (5-8%) in analysing the tissue specificity of the bovine circular transcriptome.
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Affiliation(s)
- Annie Robic
- GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet-Tolosan, France
| | - Frieder Hadlich
- Institute of Genome Biology, Research Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | | | | | - Graham Plastow
- Department of Agricultural, Food and Nutritional Science, Livestock Gentec, University of Alberta, Edmonton, AB, Canada
| | - Carole Charlier
- Unit of Animal Genomics, GIGA Institute, University of Liège, Liège, Belgium
- Faculty of Veterinary Medicine, University of Liège, Liège, Belgium
| | - Christa Kühn
- Institute of Genome Biology, Research Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
- Faculty of Agricultural and Environmental Sciences, University of Rostock, Rostock, Germany
- Friedrich Loeffler Institute, Federal Research Institute for Animal Health, Greifswald – Insel Riems, Germany
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10
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Woolley SA, Salavati M, Clark EL. Recent advances in the genomic resources for sheep. Mamm Genome 2023; 34:545-558. [PMID: 37752302 PMCID: PMC10627984 DOI: 10.1007/s00335-023-10018-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Accepted: 08/30/2023] [Indexed: 09/28/2023]
Abstract
Sheep (Ovis aries) provide a vital source of protein and fibre to human populations. In coming decades, as the pressures associated with rapidly changing climates increase, breeding sheep sustainably as well as producing enough protein to feed a growing human population will pose a considerable challenge for sheep production across the globe. High quality reference genomes and other genomic resources can help to meet these challenges by: (1) informing breeding programmes by adding a priori information about the genome, (2) providing tools such as pangenomes for characterising and conserving global genetic diversity, and (3) improving our understanding of fundamental biology using the power of genomic information to link cell, tissue and whole animal scale knowledge. In this review we describe recent advances in the genomic resources available for sheep, discuss how these might help to meet future challenges for sheep production, and provide some insight into what the future might hold.
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Affiliation(s)
- Shernae A Woolley
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
| | - Mazdak Salavati
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK
- Scotland's Rural College, Parkgate, Barony Campus, Dumfries, DG1 3NE, UK
| | - Emily L Clark
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG, UK.
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11
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Chen Y, Yuan Z, Sun L. The evolutionary diversification and antimicrobial potential of MPEG1 in Metazoa. Comput Struct Biotechnol J 2023; 21:5818-5828. [PMID: 38213882 PMCID: PMC10781884 DOI: 10.1016/j.csbj.2023.11.032] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 11/17/2023] [Accepted: 11/17/2023] [Indexed: 01/13/2024] Open
Abstract
Macrophage-expressed gene 1 (MPEG1) is an ancient immune effector known to exist in Cnidaria, Mollusca, Actinopterygii, and Mammalia. In this study, we examined the evolution and antibacterial potential of MPEG1 across Metazoa. By unbiased data-mining, MPEG1 orthologs were found in 11 of 34 screened phyla. In invertebrates, MPEG1 is present in the major phyla and exhibits intensive duplication. In vertebrates, class-based clades were formed by the major, generic MPEG1 (gMPEG1) in each class. However, there is a minority of unique MPEG1 (uMPEG1) from 71 species of 4 classes that clustered into a separate clade detached from all major class-based clades. gMPEG1 and uMPEG1 exhibit strong genomic collinearity and are surrounded by high-density transposons. gMPEG1 and uMPEG1 transcript expressions were most abundant in immune organs, but differed markedly in tissue specificity. Systematic analysis identified an antimicrobial peptide (AMP)-like segment in the C-terminal (CT) tail of MPEG1. Peptides based on the AMP-like regions of 35 representative MPEG1 were synthesized. Bactericidal activities were displayed by all peptides. Together these results suggest transposon-propelled evolutionary diversification of MPEG1 in Metazoa that has likely led to functional specialisation. This study also reveals a possible antimicrobial mechanism mediated directly and solely by the CT tail of MPEG1.
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Affiliation(s)
- Yuan Chen
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Center for Ocean Mega-Science, Chinese Academy of Sciences (CAS), Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao 266237, China
- College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zihao Yuan
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Center for Ocean Mega-Science, Chinese Academy of Sciences (CAS), Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao 266237, China
- College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
| | - Li Sun
- CAS and Shandong Province Key Laboratory of Experimental Marine Biology, Institute of Oceanology, Center for Ocean Mega-Science, Chinese Academy of Sciences (CAS), Qingdao, China
- Laboratory for Marine Biology and Biotechnology, Laoshan Laboratory, Qingdao 266237, China
- College of Earth and Planetary Sciences, University of Chinese Academy of Sciences, Beijing 100049, China
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12
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Patir A, Raper A, Fleming R, Henderson BEP, Murphy L, Henderson NC, Clark EL, Freeman TC, Barnett MW. Cellular heterogeneity of the developing worker honey bee (Apis mellifera) pupa: a single cell transcriptomics analysis. G3 (BETHESDA, MD.) 2023; 13:jkad178. [PMID: 37548242 PMCID: PMC10542211 DOI: 10.1093/g3journal/jkad178] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/30/2023] [Revised: 06/30/2023] [Accepted: 07/24/2023] [Indexed: 08/08/2023]
Abstract
It is estimated that animals pollinate 87.5% of flowering plants worldwide and that managed honey bees (Apis mellifera) account for 30-50% of this ecosystem service to agriculture. In addition to their important role as pollinators, honey bees are well-established insect models for studying learning and memory, behavior, caste differentiation, epigenetic mechanisms, olfactory biology, sex determination, and eusociality. Despite their importance to agriculture, knowledge of honey bee biology lags behind many other livestock species. In this study, we have used scRNA-Seq to map cell types to different developmental stages of the worker honey bee (prepupa at day 11 and pupa at day 15) and sought to determine their gene expression signatures. To identify cell-type populations, we examined the cell-to-cell network based on the similarity of the single-cells transcriptomic profiles. Grouping similar cells together we identified 63 different cell clusters of which 17 clusters were identifiable at both stages. To determine genes associated with specific cell populations or with a particular biological process involved in honey bee development, we used gene coexpression analysis. We combined this analysis with literature mining, the honey bee protein atlas, and gene ontology analysis to determine cell cluster identity. Of the cell clusters identified, 17 were related to the nervous system and sensory organs, 7 to the fat body, 19 to the cuticle, 5 to muscle, 4 to compound eye, 2 to midgut, 2 to hemocytes, and 1 to malpighian tubule/pericardial nephrocyte. To our knowledge, this is the first whole single-cell atlas of honey bees at any stage of development and demonstrates the potential for further work to investigate their biology at the cellular level.
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Affiliation(s)
- Anirudh Patir
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - Anna Raper
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - Robert Fleming
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - Beth E P Henderson
- The Queen's Medical Research Institute, Centre for Inflammation Research, University of Edinburgh,Edinburgh BioQuarter, Edinburgh EH16 4TJ, UK
| | - Lee Murphy
- Edinburgh Clinical Research Facility, Western General Hospital, University of Edinburgh, Edinburgh EH4 2XU, UK
| | - Neil C Henderson
- The Queen's Medical Research Institute, Centre for Inflammation Research, University of Edinburgh,Edinburgh BioQuarter, Edinburgh EH16 4TJ, UK
- Institute of Genetics and Cancer, Western General Hospital, University of Edinburgh,Edinburgh EH4 2XU, UK
| | - Emily L Clark
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - Tom C Freeman
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - Mark W Barnett
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
- Beebytes Analytics CIC, The Roslin Innovation Centre, University of Edinburgh, The Charnock Bradley Building, Easter Bush, Midlothian EH25 9RG, UK
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13
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Triant DA, Walsh AT, Hartley GA, Petry B, Stegemiller MR, Nelson BM, McKendrick MM, Fuller EP, Cockett NE, Koltes JE, McKay SD, Green JA, Murdoch BM, Hagen DE, Elsik CG. AgAnimalGenomes: browsers for viewing and manually annotating farm animal genomes. Mamm Genome 2023; 34:418-436. [PMID: 37460664 PMCID: PMC10382368 DOI: 10.1007/s00335-023-10008-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Accepted: 06/29/2023] [Indexed: 07/30/2023]
Abstract
Current genome sequencing technologies have made it possible to generate highly contiguous genome assemblies for non-model animal species. Despite advances in genome assembly methods, there is still room for improvement in the delineation of specific gene features in the genomes. Here we present genome visualization and annotation tools to support seven livestock species (bovine, chicken, goat, horse, pig, sheep, and water buffalo), available in a new resource called AgAnimalGenomes. In addition to supporting the manual refinement of gene models, these browsers provide visualization tracks for hundreds of RNAseq experiments, as well as data generated by the Functional Annotation of Animal Genomes (FAANG) Consortium. For species with predicted gene sets from both Ensembl and RefSeq, the browsers provide special tracks showing the thousands of protein-coding genes that disagree across the two gene sources, serving as a valuable resource to alert researchers to gene model issues that may affect data interpretation. We describe the data and search methods available in the new genome browsers and how to use the provided tools to edit and create new gene models.
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Affiliation(s)
- Deborah A Triant
- Division of Animal Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Amy T Walsh
- Division of Animal Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Gabrielle A Hartley
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, 06269, USA
| | - Bruna Petry
- Department of Animal Science, Iowa State University, Ames, IA, 50011, USA
| | - Morgan R Stegemiller
- Department of Animal, Veterinary and Food Sciences, University of Idaho, Moscow, ID, 83844, USA
| | - Benjamin M Nelson
- Division of Animal Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Makenna M McKendrick
- Department of Animal and Food Sciences, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Emily P Fuller
- Department of Molecular and Cell Biology, University of Connecticut, Storrs, CT, 06269, USA
| | - Noelle E Cockett
- Department of Animal, Dairy, and Veterinary Sciences, Utah State University, Logan, UT, 84322, USA
| | - James E Koltes
- Department of Animal Science, Iowa State University, Ames, IA, 50011, USA
| | - Stephanie D McKay
- Department of Animal and Veterinary Sciences, University of Vermont, Burlington, VT, 05405, USA
| | - Jonathan A Green
- Division of Animal Sciences, University of Missouri, Columbia, MO, 65211, USA
| | - Brenda M Murdoch
- Department of Animal, Veterinary and Food Sciences, University of Idaho, Moscow, ID, 83844, USA
| | - Darren E Hagen
- Department of Animal and Food Sciences, Oklahoma State University, Stillwater, OK, 74078, USA
| | - Christine G Elsik
- Division of Animal Sciences, University of Missouri, Columbia, MO, 65211, USA.
- Division of Plant Science & Technology, University of Missouri, Columbia, MO, 65211, USA.
- Institute for Data Science & Informatics, University of Missouri, Columbia, MO, 65211, USA.
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14
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Letko A, Brülisauer F, Häfliger IM, Corr E, Scholes S, Drögemüller C. Loss-of-function variant in the ovine TMCO6 gene in North Country Cheviot sheep with motor neuron disease. Genomics 2023; 115:110689. [PMID: 37488055 DOI: 10.1016/j.ygeno.2023.110689] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2023] [Revised: 06/27/2023] [Accepted: 07/21/2023] [Indexed: 07/26/2023]
Abstract
In North Country Cheviot lambs with early-onset progressive ataxia and motor neuron degeneration, whole-genome sequencing identified a homozygous loss-of-function variant in the ovine transmembrane and coiled-coil domains (TMCO6) gene. The familial recessive form of motor neuron disease in sheep is due to a pathogenic 4 bp deletion leading to a 50% protein truncation that is assumed to result in the absence of a functional TMCO6. This uncharacterised protein is proposed to interact with ubiquilin 1 which is associated with Alzheimer's disease, whereas sporadic forms of amyotrophic lateral sclerosis are caused by variants in UBQLN2. Our findings provide a first spontaneous animal model for TMCO6, which could have implications in the studies of other comparative neurodegenerative diseases. In addition, these results will allow the design of a genetic test to prevent the occurrence of this fatal disease in the affected sheep population.
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Affiliation(s)
- Anna Letko
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern 3012, Switzerland.
| | - Franz Brülisauer
- SRUC Veterinary Services, Pentlands Science Park, Bush Estate Loan, Penicuik, Midlothian EH26 0PZ, United Kingdom.
| | - Irene M Häfliger
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern 3012, Switzerland.
| | - Eilidh Corr
- SRUC Veterinary Services, Pentlands Science Park, Bush Estate Loan, Penicuik, Midlothian EH26 0PZ, United Kingdom.
| | - Sandra Scholes
- SRUC Veterinary Services, Pentlands Science Park, Bush Estate Loan, Penicuik, Midlothian EH26 0PZ, United Kingdom
| | - Cord Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern 3012, Switzerland.
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15
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Luigi-Sierra MG, Guan D, López-Béjar M, Casas E, Olvera-Maneu S, Gardela J, Palomo MJ, Osuagwuh UI, Ohaneje UL, Mármol-Sánchez E, Amills M. A protein-coding gene expression atlas from the brain of pregnant and non-pregnant goats. Front Genet 2023; 14:1114749. [PMID: 37519888 PMCID: PMC10382233 DOI: 10.3389/fgene.2023.1114749] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/02/2022] [Accepted: 06/27/2023] [Indexed: 08/01/2023] Open
Abstract
Background: The brain is an extraordinarily complex organ with multiple anatomical structures involved in highly specialized functions related with behavior and physiological homeostasis. Our goal was to build an atlas of protein-coding gene expression in the goat brain by sequencing the transcriptomes of 12 brain regions in seven female Murciano-Granadina goats, from which three of them were 1-month pregnant. Results: Between 14,889 (cerebellar hemisphere) and 15,592 (pineal gland) protein-coding genes were expressed in goat brain regions, and most of them displayed ubiquitous or broad patterns of expression across tissues. Principal component analysis and hierarchical clustering based on the patterns of mRNA expression revealed that samples from certain brain regions tend to group according to their position in the anterior-posterior axis of the neural tube, i.e., hindbrain (pons and medulla oblongata), midbrain (rostral colliculus) and forebrain (frontal neocortex, olfactory bulb, hypothalamus, and hippocampus). Exceptions to this observation were cerebellum and glandular tissues (pineal gland and hypophysis), which showed highly divergent mRNA expression profiles. Differential expression analysis between pregnant and non-pregnant goats revealed moderate changes of mRNA expression in the frontal neocortex, hippocampus, adenohypophysis and pons, and very dramatic changes in the olfactory bulb. Many genes showing differential expression in this organ are related to olfactory function and behavior in humans. Conclusion: With the exception of cerebellum and glandular tissues, there is a relationship between the cellular origin of sampled regions along the anterior-posterior axis of the neural tube and their mRNA expression patterns in the goat adult brain. Gestation induces substantial changes in the mRNA expression of the olfactory bulb, a finding consistent with the key role of this anatomical structure on the development of maternal behavior.
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Affiliation(s)
| | - Dailu Guan
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Bellaterra, Spain
| | - Manel López-Béjar
- Department of Animal Health and Anatomy, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Encarna Casas
- Department of Animal Health and Anatomy, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Sergi Olvera-Maneu
- Department of Animal Health and Anatomy, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Jaume Gardela
- Department of Animal Health and Anatomy, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - María Jesús Palomo
- Department of Animal Medicine and Surgery, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Uchebuchi Ike Osuagwuh
- Department of Animal Medicine and Surgery, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Uchechi Linda Ohaneje
- Department of Animal Medicine and Surgery, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Emilio Mármol-Sánchez
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Bellaterra, Spain
| | - Marcel Amills
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Bellaterra, Spain
- Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, Bellaterra, Spain
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16
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Li R, Gong M, Zhang X, Wang F, Liu Z, Zhang L, Yang Q, Xu Y, Xu M, Zhang H, Zhang Y, Dai X, Gao Y, Zhang Z, Fang W, Yang Y, Fu W, Cao C, Yang P, Ghanatsaman ZA, Negari NJ, Nanaei HA, Yue X, Song Y, Lan X, Deng W, Wang X, Pan C, Xiang R, Ibeagha-Awemu EM, Heslop-Harrison PJS, Rosen BD, Lenstra JA, Gan S, Jiang Y. A sheep pangenome reveals the spectrum of structural variations and their effects on tail phenotypes. Genome Res 2023; 33:463-477. [PMID: 37310928 PMCID: PMC10078295 DOI: 10.1101/gr.277372.122] [Citation(s) in RCA: 25] [Impact Index Per Article: 25.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Accepted: 02/21/2023] [Indexed: 03/29/2023]
Abstract
Structural variations (SVs) are a major contributor to genetic diversity and phenotypic variations, but their prevalence and functions in domestic animals are largely unexplored. Here we generated high-quality genome assemblies for 15 individuals from genetically diverse sheep breeds using Pacific Biosciences (PacBio) high-fidelity sequencing, discovering 130.3 Mb nonreference sequences, from which 588 genes were annotated. A total of 149,158 biallelic insertions/deletions, 6531 divergent alleles, and 14,707 multiallelic variations with precise breakpoints were discovered. The SV spectrum is characterized by an excess of derived insertions compared to deletions (94,422 vs. 33,571), suggesting recent active LINE expansions in sheep. Nearly half of the SVs display low to moderate linkage disequilibrium with surrounding single-nucleotide polymorphisms (SNPs) and most SVs cannot be tagged by SNP probes from the widely used ovine 50K SNP chip. We identified 865 population-stratified SVs including 122 SVs possibly derived in the domestication process among 690 individuals from sheep breeds worldwide. A novel 168-bp insertion in the 5' untranslated region (5' UTR) of HOXB13 is found at high frequency in long-tailed sheep. Further genome-wide association study and gene expression analyses suggest that this mutation is causative for the long-tail trait. In summary, we have developed a panel of high-quality de novo assemblies and present a catalog of structural variations in sheep. Our data capture abundant candidate functional variations that were previously unexplored and provide a fundamental resource for understanding trait biology in sheep.
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Affiliation(s)
- Ran Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Mian Gong
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xinmiao Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Fei Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zhenyu Liu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Lei Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Qimeng Yang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yuan Xu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Mengsi Xu
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, Xinjiang 832000, China
| | - Huanhuan Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yunfeng Zhang
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, Xinjiang 832000, China
| | - Xuelei Dai
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yuanpeng Gao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zhuangbiao Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Wenwen Fang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yuta Yang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Weiwei Fu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Chunna Cao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Peng Yang
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, Xinjiang 832000, China
| | - Zeinab Amiri Ghanatsaman
- Department of Animal Science, Fars Agricultural and Natural Resources Research and Education Center, Agricultural Research, Education & Extension Organization (AREEO), Shiraz 7155863511, Iran
| | | | | | - Xiangpeng Yue
- State Key Laboratory of Grassland Agro-ecosystems, Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou 730020, China
| | - Yuxuan Song
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xianyong Lan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Weidong Deng
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
| | - Xihong Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Chuanying Pan
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Ruidong Xiang
- Faculty of Veterinary & Agricultural Science, The University of Melbourne, Parkville, 3052 Victoria, Australia
| | - Eveline M Ibeagha-Awemu
- Sherbrooke Research and Development Centre, Agriculture and Agri-Food Canada, Sherbrooke, Quebec J1M 0C8, Canada
| | - Pat J S Heslop-Harrison
- Department of Genetics and Genome Biology, University of Leicester, Leicester LE1 7RH, United Kingdom
| | - Benjamin D Rosen
- Animal Genomics and Improvement Laboratory, USDA-ARS, Beltsville, Maryland 20705, USA
| | - Johannes A Lenstra
- Faculty of Veterinary Medicine, Utrecht University, Utrecht 3508 TD, The Netherlands
| | - Shangquan Gan
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Sciences, Shihezi, Xinjiang 832000, China;
- College of Coastal Agricultural Sciences, Guangdong Ocean University, Zhanjiang 524088, China
| | - Yu Jiang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi 712100, China;
- Key Laboratory of Livestock Biology, Northwest A&F University, Yangling, Shaanxi 712100, China
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17
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Kasianov AS, Klepikova AV, Mayorov AV, Buzanov GS, Logacheva MD, Penin AA. Interspecific comparison of gene expression profiles using machine learning. PLoS Comput Biol 2023; 19:e1010743. [PMID: 36626392 PMCID: PMC9879537 DOI: 10.1371/journal.pcbi.1010743] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2021] [Revised: 01/26/2023] [Accepted: 11/16/2022] [Indexed: 01/11/2023] Open
Abstract
Interspecific gene comparisons are the keystones for many areas of biological research and are especially important for the translation of knowledge from model organisms to economically important species. Currently they are hampered by the low resolution of methods based on sequence analysis and by the complex evolutionary history of eukaryotic genes. This is especially critical for plants, whose genomes are shaped by multiple whole genome duplications and subsequent gene loss. This requires the development of new methods for comparing the functions of genes in different species. Here, we report ISEEML (Interspecific Similarity of Expression Evaluated using Machine Learning)-a novel machine learning-based algorithm for interspecific gene classification. In contrast to previous studies focused on sequence similarity, our algorithm focuses on functional similarity inferred from the comparison of gene expression profiles. We propose novel metrics for expression pattern similarity-expression score (ES)-that is suitable for species with differing morphologies. As a proof of concept, we compare detailed transcriptome maps of Arabidopsis thaliana, the model species, Zea mays (maize) and Fagopyrum esculentum (common buckwheat), which are species that represent distant clades within flowering plants. The classifier resulted in an AUC of 0.91; under the ES threshold of 0.5, the specificity was 94%, and sensitivity was 72%.
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Affiliation(s)
- Artem S. Kasianov
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
| | - Anna V. Klepikova
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
| | - Alexey V. Mayorov
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
| | | | - Maria D. Logacheva
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
- Skolkovo Institute of Science and Technology, Moscow, Russia
| | - Aleksey A. Penin
- Institute for Information Transmission Problems of the Russian Academy of Sciences, Moscow, Russia
- * E-mail:
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18
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Uncovering novel MHC alleles from RNA-Seq data: expanding the spectrum of MHC class I alleles in sheep. BMC Genom Data 2023; 24:1. [PMID: 36597020 PMCID: PMC9809118 DOI: 10.1186/s12863-022-01102-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2022] [Accepted: 12/20/2022] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Major histocompatibility complex (MHC) class I glycoproteins present selected peptides or antigens to CD8 + T cells that control the cytotoxic immune response. The MHC class I genes are among the most polymorphic loci in the vertebrate genome, with more than twenty thousand alleles known in humans. In sheep, only a very small number of alleles have been described to date, making the development of genotyping systems or functional studies difficult. A cost-effective way to identify new alleles could be to use already available RNA-Seq data from sheep. Current strategies for aligning RNA-Seq reads against annotated genome sequences or transcriptomes fail to detect the majority of class I alleles. Here, I combine the alignment of RNA-Seq reads against a specific reference database with de novo assembly to identify alleles. The method allows the comprehensive discovery of novel MHC class I alleles from RNA-Seq data (DinoMfRS). RESULTS Using DinoMfRS, virtually all expressed MHC class I alleles could be determined. From 18 animals 75 MHC class I alleles were identified, of which 69 were novel. In addition, it was shown that DinoMfRS can be used to improve the annotation of MHC genes in the sheep genome sequence. CONCLUSIONS DinoMfRS allows for the first time the annotation of unknown, more divergent MHC alleles from RNA-Seq data. Successful application to RNA-Seq data from 16 animals has approximately doubled the number of known alleles in sheep. By using existing data, alleles can now be determined very inexpensively for populations that have not been well studied. In addition, MHC expression studies or evolutionary studies, for example, can be greatly improved in this way, and the method should be applicable to a broader spectrum of other multigene families or highly polymorphic genes.
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19
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Meakin AS, Amirmostofian M, Darby JRT, Holman SL, Morrison JL, Wiese MD. Characterisation of cytochrome P450 isoenzyme activity in sheep liver and placental microsomes. Placenta 2023; 131:82-89. [PMID: 36527743 DOI: 10.1016/j.placenta.2022.11.015] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/19/2022] [Revised: 10/17/2022] [Accepted: 11/30/2022] [Indexed: 12/02/2022]
Abstract
INTRODUCTION Drug metabolism during pregnancy is a complex process that involves maternal, placental and fetal sites of metabolism. Indeed, there is a lack of clarity provided from drug metabolism in human pregnancy due to ethical limitations. Large animal models of human pregnancy provide an opportunity to quantify activity of phase 1 drug metabolism mediated by cytochrome P450 (CYP) enzymes in the maternal, placental, and fetal compartments. Herein, we have validated a comprehensive assay to quantify maternal, placental, and fetal CYP activity. METHODS Isolated microsomes from sheep maternal liver, placenta, and fetal liver (140d gestation, term = 150d) were incubated with CYP-specific probe drugs to quantify the activity of CYP1A2, CYP2B6, CYP2C8, CYP2C9, CYP2C19, CYP2D6, CYP2E1 and CYP3A. Inhibition studies were performed to validate specificity of probe drugs. The validated assay was developed using liquid chromatography-tandem mass spectrometry (LC-MS/MS). RESULTS CYP1A2, CYP2B6, CYP2C8, CYP2C19, CYP2D6, CYP2E1 and CYP3A were active in maternal liver. In contrast, only CYP1A2, CYP2C8 and CYP2D6 were active in the placenta, whereas CYP2B6, CYP2C8 and CYP2D6 were active in the fetal liver. Of the placental-specific CYPs validated, CYP1A2 increased in type A compared with type D placentomes, whereas CYP2C8 activity increased in type B compared with type A and C. DISCUSSION This study has established conditions for compartment-specific CYP activity in the sheep maternal-placental-fetal unit using a validated and standardised experimental workflow. Compartment- and placentome type-specific CYP activity are important considerations when examining drug metabolism in the maternal-placental-fetal unit and in determining the impact of pregnancy complications.
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Affiliation(s)
- Ashley S Meakin
- Early Origins of Adult Health Research Group, Health and Biomedical Innovation, UniSA: Clinical and Health Sciences, University of South Australia, Adelaide, South Australia, Australia
| | - Marzieh Amirmostofian
- Centre for Pharmaceutical Innovation, UniSA: Clinical and Health Sciences, University of South Australia, Adelaide, South Australia, Australia
| | - Jack RT Darby
- Early Origins of Adult Health Research Group, Health and Biomedical Innovation, UniSA: Clinical and Health Sciences, University of South Australia, Adelaide, South Australia, Australia
| | - Stacey L Holman
- Early Origins of Adult Health Research Group, Health and Biomedical Innovation, UniSA: Clinical and Health Sciences, University of South Australia, Adelaide, South Australia, Australia
| | - Janna L Morrison
- Early Origins of Adult Health Research Group, Health and Biomedical Innovation, UniSA: Clinical and Health Sciences, University of South Australia, Adelaide, South Australia, Australia.
| | - Michael D Wiese
- Centre for Pharmaceutical Innovation, UniSA: Clinical and Health Sciences, University of South Australia, Adelaide, South Australia, Australia.
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20
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Summers KM, Bush SJ, Davis MR, Hume DA, Keshvari S, West JA. Fibrillin-1 and asprosin, novel players in metabolic syndrome. Mol Genet Metab 2023; 138:106979. [PMID: 36630758 DOI: 10.1016/j.ymgme.2022.106979] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/08/2022] [Revised: 12/13/2022] [Accepted: 12/14/2022] [Indexed: 12/23/2022]
Abstract
Fibrillin-1 is a major component of the extracellular microfibrils, where it interacts with other extracellular matrix proteins to provide elasticity to connective tissues, and regulates the bioavailability of TGFβ family members. A peptide consisting of the C-terminal 140 amino acids of fibrillin-1 has recently been identified as a glucogenic hormone, secreted from adipose tissue during fasting and targeting the liver to release glucose. This fragment, called asprosin, also signals in the hypothalamus to stimulate appetite. Asprosin levels are correlated with many of the pathologies indicative of metabolic syndrome, including insulin resistance and obesity. Previous studies and reviews have addressed the therapeutic potential of asprosin as a target in obesity, diabetes and related conditions without considering mechanisms underlying the relationship between generation of asprosin and expression of the much larger fibrillin-1 protein. Profibrillin-1 undergoes obligatory cleavage at the cell surface as part of its assembly into microfibrils, producing the asprosin peptide as well as mature fibrillin-1. Patterns of FBN1 mRNA expression are inconsistent with the necessity for regulated release of asprosin. The asprosin peptide may be protected from degradation in adipose tissue. We present evidence for an alternative possibility, that asprosin mRNA is generated independently from an internal promoter within the 3' end of the FBN1 gene, which would allow for regulation independent of fibrillin-synthesis and is more economical of cellular resources. The discovery of asprosin opened exciting possibilities for treatment of metabolic syndrome related conditions, but there is much to be understood before such therapies could be introduced into the clinic.
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Affiliation(s)
- Kim M Summers
- Mater Research Institute-University of Queensland, Translational Research Institute, 37 Kent St, Woolloongabba, Queensland 4102, Australia.
| | - Stephen J Bush
- Weatherall Institute of Molecular Medicine, University of Oxford, John Radcliffe Hospital, Headley Way, Oxford OX3 9DS, United Kingdom.
| | - Margaret R Davis
- The Roslin Institute, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, United Kingdom
| | - David A Hume
- Mater Research Institute-University of Queensland, Translational Research Institute, 37 Kent St, Woolloongabba, Queensland 4102, Australia.
| | - Sahar Keshvari
- Mater Research Institute-University of Queensland, Translational Research Institute, 37 Kent St, Woolloongabba, Queensland 4102, Australia.
| | - Jennifer A West
- Faculty of Medicine, The University of Queensland, Mayne Medical Building, 288 Herston Road, Herston, Queensland 4006, Australia.
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21
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Bozhilova-Sakova M, Dimitrova I, Stancheva N, Ignatova M, Ivanova T. 35-bp deletion in ABCG2 gene: mini-review and report on two herds of Bulgarian dairy synthetic population sheep breed. BIOTECHNOL BIOTEC EQ 2022. [DOI: 10.1080/13102818.2022.2107949] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/14/2022] Open
Affiliation(s)
- Milena Bozhilova-Sakova
- Department of Genetics, Breeding and Reproduction, Institute of Animal Science, Agricultural Academy, Kostinbrod, Bulgaria
| | - Ivona Dimitrova
- Agronomy Faculty, Department of Plant Protection, University of Forestry, Sofia, Bulgaria
| | - Nevyana Stancheva
- Department of Animal Science, Agricultural Academy, Agricultural Institute, Shumen, Bulgaria
| | - Maya Ignatova
- Department of Genetics, Breeding and Reproduction, Institute of Animal Science, Agricultural Academy, Kostinbrod, Bulgaria
| | - Tanya Ivanova
- Department of Genetics, Breeding and Reproduction, Institute of Animal Science, Agricultural Academy, Kostinbrod, Bulgaria
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22
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Pan X, Cai J, Wang Y, Xu D, Jiang Y, Gong W, Tian Y, Shen Q, Zhang Z, Yuan X, Li J. Expression Profile of Housekeeping Genes and Tissue-Specific Genes in Multiple Tissues of Pigs. Animals (Basel) 2022; 12:3539. [PMID: 36552460 PMCID: PMC9774903 DOI: 10.3390/ani12243539] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/07/2022] [Revised: 12/09/2022] [Accepted: 12/12/2022] [Indexed: 12/23/2022] Open
Abstract
Pigs have become an ideal model system for human disease research and development and an important farm animal that provides a valuable source of nutrition. To profile the all-sided gene expression and their biological functions across multiple tissues, we conducted a comprehensive analysis of gene expression on a large scale around the side of housekeeping genes (HKGs), tissue specific genes (TSGs), and the co-expressed genes in 14 various tissues. In this study, we identified 2351 HKGs and 3018 TSGs across tissues, among which 4 HKGs (COX1, UBB, OAZ1/NPFF) exhibited low variation and high expression levels, and 31 particular TSGs (e.g., PDC, FKBP6, STAT2, and COL1A1) were exclusively expressed in several tissues, including endocrine brain, ovaries, livers, backfat, jejunum, kidneys, lungs, and longissimus dorsi muscles. We also obtained 17 modules with 230 hub genes (HUBGs) by weighted gene co-expression network analysis. On the other hand, HKGs functions were enriched in the signaling pathways of the ribosome, spliceosome, thermogenesis, oxidative phosphorylation, and nucleocytoplasmic transport, which have been highly suggested to involve in the basic biological tissue activities. While TSGs were highly enriched in the signaling pathways that were involved in specific physiological processes, such as the ovarian steroidogenesis pathway in ovaries and the renin-angiotensin system pathway in kidneys. Collectively, these stable, specifical, and co-expressed genes provided useful information for the investigation of the molecular mechanism for an understanding of the genetic and biological processes of complex traits in pigs.
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Affiliation(s)
- Xiangchun Pan
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Jiali Cai
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Yifei Wang
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Dantong Xu
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Yao Jiang
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Shenzhen 518120, China
- Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518120, China
- School of Veterinary and Life Sciences, Murdoch University, Murdoch 6150, Australia
| | - Wentao Gong
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Yuhan Tian
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Qingpeng Shen
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Zhe Zhang
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Xiaolong Yuan
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
| | - Jiaqi Li
- Guangdong Provincial Key Laboratory of Agro-Animal Genomics and Molecular Breeding, National Engineering Research Center for Breeding Swine Industry, College of Animal Science, South China Agricultural University, Guangzhou 510642, China
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23
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Freeman TC, Horsewell S, Patir A, Harling-Lee J, Regan T, Shih BB, Prendergast J, Hume DA, Angus T. Graphia: A platform for the graph-based visualisation and analysis of high dimensional data. PLoS Comput Biol 2022; 18:e1010310. [PMID: 35877685 PMCID: PMC9352203 DOI: 10.1371/journal.pcbi.1010310] [Citation(s) in RCA: 23] [Impact Index Per Article: 11.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2021] [Revised: 08/04/2022] [Accepted: 06/16/2022] [Indexed: 01/04/2023] Open
Abstract
Graphia is an open-source platform created for the graph-based analysis of the huge amounts of quantitative and qualitative data currently being generated from the study of genomes, genes, proteins metabolites and cells. Core to Graphia’s functionality is support for the calculation of correlation matrices from any tabular matrix of continuous or discrete values, whereupon the software is designed to rapidly visualise the often very large graphs that result in 2D or 3D space. Following graph construction, an extensive range of measurement algorithms, routines for graph transformation, and options for the visualisation of node and edge attributes are available, for graph exploration and analysis. Combined, these provide a powerful solution for the interpretation of high-dimensional data from many sources, or data already in the form of a network or equivalent adjacency matrix. Several use cases of Graphia are described, to showcase its wide range of applications in the analysis biological data. Graphia runs on all major desktop operating systems, is extensible through the deployment of plugins and is freely available to download from https://graphia.app/. Graphia is a new visual analytics platform specifically created for the network-based analysis of large and complex data, such as that generated in huge amounts by modern biological analyses. It works in a data agnostic, hypothesis-free manner to generate correlation networks from any table of numerical or discrete values, thereafter providing a means to rapidly visualise the often very large networks that result, in either 2D or 3D space. Following network construction, the tool offers an extensive range of analysis algorithms, routines for network transformation, and options for the visualisation of metadata. This provides a powerful analysis solution for the exploration and interpretation of high-dimensional data from any source, as well as any data already defined as a network. Several use cases of Graphia are described to showcase its wide range of applications in the analysis biological data. Graphia is open source and free to all.
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Affiliation(s)
- Tom C. Freeman
- The Roslin Institute, Easter Bush Campus, The University of Edinburgh, Edinburgh, United Kingdom
- Kajeka Limited, Roslin Innovation Centre, Easter Bush Campus, The University of Edinburgh, Edinburgh, United Kingdom
- * E-mail:
| | - Sebastian Horsewell
- Kajeka Limited, Roslin Innovation Centre, Easter Bush Campus, The University of Edinburgh, Edinburgh, United Kingdom
| | - Anirudh Patir
- The Roslin Institute, Easter Bush Campus, The University of Edinburgh, Edinburgh, United Kingdom
| | - Josh Harling-Lee
- The Roslin Institute, Easter Bush Campus, The University of Edinburgh, Edinburgh, United Kingdom
| | - Tim Regan
- The Roslin Institute, Easter Bush Campus, The University of Edinburgh, Edinburgh, United Kingdom
| | - Barbara B. Shih
- The Roslin Institute, Easter Bush Campus, The University of Edinburgh, Edinburgh, United Kingdom
| | - James Prendergast
- The Roslin Institute, Easter Bush Campus, The University of Edinburgh, Edinburgh, United Kingdom
| | - David A. Hume
- Mater Research Institute-University of Queensland, Translational Research Institute, Woolloongabba, Queensland, Australia
| | - Tim Angus
- Kajeka Limited, Roslin Innovation Centre, Easter Bush Campus, The University of Edinburgh, Edinburgh, United Kingdom
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24
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Zhang T, Wang T, Niu Q, Zheng X, Li H, Gao X, Chen Y, Gao H, Zhang L, Liu GE, Li J, Xu L. Comparative transcriptomic analysis reveals region-specific expression patterns in different beef cuts. BMC Genomics 2022; 23:387. [PMID: 35596128 PMCID: PMC9123670 DOI: 10.1186/s12864-022-08527-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/13/2021] [Accepted: 03/30/2022] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Beef cuts in different regions of the carcass have different meat quality due to their distinct physiological function. The objective of this study was to characterize the region-specific expression differences using comparative transcriptomics analysis among five representative beef cuts (tenderloin, longissimus lumborum, rump, neck, chuck). RESULTS We obtained 15,701 expressed genes in 30 muscle samples across five regions from carcass meat. We identified a total of 80 region-specific genes (RSGs), ranging from three (identified in the rump cut) to thirty (identified in the longissimus lumborum cut), and detected 25 transcription factors (TFs) for RSGs. Using a co-expression network analysis, we detected seven region-specific modules, including three positively correlated modules and four negatively correlated modules. We finally obtained 91 candidate genes related to meat quality, and the functional enrichment analyses showed that these genes were mainly involved in muscle fiber structure (e.g., TNNI1, TNNT1), fatty acids (e.g., SCD, LPL), amino acids (ALDH2, IVD, ACADS), ion channel binding (PHPT1, SNTA1, SUMO1, CNBP), protein processing (e.g., CDC37, GAPDH, NRBP1), as well as energy production and conversion (e.g., ATP8, COX8B, NDUFB6). Moreover, four candidate genes (ALDH2, CANX, IVD, PHPT1) were validated using RT-qPCR analyses which further supported our RNA-seq results. CONCLUSIONS Our results provide valuable insights into understanding the transcriptome regulation of meat quality in different beef cuts, and these findings may further help to improve the selection for health-beneficial meat in beef cattle.
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Affiliation(s)
- Tianliu Zhang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Yuanmingyuan West Road 2#, Haidian District, Beijing, 100193, China
| | - Tianzhen Wang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Yuanmingyuan West Road 2#, Haidian District, Beijing, 100193, China
| | - Qunhao Niu
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Yuanmingyuan West Road 2#, Haidian District, Beijing, 100193, China
| | - Xu Zheng
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Yuanmingyuan West Road 2#, Haidian District, Beijing, 100193, China
| | - Haipeng Li
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Yuanmingyuan West Road 2#, Haidian District, Beijing, 100193, China
| | - Xue Gao
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Yuanmingyuan West Road 2#, Haidian District, Beijing, 100193, China
| | - Yan Chen
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Yuanmingyuan West Road 2#, Haidian District, Beijing, 100193, China
| | - Huijiang Gao
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Yuanmingyuan West Road 2#, Haidian District, Beijing, 100193, China
| | - Lupei Zhang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Yuanmingyuan West Road 2#, Haidian District, Beijing, 100193, China
| | - George E Liu
- Animal Genomics and Improvement Laboratory, United States Department of Agriculture-Agricultural Research Services, Beltsville, MD, 20705, USA
| | - Junya Li
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Yuanmingyuan West Road 2#, Haidian District, Beijing, 100193, China.
| | - Lingyang Xu
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Yuanmingyuan West Road 2#, Haidian District, Beijing, 100193, China.
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25
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Ballandras-Colas A, Chivukula V, Gruszka DT, Shan Z, Singh PK, Pye VE, McLean RK, Bedwell GJ, Li W, Nans A, Cook NJ, Fadel HJ, Poeschla EM, Griffiths DJ, Vargas J, Taylor IA, Lyumkis D, Yardimci H, Engelman AN, Cherepanov P. Multivalent interactions essential for lentiviral integrase function. Nat Commun 2022; 13:2416. [PMID: 35504909 PMCID: PMC9065133 DOI: 10.1038/s41467-022-29928-8] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2022] [Accepted: 04/07/2022] [Indexed: 12/24/2022] Open
Abstract
A multimer of retroviral integrase (IN) synapses viral DNA ends within a stable intasome nucleoprotein complex for integration into a host cell genome. Reconstitution of the intasome from the maedi-visna virus (MVV), an ovine lentivirus, revealed a large assembly containing sixteen IN subunits1. Herein, we report cryo-EM structures of the lentiviral intasome prior to engagement of target DNA and following strand transfer, refined at 3.4 and 3.5 Å resolution, respectively. The structures elucidate details of the protein-protein and protein-DNA interfaces involved in lentiviral intasome formation. We show that the homomeric interfaces involved in IN hexadecamer formation and the α-helical configuration of the linker connecting the C-terminal and catalytic core domains are critical for MVV IN strand transfer activity in vitro and for virus infectivity. Single-molecule microscopy in conjunction with photobleaching reveals that the MVV intasome can bind a variable number, up to sixteen molecules, of the lentivirus-specific host factor LEDGF/p75. Concordantly, ablation of endogenous LEDGF/p75 results in gross redistribution of MVV integration sites in human and ovine cells. Our data confirm the importance of the expanded architecture observed in cryo-EM studies of lentiviral intasomes and suggest that this organization underlies multivalent interactions with chromatin for integration targeting to active genes.
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Affiliation(s)
- Allison Ballandras-Colas
- Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London, UK
- Institut de Biologie Structurale (IBS) CNRS, CEA, University Grenoble, Grenoble, France
| | - Vidya Chivukula
- Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London, UK
- Department of Microbiology, NYU Grossman School of Medicine, New York, NY, 10016, USA
| | - Dominika T Gruszka
- Single Molecule Imaging of Genome Duplication and Maintenance Laboratory, The Francis Crick Institute, London, UK
- Biological Physics Research Group, Clarendon Laboratory, Department of Physics and Kavli Institute for Nanoscience Discovery, University of Oxford, Oxford, UK
| | - Zelin Shan
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA, USA
| | - Parmit K Singh
- Department of Cancer Immunology & Virology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Valerie E Pye
- Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London, UK
| | - Rebecca K McLean
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Penicuik, UK
- The Pirbright Institute, Ash Road, Pirbright, Woking, GU24 0NF, UK
| | - Gregory J Bedwell
- Department of Cancer Immunology & Virology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Wen Li
- Department of Cancer Immunology & Virology, Dana-Farber Cancer Institute, Boston, MA, USA
- Department of Medicine, Harvard Medical School, Boston, MA, USA
| | - Andrea Nans
- Structural Biology Science Technology Platform, The Francis Crick Institute, London, UK
| | - Nicola J Cook
- Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London, UK
| | - Hind J Fadel
- Division of Infectious Diseases, Mayo Clinic, Rochester, MN, USA
| | - Eric M Poeschla
- Division of Infectious Diseases, University of Colorado Anschutz Medical Campus, Aurora, CO, USA
| | - David J Griffiths
- Moredun Research Institute, Pentlands Science Park, Bush Loan, Penicuik, UK
| | - Javier Vargas
- Departmento de Óptica, Universidad Complutense de Madrid, Madrid, Spain
| | - Ian A Taylor
- Macromolecular Structure Laboratory, The Francis Crick Institute, London, UK
| | - Dmitry Lyumkis
- Laboratory of Genetics, The Salk Institute for Biological Studies, La Jolla, CA, USA.
- Department of Integrative Structural and Computational Biology, The Scripps Research Institute, La Jolla, CA, USA.
| | - Hasan Yardimci
- Single Molecule Imaging of Genome Duplication and Maintenance Laboratory, The Francis Crick Institute, London, UK.
| | - Alan N Engelman
- Department of Cancer Immunology & Virology, Dana-Farber Cancer Institute, Boston, MA, USA.
- Department of Medicine, Harvard Medical School, Boston, MA, USA.
| | - Peter Cherepanov
- Chromatin Structure and Mobile DNA Laboratory, The Francis Crick Institute, London, UK.
- Department of Infectious Disease, St-Mary's Campus, Imperial College London, London, UK.
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26
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Mohammadi A, Alijani S, Rafat S, Abdollahi-Arpanahi R. Single-step genome-wide association study and candidate genes networks affecting reproductive traits in Iranian Holstein cattle. Livest Sci 2022. [DOI: 10.1016/j.livsci.2022.104971] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/25/2022]
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27
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Chen C, Yin Y, Li H, Zhou B, Zhou J, Zhou X, Li Z, Liu G, Pan X, Zhang R, Lin Z, Chen L, Qiu Q, Zhang YE, Wang W. Ruminant-specific genes identified using high-quality genome data and their roles in rumen evolution. Sci Bull (Beijing) 2022; 67:825-835. [PMID: 36546235 DOI: 10.1016/j.scib.2022.01.023] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2021] [Revised: 10/26/2021] [Accepted: 12/13/2021] [Indexed: 01/06/2023]
Abstract
Ruminants comprise a highly successful group of mammals with striking morphological innovations, including the presence of a rumen. Many studies have shown that species-specific or lineage-specific genes (referred to as new genes) play important roles in phenotypic evolution. In this study, we identified 1064 ruminant-specific genes based on the newly assembled high-quality genomes of representative members of two ruminant families and other publically available high-quality genomes. Ruminant-specific genes shared similar evolutionary and expression patterns with new genes found in other mammals, such as primates and rodents. Most new genes were derived from gene duplication and tended to be expressed in the testes or immune-related tissues, but were depleted in the adult brain. We also found that most genes expressed in the rumen were genes predating sheep-sperm whale split (referred to as old genes), but some new genes were also involved in the evolution of the rumen, and contributed more during rumen development than in the adult rumen. Notably, expression levels of members of the ruminant-specific PRD-SPRRII gene family, which are subject to positive selection, varied throughout rumen development and may thus play important roles in the development of the keratin-rich surface of the rumen. Overall, this study generated two novel ruminant genomes and also provided novel insights into the evolution of new mammalian organs.
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Affiliation(s)
- Chunyan Chen
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710072, China
| | - Yuan Yin
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710072, China
| | - Haorong Li
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710072, China
| | - Botong Zhou
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710072, China
| | - Jiong Zhou
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710072, China
| | - Xiaofang Zhou
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710072, China
| | - Zhipeng Li
- College of Animal Science and Technology, Jilin Agricultural University, Changchun 130118, China
| | - Guichun Liu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710072, China; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China
| | - Xiangyu Pan
- Department of Gastroenterology, Guangdong Provincial People's Hospital, Guangdong Academy of Medical Sciences, Guangzhou 510080, China; Guangdong Cardiovascular Institute, Guangzhou 510080, China
| | - Ru Zhang
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710072, China
| | - Zeshan Lin
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710072, China
| | - Lei Chen
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710072, China; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China.
| | - Qiang Qiu
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710072, China.
| | - Yong E Zhang
- Key Laboratory of Zoological Systematics and Evolution, Institute of Zoology, Chinese Academy of Sciences, Beijing 100101, China; University of Chinese Academy of Sciences, Beijing 100049, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China.
| | - Wen Wang
- School of Ecology and Environment, Northwestern Polytechnical University, Xi'an 710072, China; State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming 650223, China; Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming 650223, China.
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28
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Zhang T, Wang T, Niu Q, Xu L, Chen Y, Gao X, Gao H, Zhang L, Liu GE, Li J, Xu L. Transcriptional atlas analysis from multiple tissues reveals the expression specificity patterns in beef cattle. BMC Biol 2022; 20:79. [PMID: 35351103 PMCID: PMC8966188 DOI: 10.1186/s12915-022-01269-4] [Citation(s) in RCA: 16] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2021] [Accepted: 03/03/2022] [Indexed: 11/12/2022] Open
Abstract
BACKGROUND A comprehensive analysis of gene expression profiling across tissues can provide necessary information for an in-depth understanding of their biological functions. We performed a large-scale gene expression analysis and generated a high-resolution atlas of the transcriptome in beef cattle. RESULTS Our transcriptome atlas was generated from 135 bovine tissues in adult beef cattle, covering 51 tissue types of major organ systems (e.g., muscular system, digestive system, immune system, reproductive system). Approximately 94.76% of sequencing reads were successfully mapped to the reference genome assembly ARS-UCD1.2. We detected a total of 60,488 transcripts, and 32% of them were not reported before. We identified 2654 housekeeping genes (HKGs) and 477 tissue-specific genes (TSGs) across tissues. Using weighted gene co-expression network analysis, we obtained 24 modules with 237 hub genes (HUBGs). Functional enrichment analysis showed that HKGs mainly maintain the basic biological activities of cells, while TSGs were involved in tissue differentiation and specific physiological processes. HKGs in bovine tissues were more conserved in terms of expression pattern as compared to TSGs and HUBGs among multiple species. Finally, we obtained a subset of tissue-specific differentially expressed genes (DEGs) between beef and dairy cattle and several functional pathways, which may be involved in production and health traits. CONCLUSIONS We generated a large-scale gene expression atlas across the major tissues in beef cattle, providing valuable information for enhancing genome assembly and annotation. HKGs, TSGs, and HUBGs further contribute to better understanding the biology and evolution of multiple tissues in cattle. DEGs between beef and dairy cattle also fill in the knowledge gaps about differential transcriptome regulation of bovine tissues underlying economically important traits.
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Affiliation(s)
- Tianliu Zhang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193 People’s Republic of China
| | - Tianzhen Wang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193 People’s Republic of China
| | - Qunhao Niu
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193 People’s Republic of China
| | - Lei Xu
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193 People’s Republic of China
| | - Yan Chen
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193 People’s Republic of China
| | - Xue Gao
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193 People’s Republic of China
| | - Huijiang Gao
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193 People’s Republic of China
| | - Lupei Zhang
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193 People’s Republic of China
| | - George E. Liu
- Animal Genomics and Improvement Laboratory, United States Department of Agriculture, Agricultural Research Service, Beltsville, Maryland 20705 USA
| | - Junya Li
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193 People’s Republic of China
| | - Lingyang Xu
- Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, 100193 People’s Republic of China
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29
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Wang H, Feng X, Muhatai G, Wang L. Expression profile analysis of sheep ovary after superovulation and estrus synchronisation treatment. Vet Med Sci 2022; 8:1276-1287. [PMID: 35305293 PMCID: PMC9122410 DOI: 10.1002/vms3.783] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
Superovulation is a widely used reproductive technique in livestock production, but the mechanism of sheep's superovulation is not yet clear. Here, a method of superovulation and estrus synchronisation was used to treat female Duolang sheep. After treatment, there were significant differences in serum FSH and LH levels and the number of dominant follicles between the two groups of sheep. We identified a total of 5021 differentially expressed genes (11, 13 and 15 days after treatment) and performed RT‐qPCR analysis to identify several mRNA expression levels. GO and KEGG enrichment analysis revealed that differentially expressed genes were involved in the regulation of signalling pathways of follicular development, cell cycle, material synthesis, energy metabolism, such as COL3A1, RPS8, ACTA2, RPL7 RPS6 and TNFAIP6 may play a key role in regulating the development of follicles. Our results show a comprehensive expression profile after superovulation and estrus synchronisation treatment. We provide the basis for further research on breeding techniques to improve the ovulation rate and birth rate of livestock.
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Affiliation(s)
- Huie Wang
- College of Animal Science, Tarim University, Alar, Xinjiang, China
| | - Xinwei Feng
- College of Animal Science, Tarim University, Alar, Xinjiang, China
| | | | - Lan Wang
- College of Animal Science, Tarim University, Alar, Xinjiang, China
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30
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Summers KM, Bush SJ, Wu C, Hume DA. Generation and network analysis of an RNA-seq transcriptional atlas for the rat. NAR Genom Bioinform 2022; 4:lqac017. [PMID: 35265836 PMCID: PMC8900154 DOI: 10.1093/nargab/lqac017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2021] [Revised: 01/13/2022] [Accepted: 02/15/2022] [Indexed: 12/19/2022] Open
Abstract
Abstract
The laboratory rat is an important model for biomedical research. To generate a comprehensive rat transcriptomic atlas, we curated and downloaded 7700 rat RNA-seq datasets from public repositories, downsampled them to a common depth and quantified expression. Data from 585 rat tissues and cells, averaged from each BioProject, can be visualized and queried at http://biogps.org/ratatlas. Gene co-expression network (GCN) analysis revealed clusters of transcripts that were tissue or cell type restricted and contained transcription factors implicated in lineage determination. Other clusters were enriched for transcripts associated with biological processes. Many of these clusters overlap with previous data from analysis of other species, while some (e.g. expressed specifically in immune cells, retina/pineal gland, pituitary and germ cells) are unique to these data. GCN analysis on large subsets of the data related specifically to liver, nervous system, kidney, musculoskeletal system and cardiovascular system enabled deconvolution of cell type-specific signatures. The approach is extensible and the dataset can be used as a point of reference from which to analyse the transcriptomes of cell types and tissues that have not yet been sampled. Sets of strictly co-expressed transcripts provide a resource for critical interpretation of single-cell RNA-seq data.
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Affiliation(s)
- Kim M Summers
- Mater Research Institute—University of Queensland, Translational Research Institute, 37 Kent St, Woolloongabba, QLD 4102, Australia
| | - Stephen J Bush
- Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, OX3 9DS, UK
| | - Chunlei Wu
- Department of Integrative and Computational Biology, The Scripps Research Institute, La Jolla, CA 92037, USA
| | - David A Hume
- Mater Research Institute—University of Queensland, Translational Research Institute, 37 Kent St, Woolloongabba, QLD 4102, Australia
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31
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Murray SJ, Mitchell NL. The Translational Benefits of Sheep as Large Animal Models of Human Neurological Disorders. Front Vet Sci 2022; 9:831838. [PMID: 35242840 PMCID: PMC8886239 DOI: 10.3389/fvets.2022.831838] [Citation(s) in RCA: 13] [Impact Index Per Article: 6.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2021] [Accepted: 01/21/2022] [Indexed: 12/15/2022] Open
Abstract
The past two decades have seen a considerable rise in the use of sheep to model human neurological disorders. While each animal model has its merits, sheep have many advantages over small animal models when it comes to studies on the brain. In particular, sheep have brains more comparable in size and structure to the human brain. They also have much longer life spans and are docile animals, making them useful for a wide range of in vivo studies. Sheep are amenable to regular blood and cerebrospinal fluid sampling which aids in biomarker discovery and monitoring of treatment efficacy. Several neurological diseases have been found to occur naturally in sheep, however sheep can also be genetically engineered or experimentally manipulated to recapitulate disease or injury. Many of these types of sheep models are currently being used for pre-clinical therapeutic trials, particularly gene therapy, with studies from several models culminating in potential treatments moving into clinical trials. This review will provide an overview of the benefits of using sheep to model neurological conditions, and highlight naturally occurring and experimentally induced sheep models that have demonstrated translational validity.
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Affiliation(s)
- Samantha J. Murray
- Faculty of Agriculture and Life Sciences, Lincoln University, Canterbury, New Zealand
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32
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Training associated alterations in equine respiratory immunity using a multiomics comparative approach. Sci Rep 2022; 12:427. [PMID: 35013475 PMCID: PMC8748960 DOI: 10.1038/s41598-021-04137-3] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2021] [Accepted: 12/07/2021] [Indexed: 12/19/2022] Open
Abstract
Neutrophilic airway inflammation is highly prevalent in racehorses in training, with the term mild to moderate equine asthma (MMEA) being applied to the majority of such cases. Our proposed study is largely derived from the strong association between MMEA in racehorses and their entry into a race training program. The objectives of this study are to characterise the effect of training on the local pulmonary immune system by defining the gene and protein expression of tracheal wash (TW) derived samples from Thoroughbred racehorses prior to and following commencement of race training. Multiomics analysis detected 2138 differentially expressed genes and 260 proteins during the training period. Gene and protein sets were enriched for biological processes related to acute phase response, oxidative stress, haemopoietic processes, as well as to immune response and inflammation. This study demonstrated TW samples to represent a rich source of airway cells, protein and RNA to study airway immunity in the horse and highlighted the benefits of a multiomics methodological approach to studying the dynamics of equine airway immunity. Findings likely reflect the known associations between race-training and both airway inflammation and bleeding, offering further insight into the potential mechanisms which underpin training associated airway inflammation.
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33
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Ben Braiek M, Moreno-Romieux C, Allain C, Bardou P, Bordes A, Debat F, Drögemüller C, Plisson-Petit F, Portes D, Sarry J, Tadi N, Woloszyn F, Fabre S. A Nonsense Variant in CCDC65 Gene Causes Respiratory Failure Associated with Increased Lamb Mortality in French Lacaune Dairy Sheep. Genes (Basel) 2021; 13:genes13010045. [PMID: 35052387 PMCID: PMC8774411 DOI: 10.3390/genes13010045] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 12/16/2021] [Accepted: 12/20/2021] [Indexed: 12/04/2022] Open
Abstract
We recently demonstrated that the Lacaune deficient homozygous haplotype 6 (LDHH6) potentially hosts a recessive perinatal lethal mutation in Lacaune dairy sheep mapped on OAR3. In the present study, we have analyzed the whole-genome sequences of two Lacaune ram heterozygous carriers of LDHH6. After variant calling and filtering against the variants of 86 non-carrier rams, we have identified a single nucleotide variant (SNV) in the two LDHH6 carriers whose variant allele induced a premature stop codon (p.Glu111*) in the Coiled-Coil Domain Containing 65 (CCDC65) gene. CCDC65 is involved in the assembly of the nexin-dynein regulatory complex for the formation of microtubules in ciliated cells. In order to identify the phenotype in homozygous sheep, we generated at-risk matings (n = 17) between rams and ewes heterozygous for the candidate variant in CCDC65. A total of 16 lambs were born alive with five genotyped as homozygous carriers. The homozygous lambs suffered from respiratory problems, and four of them died within the first month of life. At necropsy, we observed a broad hepatization of lung lobes possibly induced by infectious pneumonia. The management of this lethal recessive allele (frequency of 0.06) through reasoned mating in the Lacaune sheep selection schemes could reduce lamb mortality by 2%.
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Affiliation(s)
- Maxime Ben Braiek
- GenPhySE, Université de Toulouse, Institut National de Recherche Pour L’agriculture, L’alimentation et l’environnement (INRAE), Ecole Nationale Vétérinaire de Toulouse (ENVT), 31326 Castanet-Tolosan, France; (M.B.B.); (C.M.-R.); (A.B.); (F.D.); (F.P.-P.); (J.S.); (N.T.); (F.W.)
| | - Carole Moreno-Romieux
- GenPhySE, Université de Toulouse, Institut National de Recherche Pour L’agriculture, L’alimentation et l’environnement (INRAE), Ecole Nationale Vétérinaire de Toulouse (ENVT), 31326 Castanet-Tolosan, France; (M.B.B.); (C.M.-R.); (A.B.); (F.D.); (F.P.-P.); (J.S.); (N.T.); (F.W.)
| | - Charlotte Allain
- UE Domaine de La Fage, Institut National de Recherche Pour L’agriculture, L’alimentation et L’environnement (INRAE), 12250 Saint-Jean et Saint-Paul, France; (C.A.); (D.P.)
| | - Philippe Bardou
- Sigenae, Institut National de Recherche Pour L’agriculture, L’alimentation et L’environnement (INRAE), 31326 Castanet-Tolosan, France;
| | - Arnaud Bordes
- GenPhySE, Université de Toulouse, Institut National de Recherche Pour L’agriculture, L’alimentation et l’environnement (INRAE), Ecole Nationale Vétérinaire de Toulouse (ENVT), 31326 Castanet-Tolosan, France; (M.B.B.); (C.M.-R.); (A.B.); (F.D.); (F.P.-P.); (J.S.); (N.T.); (F.W.)
| | - Frédéric Debat
- GenPhySE, Université de Toulouse, Institut National de Recherche Pour L’agriculture, L’alimentation et l’environnement (INRAE), Ecole Nationale Vétérinaire de Toulouse (ENVT), 31326 Castanet-Tolosan, France; (M.B.B.); (C.M.-R.); (A.B.); (F.D.); (F.P.-P.); (J.S.); (N.T.); (F.W.)
| | - Cord Drögemüller
- Institute of Genetics, Vetsuisse Faculty, University of Bern, 3012 Bern, Switzerland;
| | - Florence Plisson-Petit
- GenPhySE, Université de Toulouse, Institut National de Recherche Pour L’agriculture, L’alimentation et l’environnement (INRAE), Ecole Nationale Vétérinaire de Toulouse (ENVT), 31326 Castanet-Tolosan, France; (M.B.B.); (C.M.-R.); (A.B.); (F.D.); (F.P.-P.); (J.S.); (N.T.); (F.W.)
| | - David Portes
- UE Domaine de La Fage, Institut National de Recherche Pour L’agriculture, L’alimentation et L’environnement (INRAE), 12250 Saint-Jean et Saint-Paul, France; (C.A.); (D.P.)
| | - Julien Sarry
- GenPhySE, Université de Toulouse, Institut National de Recherche Pour L’agriculture, L’alimentation et l’environnement (INRAE), Ecole Nationale Vétérinaire de Toulouse (ENVT), 31326 Castanet-Tolosan, France; (M.B.B.); (C.M.-R.); (A.B.); (F.D.); (F.P.-P.); (J.S.); (N.T.); (F.W.)
| | - Némuel Tadi
- GenPhySE, Université de Toulouse, Institut National de Recherche Pour L’agriculture, L’alimentation et l’environnement (INRAE), Ecole Nationale Vétérinaire de Toulouse (ENVT), 31326 Castanet-Tolosan, France; (M.B.B.); (C.M.-R.); (A.B.); (F.D.); (F.P.-P.); (J.S.); (N.T.); (F.W.)
| | - Florent Woloszyn
- GenPhySE, Université de Toulouse, Institut National de Recherche Pour L’agriculture, L’alimentation et l’environnement (INRAE), Ecole Nationale Vétérinaire de Toulouse (ENVT), 31326 Castanet-Tolosan, France; (M.B.B.); (C.M.-R.); (A.B.); (F.D.); (F.P.-P.); (J.S.); (N.T.); (F.W.)
| | - Stéphane Fabre
- GenPhySE, Université de Toulouse, Institut National de Recherche Pour L’agriculture, L’alimentation et l’environnement (INRAE), Ecole Nationale Vétérinaire de Toulouse (ENVT), 31326 Castanet-Tolosan, France; (M.B.B.); (C.M.-R.); (A.B.); (F.D.); (F.P.-P.); (J.S.); (N.T.); (F.W.)
- Correspondence:
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34
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McRae KM, Rowe SJ, Johnson PL, Baird HJ, Cullen NG, Bixley MJ, Plowman JE, Deb-Choudhury S, Brauning R, Amyes NC, Dodds KG, Newman SAN, McEwan JC, Clarke SM. Genomic Tools for the Identification of Loci Associated with Facial Eczema in New Zealand Sheep. Genes (Basel) 2021; 12:genes12101560. [PMID: 34680955 PMCID: PMC8536008 DOI: 10.3390/genes12101560] [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: 09/10/2021] [Revised: 09/28/2021] [Accepted: 09/29/2021] [Indexed: 11/16/2022] Open
Abstract
Facial eczema (FE) is a significant metabolic disease that affects New Zealand ruminants. Ingestion of the mycotoxin sporidesmin leads to liver and bile duct damage, which can result in photosensitisation, reduced productivity and death. Strategies used to manage the incidence and severity of the disease include breeding. In sheep, there is considerable genetic variation in the response to FE. A commercial testing program is available for ram breeders who aim to increase tolerance, determined by the concentration of the serum enzyme, gamma-glutamyltransferase 21 days after a measured sporidesmin challenge (GGT21). Genome-wide association studies were carried out to determine regions of the genome associated with GGT21. Two regions on chromosomes 15 and 24 are reported, which explain 5% and 1% of the phenotypic variance in the response to FE, respectively. The region on chromosome 15 contains the β-globin locus. Of the significant SNPs in the region, one is a missense variant within the haemoglobin subunit β (HBB) gene. Mass spectrometry of haemoglobin from animals with differing genotypes at this locus indicated that genotypes are associated with different forms of adult β-globin. Haemoglobin haplotypes have previously been associated with variation in several health-related traits in sheep and warrant further investigation regarding their role in tolerance to FE in sheep. We show a strategic approach to the identification of regions of importance for commercial breeding programs with a combination of discovery, statistical and biological validation. This study highlights the power of using increased density genotyping for the identification of influential genomic regions, combined with subsequent inclusion on lower density genotyping platforms.
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Affiliation(s)
- Kathryn M. McRae
- AgResearch Limited, Invermay Agricultural Centre, Puddle Alley, Mosgiel, Private Bag 50034, New Zealand; (S.J.R.); (P.L.J.); (H.J.B.); (M.J.B.); (R.B.); (K.G.D.); (J.C.M.); (S.M.C.)
- Correspondence:
| | - Suzanne J. Rowe
- AgResearch Limited, Invermay Agricultural Centre, Puddle Alley, Mosgiel, Private Bag 50034, New Zealand; (S.J.R.); (P.L.J.); (H.J.B.); (M.J.B.); (R.B.); (K.G.D.); (J.C.M.); (S.M.C.)
| | - Patricia L. Johnson
- AgResearch Limited, Invermay Agricultural Centre, Puddle Alley, Mosgiel, Private Bag 50034, New Zealand; (S.J.R.); (P.L.J.); (H.J.B.); (M.J.B.); (R.B.); (K.G.D.); (J.C.M.); (S.M.C.)
| | - Hayley J. Baird
- AgResearch Limited, Invermay Agricultural Centre, Puddle Alley, Mosgiel, Private Bag 50034, New Zealand; (S.J.R.); (P.L.J.); (H.J.B.); (M.J.B.); (R.B.); (K.G.D.); (J.C.M.); (S.M.C.)
| | - Neil G. Cullen
- AgResearch Limited Ruakura Agricultural Centre, Bisley Road, Hamilton 3214, New Zealand; (N.G.C.); (N.C.A.)
| | - Matthew J. Bixley
- AgResearch Limited, Invermay Agricultural Centre, Puddle Alley, Mosgiel, Private Bag 50034, New Zealand; (S.J.R.); (P.L.J.); (H.J.B.); (M.J.B.); (R.B.); (K.G.D.); (J.C.M.); (S.M.C.)
| | - Jeffrey E. Plowman
- AgResearch Limited, Lincoln Research Centre, Springs Road, Lincoln, Private Bag 4749, New Zealand; (J.E.P.); (S.D.-C.); (S.-A.N.N.)
| | - Santanu Deb-Choudhury
- AgResearch Limited, Lincoln Research Centre, Springs Road, Lincoln, Private Bag 4749, New Zealand; (J.E.P.); (S.D.-C.); (S.-A.N.N.)
| | - Rudiger Brauning
- AgResearch Limited, Invermay Agricultural Centre, Puddle Alley, Mosgiel, Private Bag 50034, New Zealand; (S.J.R.); (P.L.J.); (H.J.B.); (M.J.B.); (R.B.); (K.G.D.); (J.C.M.); (S.M.C.)
| | - Neville C. Amyes
- AgResearch Limited Ruakura Agricultural Centre, Bisley Road, Hamilton 3214, New Zealand; (N.G.C.); (N.C.A.)
| | - Ken G. Dodds
- AgResearch Limited, Invermay Agricultural Centre, Puddle Alley, Mosgiel, Private Bag 50034, New Zealand; (S.J.R.); (P.L.J.); (H.J.B.); (M.J.B.); (R.B.); (K.G.D.); (J.C.M.); (S.M.C.)
| | - Sheryl-Anne N. Newman
- AgResearch Limited, Lincoln Research Centre, Springs Road, Lincoln, Private Bag 4749, New Zealand; (J.E.P.); (S.D.-C.); (S.-A.N.N.)
| | - John C. McEwan
- AgResearch Limited, Invermay Agricultural Centre, Puddle Alley, Mosgiel, Private Bag 50034, New Zealand; (S.J.R.); (P.L.J.); (H.J.B.); (M.J.B.); (R.B.); (K.G.D.); (J.C.M.); (S.M.C.)
| | - Shannon M. Clarke
- AgResearch Limited, Invermay Agricultural Centre, Puddle Alley, Mosgiel, Private Bag 50034, New Zealand; (S.J.R.); (P.L.J.); (H.J.B.); (M.J.B.); (R.B.); (K.G.D.); (J.C.M.); (S.M.C.)
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35
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Zhao B, Luo H, He J, Huang X, Chen S, Fu X, Zeng W, Tian Y, Liu S, Li CJ, Liu GE, Fang L, Zhang S, Tian K. Comprehensive transcriptome and methylome analysis delineates the biological basis of hair follicle development and wool-related traits in Merino sheep. BMC Biol 2021; 19:197. [PMID: 34503498 PMCID: PMC8427949 DOI: 10.1186/s12915-021-01127-9] [Citation(s) in RCA: 32] [Impact Index Per Article: 10.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2021] [Accepted: 08/18/2021] [Indexed: 12/13/2022] Open
Abstract
Background Characterization of the molecular mechanisms underlying hair follicle development is of paramount importance in the genetic improvement of wool-related traits in sheep and skin-related traits in humans. The Merino is the most important breed of fine-wooled sheep in the world. In this study, we systematically investigated the complexity of sheep hair follicle development by integrating transcriptome and methylome datasets from Merino sheep skin. Results We analysed 72 sequence datasets, including DNA methylome and the whole transcriptome of four gene types, i.e. protein-coding genes (PCGs), lncRNAs, circRNAs, and miRNAs, across four embryonic days (E65, E85, E105, and E135) and two postnatal days (P7 and P30) from the skin tissue of 18 Merino sheep. We revealed distinct expression profiles of these four gene types across six hair follicle developmental stages, and demonstrated their complex interactions with DNA methylation. PCGs with stage-specific expression or regulated by stage-specific lncRNAs, circRNAs, and miRNAs were significantly enriched in epithelial differentiation and hair follicle morphogenesis. Regulatory network and gene co-expression analyses identified key transcripts controlling hair follicle development. We further predicted transcriptional factors (e.g. KLF4, LEF1, HOXC13, RBPJ, VDR, RARA, and STAT3) with stage-specific involvement in hair follicle morphogenesis. Through integrating these stage-specific genomic features with results from genome-wide association studies (GWAS) of five wool-related traits in 7135 Merino sheep, we detected developmental stages and genes that were relevant with wool-related traits in sheep. For instance, genes that were specifically upregulated at E105 were significantly associated with most of wool-related traits. A phenome-wide association study (PheWAS) demonstrated that candidate genes of wool-related traits (e.g. SPHK1, GHR, PPP1R27, CSRP2, EEF1A2, and PTPN1) in sheep were also significantly associated with dermatological, metabolic, and immune traits in humans. Conclusions Our study provides novel insights into the molecular basis of hair follicle morphogenesis and will serve as a foundation to improve breeding for wool traits in sheep. It also indicates the importance of studying gene expression in the normal development of organs in understanding the genetic architecture of economically important traits in livestock. The datasets generated here are useful resources for functionally annotating the sheep genome, and for elucidating early skin development in mammals, including humans. Supplementary Information The online version contains supplementary material available at 10.1186/s12915-021-01127-9.
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Affiliation(s)
- Bingru Zhao
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding, and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Hanpeng Luo
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding, and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Junmin He
- Key Laboratory of Genetics Breeding and Reproduction of the Fine Wool Sheep & Cashmere Goat in Xinjiang, Institute of Animal Science, Xinjiang Academy of Animal Sciences, Urumqi, China
| | - Xixia Huang
- College of Animal Science, Xinjiang Agricultural University, Urumqi, China
| | - Siqian Chen
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding, and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xuefeng Fu
- Key Laboratory of Genetics Breeding and Reproduction of the Fine Wool Sheep & Cashmere Goat in Xinjiang, Institute of Animal Science, Xinjiang Academy of Animal Sciences, Urumqi, China
| | - Weidan Zeng
- College of Animal Science, Xinjiang Agricultural University, Urumqi, China
| | - Yuezhen Tian
- Key Laboratory of Genetics Breeding and Reproduction of the Fine Wool Sheep & Cashmere Goat in Xinjiang, Institute of Animal Science, Xinjiang Academy of Animal Sciences, Urumqi, China
| | - Shuli Liu
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding, and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Cong-Jun Li
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, Agricultural Research Service, USDA, Beltsville, Maryland, USA
| | - George E Liu
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, Agricultural Research Service, USDA, Beltsville, Maryland, USA
| | - Lingzhao Fang
- MRC Human Genetics Unit at the Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK.
| | - Shengli Zhang
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding, and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China.
| | - Kechuan Tian
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China.
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Nosková A, Hiltpold M, Janett F, Echtermann T, Fang ZH, Sidler X, Selige C, Hofer A, Neuenschwander S, Pausch H. Infertility due to defective sperm flagella caused by an intronic deletion in DNAH17 that perturbs splicing. Genetics 2021; 217:6041611. [PMID: 33724408 DOI: 10.1093/genetics/iyaa033] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2020] [Accepted: 12/08/2020] [Indexed: 12/30/2022] Open
Abstract
Artificial insemination in pig (Sus scrofa domesticus) breeding involves the evaluation of the semen quality of breeding boars. Ejaculates that fulfill predefined quality requirements are processed, diluted and used for inseminations. Within short time, eight Swiss Large White boars producing immotile sperm that had multiple morphological abnormalities of the sperm flagella were noticed at a semen collection center. The eight boars were inbred on a common ancestor suggesting that the novel sperm flagella defect is a recessive trait. Transmission electron microscopy cross-sections revealed that the immotile sperm had disorganized flagellar axonemes. Haplotype-based association testing involving microarray-derived genotypes at 41,094 SNPs of six affected and 100 fertile boars yielded strong association (P = 4.22 × 10-15) at chromosome 12. Autozygosity mapping enabled us to pinpoint the causal mutation on a 1.11 Mb haplotype located between 3,473,632 and 4,587,759 bp. The haplotype carries an intronic 13-bp deletion (Chr12:3,556,401-3,556,414 bp) that is compatible with recessive inheritance. The 13-bp deletion excises the polypyrimidine tract upstream exon 56 of DNAH17 (XM_021066525.1: c.8510-17_8510-5del) encoding dynein axonemal heavy chain 17. Transcriptome analysis of the testis of two affected boars revealed that the loss of the polypyrimidine tract causes exon skipping which results in the in-frame loss of 89 amino acids from DNAH17. Disruption of DNAH17 impairs the assembly of the flagellar axoneme and manifests in multiple morphological abnormalities of the sperm flagella. Direct gene testing may now be implemented to monitor the defective allele in the Swiss Large White population and prevent the frequent manifestation of a sterilizing sperm tail disorder in breeding boars.
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Affiliation(s)
- Adéla Nosková
- Animal Genomics, Institute of Agricultural Sciences, ETH Zürich, 8315 Lindau, Switzerland
| | - Maya Hiltpold
- Animal Genomics, Institute of Agricultural Sciences, ETH Zürich, 8315 Lindau, Switzerland
| | - Fredi Janett
- Clinic of Reproductive Medicine, Vetsuisse Faculty, University of Zurich, 8057 Zurich, Switzerland
| | - Thomas Echtermann
- Division of Swine Medicine, Vetsuisse Faculty, University of Zurich, 8057 Zurich, Switzerland
| | - Zih-Hua Fang
- Animal Genomics, Institute of Agricultural Sciences, ETH Zürich, 8315 Lindau, Switzerland
| | - Xaver Sidler
- Division of Swine Medicine, Vetsuisse Faculty, University of Zurich, 8057 Zurich, Switzerland
| | | | | | - Stefan Neuenschwander
- Animal Genetics, Institute of Agricultural Science, ETH Zürich, 8092 Zürich, Switzerland
| | - Hubert Pausch
- Animal Genomics, Institute of Agricultural Sciences, ETH Zürich, 8315 Lindau, Switzerland
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37
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Wang Y, Miao X, Zhao Z, Wang Y, Li S, Wang C. Transcriptome Atlas of 16 Donkey Tissues. Front Genet 2021; 12:682734. [PMID: 34434218 PMCID: PMC8381363 DOI: 10.3389/fgene.2021.682734] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 07/19/2021] [Indexed: 12/15/2022] Open
Abstract
Donkeys (Equus asinus) are important livestock with great economic value in meat, skin, and milk production. However, a lack of knowledge of the transcriptome landscape across a wide range of donkey tissues limits genetic selective breeding and conservation. Here we used transcriptomics to describe the transcriptome landscape, classify the tissue-specific gene expression across all primary donkey tissues, and present supplementary analyses on the protein level of additional donkey milk samples. Overall, 16,013 protein-coding genes and 21,983 transcripts were mapped to the reference genome, including 6,778 ubiquitously expressed genes and 2,601 tissue-enriched genes. Functional analysis revealed that the function of the tissue-enriched genes was highly tissue specific. Tissue-elevated genes that could be associated with unique phenotypes in donkey were analyzed. The results showed that, compared with those in human and other livestock, the lysozyme gene in donkey breast was specifically and highly expressed. The calcium-binding lysozyme, encoded by the lysozyme gene, was also detected in high amounts in donkey milk. Given those intact lysozyme genes that predict potentially functional calcium-binding lysozyme found in only a few species (e.g., donkey and horse), the high expression of the lysozyme gene in donkey breast may contribute to the high lysozyme content in donkey milk. Furthermore, 71% of the proteins in donkey milk overlapped with human milk protein, higher than the overlapping rates of bovine, sheep, and swine with humans. The donkey transcriptomic resource contributes to the available genomic resources to interpret the molecular mechanisms underlying phenotype traits.
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Affiliation(s)
- Yinan Wang
- Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Liaocheng University, Liaocheng, China.,College of Forensic Medicine, Xi'an Jiaotong University, Xi'an, China
| | - Xinyao Miao
- College of Forensic Medicine, Xi'an Jiaotong University, Xi'an, China.,Department of Computer Science, City University of Hong Kong, Hong Kong, China
| | - Zicheng Zhao
- Shenzhen Byoryn Technology Co., Ltd, Shenzhen, China
| | - Yonghui Wang
- Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Liaocheng University, Liaocheng, China
| | - Shuaicheng Li
- Department of Computer Science, City University of Hong Kong, Hong Kong, China
| | - Changfa Wang
- Liaocheng Research Institute of Donkey High-Efficiency Breeding and Ecological Feeding, Liaocheng University, Liaocheng, China
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38
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Lévesque JP, Summers KM, Millard SM, Bisht K, Winkler IG, Pettit AR. Role of macrophages and phagocytes in orchestrating normal and pathologic hematopoietic niches. Exp Hematol 2021; 100:12-31.e1. [PMID: 34298116 DOI: 10.1016/j.exphem.2021.07.001] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2021] [Revised: 07/02/2021] [Accepted: 07/06/2021] [Indexed: 12/13/2022]
Abstract
The bone marrow (BM) contains a mosaic of niches specialized in supporting different maturity stages of hematopoietic stem and progenitor cells such as hematopoietic stem cells and myeloid, lymphoid, and erythroid progenitors. Recent advances in BM imaging and conditional gene knockout mice have revealed that niches are a complex network of cells of mesenchymal, endothelial, neuronal, and hematopoietic origins, together with local physicochemical parameters. Within these complex structures, phagocytes, such as neutrophils, macrophages, and dendritic cells, all of which are of hematopoietic origin, have been found to be important in regulating several niches in the BM, including hematopoietic stem cell niches, erythropoietic niches, and niches involved in endosteal bone formation. There is also increasing evidence that these macrophages have an important role in adapting hematopoiesis, erythropoiesis, and bone formation in response to inflammatory stressors and play a key part in maintaining the integrity and function of these. Likewise, there is also accumulating evidence that subsets of monocytes, macrophages, and other phagocytes contribute to the progression and response to treatment of several lymphoid malignancies such as multiple myeloma, Hodgkin lymphoma, and non-Hodgkin lymphoma, as well as lymphoblastic leukemia, and may also play a role in myelodysplastic syndrome and myeloproliferative neoplasms associated with Noonan syndrome and aplastic anemia. In this review, the potential functions of macrophages and other phagocytes in normal and pathologic niches are discussed, as are the challenges in studying BM and other tissue-resident macrophages at the molecular level.
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Affiliation(s)
- Jean-Pierre Lévesque
- Mater Research Institute, University of Queensland, Woolloongabba, QLD, Australia.
| | - Kim M Summers
- Mater Research Institute, University of Queensland, Woolloongabba, QLD, Australia
| | - Susan M Millard
- Mater Research Institute, University of Queensland, Woolloongabba, QLD, Australia
| | - Kavita Bisht
- Mater Research Institute, University of Queensland, Woolloongabba, QLD, Australia
| | - Ingrid G Winkler
- Mater Research Institute, University of Queensland, Woolloongabba, QLD, Australia
| | - Allison R Pettit
- Mater Research Institute, University of Queensland, Woolloongabba, QLD, Australia
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39
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Zhao B, Luo H, Huang X, Wei C, Di J, Tian Y, Fu X, Li B, Liu GE, Fang L, Zhang S, Tian K. Integration of a single-step genome-wide association study with a multi-tissue transcriptome analysis provides novel insights into the genetic basis of wool and weight traits in sheep. Genet Sel Evol 2021; 53:56. [PMID: 34193030 PMCID: PMC8247193 DOI: 10.1186/s12711-021-00649-8] [Citation(s) in RCA: 14] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/13/2021] [Accepted: 06/22/2021] [Indexed: 12/16/2022] Open
Abstract
BACKGROUND Genetic improvement of wool and growth traits is a major goal in the sheep industry, but their underlying genetic architecture remains elusive. To improve our understanding of these mechanisms, we conducted a weighted single-step genome-wide association study (WssGWAS) and then integrated the results with large-scale transcriptome data for five wool traits and one growth trait in Merino sheep: mean fibre diameter (MFD), coefficient of variation of the fibre diameter (CVFD), crimp number (CN), mean staple length (MSL), greasy fleece weight (GFW), and live weight (LW). RESULTS Our dataset comprised 7135 individuals with phenotype data, among which 1217 had high-density (HD) genotype data (n = 372,534). The genotypes of 707 of these animals were imputed from the Illumina Ovine single nucleotide polymorphism (SNP) 54 BeadChip to the HD Array. The heritability of these traits ranged from 0.05 (CVFD) to 0.36 (MFD), and between-trait genetic correlations ranged from - 0.44 (CN vs. LW) to 0.77 (GFW vs. LW). By integrating the GWAS signals with RNA-seq data from 500 samples (representing 87 tissue types from 16 animals), we detected tissues that were relevant to each of the six traits, e.g. liver, muscle and the gastrointestinal (GI) tract were the most relevant tissues for LW, and leukocytes and macrophages were the most relevant cells for CN. For the six traits, 54 quantitative trait loci (QTL) were identified covering 81 candidate genes on 21 ovine autosomes. Multiple candidate genes showed strong tissue-specific expression, e.g. BNC1 (associated with MFD) and CHRNB1 (LW) were specifically expressed in skin and muscle, respectively. By conducting phenome-wide association studies (PheWAS) in humans, we found that orthologues of several of these candidate genes were significantly (FDR < 0.05) associated with similar traits in humans, e.g. BNC1 was significantly associated with MFD in sheep and with hair colour in humans, and CHRNB1 was significantly associated with LW in sheep and with body mass index in humans. CONCLUSIONS Our findings provide novel insights into the biological and genetic mechanisms underlying wool and growth traits, and thus will contribute to the genetic improvement and gene mapping of complex traits in sheep.
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Affiliation(s)
- Bingru Zhao
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding, and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Hanpeng Luo
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding, and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xixia Huang
- College of Animal Science, Xinjiang Agricultural University, Urumqi, China
| | - Chen Wei
- College of Animal Science, Xinjiang Agricultural University, Urumqi, China
| | - Jiang Di
- Key Laboratory of Genetics Breeding and Reproduction of the Fine Wool Sheep & Cashmere Goat in Xinjiang, Institute of Animal Science, Xinjiang Academy of Animal Sciences, Urumqi, China
| | - Yuezhen Tian
- Key Laboratory of Genetics Breeding and Reproduction of the Fine Wool Sheep & Cashmere Goat in Xinjiang, Institute of Animal Science, Xinjiang Academy of Animal Sciences, Urumqi, China
| | - Xuefeng Fu
- Key Laboratory of Genetics Breeding and Reproduction of the Fine Wool Sheep & Cashmere Goat in Xinjiang, Institute of Animal Science, Xinjiang Academy of Animal Sciences, Urumqi, China
| | - Bingjie Li
- Scotland's Rural College (SRUC), Roslin Institute Building, Midlothian, EH25 9RG, UK
| | - George E Liu
- Animal Genomics and Improvement Laboratory, Henry A. Wallace Beltsville Agricultural Research Center, Agricultural Research Service, Agricultural Research Service, USDA, Beltsville, MD, USA
| | - Lingzhao Fang
- MRC Human Genetics Unit at the Institute of Genetics and Cancer, University of Edinburgh, Edinburgh, UK.
| | - Shengli Zhang
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding, and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing, China.
| | - Kechuan Tian
- Institute of Animal Science and Veterinary Medicine, Shandong Academy of Agricultural Sciences, Jinan, China.
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40
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A DNA Regulatory Element Haplotype at Zinc Finger Genes Is Associated with Host Resilience to Small Ruminant Lentivirus in Two Sheep Populations. Animals (Basel) 2021; 11:ani11071907. [PMID: 34206933 PMCID: PMC8300134 DOI: 10.3390/ani11071907] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/28/2021] [Revised: 06/22/2021] [Accepted: 06/22/2021] [Indexed: 12/13/2022] Open
Abstract
Small ruminant lentivirus (SRLV) causes Maedi-Visna or Ovine Progressive Pneumonia in sheep and creates insidious livestock production losses. This retrovirus is closely related to human immunodeficiency virus and currently has no vaccines or cure. Genetic marker assisted selection for sheep disease resiliency presents an attractive management solution. Previously, we identified a region containing a cluster of zinc finger genes that had association with ovine SRLV proviral concentration. Trait-association analysis validated a small insertion/deletion variant near ZNF389 (rs397514112) in multiple sheep breeds. In the current study, 543 sheep from two distinct populations were genotyped at 34 additional variants for fine mapping of the regulatory elements within this locus. Variants were selected based on ChIP-seq annotation data from sheep alveolar macrophages that defined active cis-regulatory elements predicted to influence zinc finger gene expression. We present a haplotype block of variants within regulatory elements that have improved associations and larger effect sizes (up to 4.7-fold genotypic difference in proviral concentration) than the previously validated ZNF389 deletion marker. Hypotheses for the underlying causal mutation or mutations are presented based on changes to in silico transcription factor binding sites. These variants offer alternative markers for selective breeding and are targets for future functional mutation assays.
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41
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Chitneedi PK, Weikard R, Arranz JJ, Martínez-Valladares M, Kuehn C, Gutiérrez-Gil B. Identification of Regulatory Functions of LncRNAs Associated With T. circumcincta Infection in Adult Sheep. Front Genet 2021; 12:685341. [PMID: 34194481 PMCID: PMC8236958 DOI: 10.3389/fgene.2021.685341] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 05/20/2021] [Indexed: 12/13/2022] Open
Abstract
Several recent studies have demonstrated the role of long non-coding RNAs (lncRNAs) in regulating the defense mechanism against parasite infections, but no studies are available that investigated their relevance for immune response to nematode infection in sheep. Thus, the aim of the current study was to (i) detect putative lncRNAs that are expressed in the abomasal lymph node of adult sheep after an experimental infection with the gastrointestinal nematode (GIN) Teladorsagia circumcincta and (ii) to elucidate their potential functional role associated with the differential host immune response. We hypothesized that putative lncRNAs differentially expressed (DE) between samples from animals that differ in resistance to infection may play a significant regulatory role in response to nematode infection in adult sheep. To obtain further support for our hypothesis, we performed co-expression and functional gene enrichment analyses with the differentially expressed lncRNAs (DE lncRNAs). In a conservative approach, we included for this predictive analysis only those lncRNAs that are confirmed and supported by documentation of expression in gastrointestinal tissues in the current sheep gene atlas. We identified 9,105 putative lncRNA transcripts corresponding to 7,124 gene loci. Of these, 457 were differentially expressed lncRNA loci (DELs) with 683 lncRNA transcripts. Based on a gene co-expression analysis via weighted gene co-expression network analysis, 12 gene network modules (GNMs) were found significantly correlated with at least one of 10 selected target DE lncRNAs. Based on the principle of “guilt-by-association,” the DE genes from each of the three most significantly correlated GNMs were subjected to a gene enrichment analysis. The significant pathways associated with DE lncRNAs included ERK5 Signaling, SAPK/JNK Signaling, RhoGDI Signaling, EIF2 Signaling, Regulation of eIF4 and p70S6K Signaling and Oxidative Phosphorylation pathways. They belong to signaling pathway categories like Cellular Growth, Proliferation and Development, Cellular Stress and Injury, Intracellular and Second Messenger Signaling and Apoptosis. Overall, this lncRNA study conducted in adult sheep after GIN infection provided first insights into the potential functional role of lncRNAs in the differential host response to nematode infection.
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Affiliation(s)
| | - Rosemarie Weikard
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany
| | - Juan J Arranz
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, León, Spain
| | - María Martínez-Valladares
- Departamento de Sanidad Animal, Facultad de Veterinaria, Universidad de León, León, Spain.,Instituto de Ganadería de Montaña, CSIC-Universidad de León, León, Spain
| | - Christa Kuehn
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany.,Faculty of Agricultural and Environmental Sciences, University of Rostock, Rostock, Germany
| | - Beatriz Gutiérrez-Gil
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, León, Spain
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Davenport KM, Massa AT, Bhattarai S, McKay SD, Mousel MR, Herndon MK, White SN, Cockett NE, Smith TPL, Murdoch BM. Characterizing Genetic Regulatory Elements in Ovine Tissues. Front Genet 2021; 12:628849. [PMID: 34093640 PMCID: PMC8173140 DOI: 10.3389/fgene.2021.628849] [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: 11/13/2020] [Accepted: 03/25/2021] [Indexed: 12/11/2022] Open
Abstract
The Ovine Functional Annotation of Animal Genomes (FAANG) project, part of the broader livestock species FAANG initiative, aims to identify and characterize gene regulatory elements in domestic sheep. Regulatory element annotation is essential for identifying genetic variants that affect health and production traits in this important agricultural species, as greater than 90% of variants underlying genetic effects are estimated to lie outside of transcribed regions. Histone modifications that distinguish active or repressed chromatin states, CTCF binding, and DNA methylation were used to characterize regulatory elements in liver, spleen, and cerebellum tissues from four yearling sheep. Chromatin immunoprecipitation with sequencing (ChIP-seq) was performed for H3K4me3, H3K27ac, H3K4me1, H3K27me3, and CTCF. Nine chromatin states including active promoters, active enhancers, poised enhancers, repressed enhancers, and insulators were characterized in each tissue using ChromHMM. Whole-genome bisulfite sequencing (WGBS) was performed to determine the complement of whole-genome DNA methylation with the ChIP-seq data. Hypermethylated and hypomethylated regions were identified across tissues, and these locations were compared with chromatin states to better distinguish and validate regulatory elements in these tissues. Interestingly, chromatin states with the poised enhancer mark H3K4me1 in the spleen and cerebellum and CTCF in the liver displayed the greatest number of hypermethylated sites. Not surprisingly, active enhancers in the liver and spleen, and promoters in the cerebellum, displayed the greatest number of hypomethylated sites. Overall, chromatin states defined by histone marks and CTCF occupied approximately 22% of the genome in all three tissues. Furthermore, the liver and spleen displayed in common the greatest percent of active promoter (65%) and active enhancer (81%) states, and the liver and cerebellum displayed in common the greatest percent of poised enhancer (53%), repressed enhancer (68%), hypermethylated sites (75%), and hypomethylated sites (73%). In addition, both known and de novo CTCF-binding motifs were identified in all three tissues, with the highest number of unique motifs identified in the cerebellum. In summary, this study has identified the regulatory regions of genes in three tissues that play key roles in defining health and economically important traits and has set the precedent for the characterization of regulatory elements in ovine tissues using the Rambouillet reference genome.
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Affiliation(s)
- Kimberly M. Davenport
- Department of Animal, Veterinary, and Food Science, University of Idaho, Moscow, ID, United States
| | - Alisha T. Massa
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, WA, United States
| | | | | | - Michelle R. Mousel
- USDA, ARS, Animal Disease Research Unit, Pullman, WA, United States
- Paul G. Allen School for Global Animal Health, Washington State University, Pullman, WA, United States
| | - Maria K. Herndon
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, WA, United States
| | - Stephen N. White
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, WA, United States
- USDA, ARS, Animal Disease Research Unit, Pullman, WA, United States
- Center for Reproductive Biology, Washington State University, Pullman, WA, United States
| | | | - Timothy P. L. Smith
- USDA, ARS, U.S. Meat Animal Research Center (USMARC), Clay Center, NE, United States
| | - Brenda M. Murdoch
- Department of Animal, Veterinary, and Food Science, University of Idaho, Moscow, ID, United States
- Center for Reproductive Biology, Washington State University, Pullman, WA, United States
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Robic A, Cerutti C, Kühn C, Faraut T. Comparative Analysis of the Circular Transcriptome in Muscle, Liver, and Testis in Three Livestock Species. Front Genet 2021; 12:665153. [PMID: 34040640 PMCID: PMC8141914 DOI: 10.3389/fgene.2021.665153] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/07/2021] [Accepted: 04/07/2021] [Indexed: 12/13/2022] Open
Abstract
Circular RNAs have been observed in a large number of species and tissues and are now recognized as a clear component of the transcriptome. Our study takes advantage of functional datasets produced within the FAANG consortium to investigate the pervasiveness of circular RNA transcription in farm animals. We describe here the circular transcriptional landscape in pig, sheep and bovine testicular, muscular and liver tissues using total 66 RNA-seq datasets. After an exhaustive detection of circular RNAs, we propose an annotation of exonic, intronic and sub-exonic circRNAs and comparative analyses of circRNA content to evaluate the variability between individuals, tissues and species. Despite technical bias due to the various origins of the datasets, we were able to characterize some features (i) (ruminant) liver contains more exonic circRNAs than muscle (ii) in testis, the number of exonic circRNAs seems associated with the sexual maturity of the animal. (iii) a particular class of circRNAs, sub-exonic circRNAs, are produced by a large variety of multi-exonic genes (protein-coding genes, long non-coding RNAs and pseudogenes) and mono-exonic genes (protein-coding genes from mitochondrial genome and small non-coding genes). Moreover, for multi-exonic genes there seems to be a relationship between the sub-exonic circRNAs transcription level and the linear transcription level. Finally, sub-exonic circRNAs produced by mono-exonic genes (mitochondrial protein-coding genes, ribozyme, and sno) exhibit a particular behavior. Caution has to be taken regarding the interpretation of the unannotated circRNA proportion in a given tissue/species: clusters of circRNAs without annotation were characterized in genomic regions with annotation and/or assembly problems of the respective animal genomes. This study highlights the importance of improving genome annotation to better consider candidate circRNAs and to better understand the circular transcriptome. Furthermore, it emphasizes the need for considering the relative “weight” of circRNAs/parent genes for comparative analyses of several circular transcriptomes. Although there are points of agreement in the circular transcriptome of the same tissue in two species, it will be not possible to do without the characterization of it in both species.
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Affiliation(s)
- Annie Robic
- INRAE, ENVT, GenPhySE, Université de Toulouse, Castanet-Tolosan, France
| | - Chloé Cerutti
- INRAE, ENVT, GenPhySE, Université de Toulouse, Castanet-Tolosan, France
| | - Christa Kühn
- Institute Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Dummerstorf, Germany.,Faculty of Agricultural and Environmental Sciences, University of Rostock, Rostock, Germany
| | - Thomas Faraut
- INRAE, ENVT, GenPhySE, Université de Toulouse, Castanet-Tolosan, France
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44
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Hume DA, Caruso M, Keshvari S, Patkar OL, Sehgal A, Bush SJ, Summers KM, Pridans C, Irvine KM. The Mononuclear Phagocyte System of the Rat. THE JOURNAL OF IMMUNOLOGY 2021; 206:2251-2263. [PMID: 33965905 DOI: 10.4049/jimmunol.2100136] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/10/2021] [Accepted: 03/01/2021] [Indexed: 12/14/2022]
Abstract
The laboratory rat continues to be the model of choice for many studies of physiology, behavior, and complex human diseases. Cells of the mononuclear phagocyte system (MPS; monocytes, macrophages, and dendritic cells) are abundant residents in every tissue in the body and regulate postnatal development, homeostasis, and innate and acquired immunity. Recruitment and proliferation of MPS cells is an essential component of both initiation and resolution of inflammation. The large majority of current knowledge of MPS biology is derived from studies of inbred mice, but advances in technology and resources have eliminated many of the advantages of the mouse as a model. In this article, we review the tools available and the current state of knowledge of development, homeostasis, regulation, and diversity within the MPS of the rat.
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Affiliation(s)
- David A Hume
- Mater Research Institute-University of Queensland, Translational Research Institute, Brisbane, Queensland, Australia
| | - Melanie Caruso
- Mater Research Institute-University of Queensland, Translational Research Institute, Brisbane, Queensland, Australia
| | - Sahar Keshvari
- Mater Research Institute-University of Queensland, Translational Research Institute, Brisbane, Queensland, Australia
| | - Omkar L Patkar
- Mater Research Institute-University of Queensland, Translational Research Institute, Brisbane, Queensland, Australia
| | - Anuj Sehgal
- Mater Research Institute-University of Queensland, Translational Research Institute, Brisbane, Queensland, Australia
| | - Stephen J Bush
- Nuffield Department of Clinical Medicine, John Radcliffe Hospital, University of Oxford, Oxford, United Kingdom
| | - Kim M Summers
- Mater Research Institute-University of Queensland, Translational Research Institute, Brisbane, Queensland, Australia
| | - Clare Pridans
- Centre for Inflammation Research, University of Edinburgh, Edinburgh, United Kingdom.,Simons Initiative for the Developing Brain, Centre for Discovery Brain Sciences, University of Edinburgh, Edinburgh, United Kingdom
| | - Katharine M Irvine
- Mater Research Institute-University of Queensland, Translational Research Institute, Brisbane, Queensland, Australia
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45
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British Sheep Breeds as a Part of World Sheep Gene Pool Landscape: Looking into Genomic Applications. Animals (Basel) 2021; 11:ani11040994. [PMID: 33916207 PMCID: PMC8103502 DOI: 10.3390/ani11040994] [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: 03/16/2021] [Revised: 03/27/2021] [Accepted: 03/29/2021] [Indexed: 01/18/2023] Open
Abstract
Sheep farming has been an important sector of the UK's economy and rural life for many centuries. It is the favored source of wool, meat and milk products. In the era of exponential progress in genomic technologies, we can now address the questions of what is special about UK sheep breed genotypes and how they differ genetically form one another and from other countries. We can reflect how their natural history has been determined at the level of their genetic code and what traces have been left in their genomes because of selection for phenotypic traits. These include adaptability to certain environmental conditions and management, as well as resistance to disease. Application of these advancements in genetics and genomics to study sheep breeds of British domestic selection has begun and will continue in order to facilitate conservation solutions and production improvement.
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46
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Wiener P, Robert C, Ahbara A, Salavati M, Abebe A, Kebede A, Wragg D, Friedrich J, Vasoya D, Hume DA, Djikeng A, Watson M, Prendergast JGD, Hanotte O, Mwacharo JM, Clark EL. Whole-Genome Sequence Data Suggest Environmental Adaptation of Ethiopian Sheep Populations. Genome Biol Evol 2021; 13:evab014. [PMID: 33501931 PMCID: PMC7955157 DOI: 10.1093/gbe/evab014] [Citation(s) in RCA: 16] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/19/2021] [Indexed: 12/13/2022] Open
Abstract
Great progress has been made over recent years in the identification of selection signatures in the genomes of livestock species. This work has primarily been carried out in commercial breeds for which the dominant selection pressures are associated with artificial selection. As agriculture and food security are likely to be strongly affected by climate change, a better understanding of environment-imposed selection on agricultural species is warranted. Ethiopia is an ideal setting to investigate environmental adaptation in livestock due to its wide variation in geo-climatic characteristics and the extensive genetic and phenotypic variation of its livestock. Here, we identified over three million single nucleotide variants across 12 Ethiopian sheep populations and applied landscape genomics approaches to investigate the association between these variants and environmental variables. Our results suggest that environmental adaptation for precipitation-related variables is stronger than that related to altitude or temperature, consistent with large-scale meta-analyses of selection pressure across species. The set of genes showing association with environmental variables was enriched for genes highly expressed in human blood and nerve tissues. There was also evidence of enrichment for genes associated with high-altitude adaptation although no strong association was identified with hypoxia-inducible-factor (HIF) genes. One of the strongest altitude-related signals was for a collagen gene, consistent with previous studies of high-altitude adaptation. Several altitude-associated genes also showed evidence of adaptation with temperature, suggesting a relationship between responses to these environmental factors. These results provide a foundation to investigate further the effects of climatic variables on small ruminant populations.
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Affiliation(s)
- Pamela Wiener
- Roslin Institute, University of Edinburgh, Midlothian, United Kingdom
| | - Christelle Robert
- Roslin Institute, University of Edinburgh, Midlothian, United Kingdom
- Centre for Tropical Livestock Genetics and Health (CTLGH), Midlothian, United Kingdom
| | - Abulgasim Ahbara
- School of Life Sciences, University of Nottingham, United Kingdom
- Department of Zoology, Misurata University, Misurata, Libya
| | - Mazdak Salavati
- Roslin Institute, University of Edinburgh, Midlothian, United Kingdom
- Centre for Tropical Livestock Genetics and Health (CTLGH), Midlothian, United Kingdom
| | - Ayele Abebe
- Debre Berhan Research Centre, Debre Berhan, Ethiopia
| | - Adebabay Kebede
- Amhara Regional Agricultural Research Institute, Bahir Dar, Ethiopia
- LiveGene, International Livestock Research Institute, Addis Ababa, Ethiopia
| | - David Wragg
- Roslin Institute, University of Edinburgh, Midlothian, United Kingdom
- Centre for Tropical Livestock Genetics and Health (CTLGH), Midlothian, United Kingdom
| | - Juliane Friedrich
- Roslin Institute, University of Edinburgh, Midlothian, United Kingdom
| | - Deepali Vasoya
- Roslin Institute, University of Edinburgh, Midlothian, United Kingdom
| | - David A Hume
- Mater Research Institute-University of Queensland, Translational Research Institute, Brisbane, Australia
| | - Appolinaire Djikeng
- Roslin Institute, University of Edinburgh, Midlothian, United Kingdom
- Centre for Tropical Livestock Genetics and Health (CTLGH), Midlothian, United Kingdom
| | - Mick Watson
- Roslin Institute, University of Edinburgh, Midlothian, United Kingdom
- Centre for Tropical Livestock Genetics and Health (CTLGH), Midlothian, United Kingdom
| | - James G D Prendergast
- Roslin Institute, University of Edinburgh, Midlothian, United Kingdom
- Centre for Tropical Livestock Genetics and Health (CTLGH), Midlothian, United Kingdom
| | - Olivier Hanotte
- Centre for Tropical Livestock Genetics and Health (CTLGH), Midlothian, United Kingdom
- School of Life Sciences, University of Nottingham, United Kingdom
- LiveGene, International Livestock Research Institute, Addis Ababa, Ethiopia
| | - Joram M Mwacharo
- Centre for Tropical Livestock Genetics and Health (CTLGH), Midlothian, United Kingdom
- Animal and Veterinary Sciences Group, Scotland’s Rural College (SRUC), Midlothian, United Kingdom
- Small Ruminant Genomics, International Centre for Agricultural Research in the Dry Areas (ICARDA), Addis Ababa, Ethiopia
| | - Emily L Clark
- Roslin Institute, University of Edinburgh, Midlothian, United Kingdom
- Centre for Tropical Livestock Genetics and Health (CTLGH), Midlothian, United Kingdom
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47
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Yuan Z, Sunduimijid B, Xiang R, Behrendt R, Knight MI, Mason BA, Reich CM, Prowse-Wilkins C, Vander Jagt CJ, Chamberlain AJ, MacLeod IM, Li F, Yue X, Daetwyler HD. Expression quantitative trait loci in sheep liver and muscle contribute to variations in meat traits. Genet Sel Evol 2021; 53:8. [PMID: 33461502 PMCID: PMC7812657 DOI: 10.1186/s12711-021-00602-9] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 01/08/2021] [Indexed: 11/10/2022] Open
Abstract
Background Variants that regulate transcription, such as expression quantitative trait loci (eQTL), have shown enrichment in genome-wide association studies (GWAS) for mammalian complex traits. However, no study has reported eQTL in sheep, although it is an important agricultural species for which many GWAS of complex meat traits have been conducted. Using RNA sequence data produced from liver and muscle from 149 sheep and imputed whole-genome single nucleotide polymorphisms (SNPs), our aim was to dissect the genetic architecture of the transcriptome by associating sheep genotypes with three major molecular phenotypes including gene expression (geQTL), exon expression (eeQTL) and RNA splicing (sQTL). We also examined these three types of eQTL for their enrichment in GWAS of multi-meat traits and fatty acid profiles. Results Whereas a relatively small number of molecular phenotypes were significantly heritable (h2 > 0, P < 0.05), their mean heritability ranged from 0.67 to 0.73 for liver and from 0.71 to 0.77 for muscle. Association analysis between molecular phenotypes and SNPs within ± 1 Mb identified many significant cis-eQTL (false discovery rate, FDR < 0.01). The median distance between the eQTL and transcription start sites (TSS) ranged from 68 to 153 kb across the three eQTL types. The number of common variants between geQTL, eeQTL and sQTL within each tissue, and the number of common variants between liver and muscle within each eQTL type were all significantly (P < 0.05) larger than expected by chance. The identified eQTL were significantly (P < 0.05) enriched in GWAS hits associated with 56 carcass traits and fatty acid profiles. For example, several geQTL in muscle mapped to the FAM184B gene, hundreds of sQTL in liver and muscle mapped to the CAST gene, and hundreds of sQTL in liver mapped to the C6 gene. These three genes are associated with body composition or fatty acid profiles. Conclusions We detected a large number of significant eQTL and found that the overlap of variants between eQTL types and tissues was prevalent. Many eQTL were also QTL for meat traits. Our study fills a gap in the knowledge on the regulatory variants and their role in complex traits for the sheep model.
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Affiliation(s)
- Zehu Yuan
- State Key Laboratory of Grassland Agro-ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; Grassland Agriculture Engineering Center, Ministry of Education; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, People's Republic of China.,Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia.,Institutes of Agricultural Science and Technology Development (Joint International Research Laboratory of Agriculture & Agri-Product Safety), Yangzhou University, Yangzhou, 225000, People's Republic of China
| | - Bolormaa Sunduimijid
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
| | - Ruidong Xiang
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia.,Faculty of Veterinary & Agricultural Science, University of Melbourne, Parkville, VIC, 3010, Australia
| | - Ralph Behrendt
- Agriculture Victoria, Hamilton Centre, Hamilton, VIC, 3300, Australia
| | - Matthew I Knight
- Agriculture Victoria, Hamilton Centre, Hamilton, VIC, 3300, Australia
| | - Brett A Mason
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
| | - Coralie M Reich
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
| | - Claire Prowse-Wilkins
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
| | - Christy J Vander Jagt
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
| | - Amanda J Chamberlain
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
| | - Iona M MacLeod
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia
| | - Fadi Li
- State Key Laboratory of Grassland Agro-ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; Grassland Agriculture Engineering Center, Ministry of Education; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, People's Republic of China
| | - Xiangpeng Yue
- State Key Laboratory of Grassland Agro-ecosystems; Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs; Grassland Agriculture Engineering Center, Ministry of Education; College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, 730020, People's Republic of China.
| | - Hans D Daetwyler
- Agriculture Victoria, AgriBio, Centre for AgriBioscience, Bundoora, VIC, 3083, Australia. .,School of Applied Systems Biology, La Trobe University, Bundoora, VIC, 3083, Australia.
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48
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Massa AT, Mousel MR, Herndon MK, Herndon DR, Murdoch BM, White SN. Genome-Wide Histone Modifications and CTCF Enrichment Predict Gene Expression in Sheep Macrophages. Front Genet 2021; 11:612031. [PMID: 33488675 PMCID: PMC7817998 DOI: 10.3389/fgene.2020.612031] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Accepted: 11/30/2020] [Indexed: 12/14/2022] Open
Abstract
Alveolar macrophages function in innate and adaptive immunity, wound healing, and homeostasis in the lungs dependent on tissue-specific gene expression under epigenetic regulation. The functional diversity of tissue resident macrophages, despite their common myeloid lineage, highlights the need to study tissue-specific regulatory elements that control gene expression. Increasing evidence supports the hypothesis that subtle genetic changes alter sheep macrophage response to important production pathogens and zoonoses, for example, viruses like small ruminant lentiviruses and bacteria like Coxiella burnetii. Annotation of transcriptional regulatory elements will aid researchers in identifying genetic mutations of immunological consequence. Here we report the first genome-wide survey of regulatory elements in any sheep immune cell, utilizing alveolar macrophages. We assayed histone modifications and CTCF enrichment by chromatin immunoprecipitation with deep sequencing (ChIP-seq) in two sheep to determine cis-regulatory DNA elements and chromatin domain boundaries that control immunity-related gene expression. Histone modifications included H3K4me3 (denoting active promoters), H3K27ac (active enhancers), H3K4me1 (primed and distal enhancers), and H3K27me3 (broad silencers). In total, we identified 248,674 reproducible regulatory elements, which allowed assignment of putative biological function in macrophages to 12% of the sheep genome. Data exceeded the FAANG and ENCODE standards of 20 million and 45 million useable fragments for narrow and broad marks, respectively. Active elements showed consensus with RNA-seq data and were predictive of gene expression in alveolar macrophages from the publicly available Sheep Gene Expression Atlas. Silencer elements were not enriched for expressed genes, but rather for repressed developmental genes. CTCF enrichment enabled identification of 11,000 chromatin domains with mean size of 258 kb. To our knowledge, this is the first report to use immunoprecipitated CTCF to determine putative topological domains in sheep immune cells. Furthermore, these data will empower phenotype-associated mutation discovery since most causal variants are within regulatory elements.
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Affiliation(s)
- Alisha T Massa
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, WA, United States
| | - Michelle R Mousel
- Animal Disease Research Unit, Agricultural Research Service, United States Department of Agriculture, Pullman, WA, United States.,Paul G. Allen School for Global Animal Health, Washington State University, Pullman, WA, United States
| | - Maria K Herndon
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, WA, United States
| | - David R Herndon
- Animal Disease Research Unit, Agricultural Research Service, United States Department of Agriculture, Pullman, WA, United States
| | - Brenda M Murdoch
- Department of Animal and Veterinary Science, University of Idaho, Moscow, ID, United States.,Center for Reproductive Biology, Washington State University, Pullman, WA, United States
| | - Stephen N White
- Department of Veterinary Microbiology and Pathology, Washington State University, Pullman, WA, United States.,Animal Disease Research Unit, Agricultural Research Service, United States Department of Agriculture, Pullman, WA, United States.,Center for Reproductive Biology, Washington State University, Pullman, WA, United States
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49
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Veiga-Lopez A, Sethuraman V, Navasiolava N, Makela B, Olomu I, Long R, van de Wetering K, Martin L, Aranyi T, Szeri F. Plasma Inorganic Pyrophosphate Deficiency Links Multiparity to Cardiovascular Disease Risk. Front Cell Dev Biol 2020; 8:573727. [PMID: 33363139 PMCID: PMC7755719 DOI: 10.3389/fcell.2020.573727] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 11/18/2020] [Indexed: 12/17/2022] Open
Abstract
Epidemiological studies indicate that elevated alkaline phosphatase activity is associated with increased cardiovascular disease risk. Other epidemiological data demonstrate that mothers giving multiple childbirths (multipara) are also at increased risk of developing late-onset cardiovascular disease. We hypothesized that these two associations stem from a common cause, the insufficient plasma level of the ectopic mineralization inhibitor inorganic pyrophosphate, which is a substrate of alkaline phosphatase. As alkaline phosphatase activity is elevated in pregnancy, we hypothesized that pyrophosphate concentrations decrease gestationally, potentially leading to increased maternal vascular calcification and cardiovascular disease risk in multipara. We investigated plasma pyrophosphate kinetics pre- and postpartum in sheep and at term in humans and demonstrated its shortage in pregnancy, mirroring alkaline phosphatase activity. Next, we tested whether multiparity is associated with increased vascular calcification in pseudoxanthoma elasticum patients, characterized by low intrinsic plasma pyrophosphate levels. We demonstrated that these patients had increased vascular calcification when they give birth multiple times. We propose that transient shortages of pyrophosphate during repeated pregnancies might contribute to vascular calcification and multiparity-associated cardiovascular disease risk threatening hundreds of millions of healthy women worldwide. Future trials are needed to assess if gestational pyrophosphate supplementation might be a suitable prophylactic treatment to mitigate maternal cardiovascular disease risk in multiparous women.
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Affiliation(s)
- Almudena Veiga-Lopez
- Department of Pathology, The University of Illinois at Chicago, Chicago, IL, United States.,Department of Animal Science, Michigan State University, East Lansing, MI, United States
| | - Visalakshi Sethuraman
- Department of Pediatrics and Human Development, Michigan State University, Lansing, MI, United States.,Department of Pediatrics, Texas Tech University Health Sciences Center, Odessa, TX, United States
| | | | - Barbara Makela
- Department of Animal Science, Michigan State University, East Lansing, MI, United States
| | - Isoken Olomu
- Department of Pediatrics and Human Development, Michigan State University, Lansing, MI, United States
| | - Robert Long
- Department of Obstetrics and Gynecology, Sparrow Hospital, Lansing, MI, United States
| | - Koen van de Wetering
- Department of Dermatology and Cutaneous Biology, PXE International Center of Excellence in Research and Clinical Care, Thomas Jefferson University, Philadelphia, PA, United States
| | - Ludovic Martin
- Department of Pediatrics, Texas Tech University Health Sciences Center, Odessa, TX, United States
| | - Tamas Aranyi
- Department of Molecular Biology, Semmelweis University, Budapest, Hungary.,Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary
| | - Flora Szeri
- Department of Dermatology and Cutaneous Biology, PXE International Center of Excellence in Research and Clinical Care, Thomas Jefferson University, Philadelphia, PA, United States.,Institute of Enzymology, Research Centre for Natural Sciences, Budapest, Hungary.,Department of Biochemistry, Semmelweis University, Budapest, Hungary
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50
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Modes of genetic adaptations underlying functional innovations in the rumen. SCIENCE CHINA-LIFE SCIENCES 2020; 64:1-21. [PMID: 33165812 DOI: 10.1007/s11427-020-1828-8] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/17/2020] [Accepted: 09/29/2020] [Indexed: 10/23/2022]
Abstract
The rumen is the hallmark organ of ruminants and hosts a diverse ecosystem of microorganisms that facilitates efficient digestion of plant fibers. We analyzed 897 transcriptomes from three Cetartiodactyla lineages: ruminants, camels and cetaceans, as well as data from ruminant comparative genomics and functional assays to explore the genetic basis of rumen functional innovations. We identified genes with relatively high expression in the rumen, of which many appeared to be recruited from other tissues. These genes show functional enrichment in ketone body metabolism, regulation of microbial community, and epithelium absorption, which are the most prominent biological processes involved in rumen innovations. Several modes of genetic change underlying rumen functional innovations were uncovered, including coding mutations, genes newly evolved, and changes of regulatory elements. We validated that the key ketogenesis rate-limiting gene (HMGCS2) with five ruminant-specific mutations was under positive selection and exhibits higher synthesis activity than those of other mammals. Two newly evolved genes (LYZ1 and DEFB1) are resistant to Gram-positive bacteria and thereby may regulate microbial community equilibrium. Furthermore, we confirmed that the changes of regulatory elements accounted for the majority of rumen gene recruitment. These results greatly improve our understanding of rumen evolution and organ evo-devo in general.
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