1
|
Lowe JWE. Humanising and dehumanising pigs in genomic and transplantation research. HISTORY AND PHILOSOPHY OF THE LIFE SCIENCES 2022; 44:66. [PMID: 36417007 PMCID: PMC9684229 DOI: 10.1007/s40656-022-00545-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/18/2020] [Accepted: 10/16/2022] [Indexed: 06/16/2023]
Abstract
Biologists who work on the pig (Sus scrofa) take advantage of its similarity to humans by constructing the inferential and material means to traffic data, information and knowledge across the species barrier. Their research has been funded due to its perceived value for agriculture and medicine. Improving selective breeding practices, for instance, has been a driver of genomics research. The pig is also an animal model for biomedical research and practice, and is proposed as a source of organs for cross-species transplantation: xenotransplantation. Genomics research has informed transplantation biology, which has itself motivated developments in genomics. Both have generated models of correspondences between the genomes of pigs and humans. Concerning genomics, I detail how researchers traverse species boundaries to develop representations of the pig genome, alongside ensuring that such representations are sufficiently porcine. In transplantation biology, the representations of the genomes of humans and pigs are used to detect and investigate immunologically-pertinent differences between the two species. These key differences can then be removed, to 'humanise' donor pigs so that they can become a safe and effective source of organs. In both of these endeavours, there is a tension between practices that 'humanise' the pig (or representations thereof) through using resources from human genomics, and the need to 'dehumanise' the pig to maintain distinctions for legal, ethical and scientific reasons. This paper assesses the ways in which this tension has been managed, observing the differences between its realisations across comparative pig genomics and transplantation biology, and considering the consequences of this.
Collapse
Affiliation(s)
- James W E Lowe
- Science, Technology and Innovation Studies, University of Edinburgh, Old Surgeons' Hall, High School Yards, Edinburgh, EH1 1LZ, UK.
| |
Collapse
|
2
|
Auch H, Klymiuk N, Runa-Vochozkova P. Modifying Bacterial Artificial Chromosomes for Extended Genome Modification. Methods Mol Biol 2022; 2495:67-90. [PMID: 35696028 DOI: 10.1007/978-1-0716-2301-5_4] [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] [Indexed: 06/15/2023]
Abstract
Bacterial artificial chromosomes have been used extensively for the exploration of mammalian genomes. Although novel approaches made their initial function expendable, the available BAC libraries are a precious source for life science. Their comprising of extended genomic regions provides an ideal basis for creating a large targeting vector. Here, we describe the identification of suitable BACs from their libraries and their verification prior to manipulation. Further, protocols for modifying BAC, confirming the desired modification and the preparation of transfection into mammalian cells are given.
Collapse
Affiliation(s)
- Hannah Auch
- Large Animal Models in Cardiovascular Research, Internal Medical Department I, TU Munich, Munich, Germany
- Center for Innovative Medical Models, LMU Munich, Munich, Germany
| | - Nikolai Klymiuk
- Large Animal Models in Cardiovascular Research, Internal Medical Department I, TU Munich, Munich, Germany
- Center for Innovative Medical Models, LMU Munich, Munich, Germany
| | - Petra Runa-Vochozkova
- Large Animal Models in Cardiovascular Research, Internal Medical Department I, TU Munich, Munich, Germany.
- Center for Innovative Medical Models, LMU Munich, Munich, Germany.
| |
Collapse
|
3
|
Mompart F, Kamgoué A, Lahbib-Mansais Y, Robelin D, Bonnet A, Rogel-Gaillard C, Kocanova S, Yerle-Bouissou M. The 3D nuclear conformation of the major histocompatibility complex changes upon cell activation both in porcine and human macrophages. BMC Mol Cell Biol 2021; 22:45. [PMID: 34521351 PMCID: PMC8442435 DOI: 10.1186/s12860-021-00384-4] [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: 04/21/2021] [Accepted: 08/30/2021] [Indexed: 11/27/2022] Open
Abstract
BACKGROUND The crucial role of the major histocompatibility complex (MHC) for the immune response to infectious diseases is well-known, but no information is available on the 3D nuclear organization of this gene-dense region in immune cells, whereas nuclear architecture is known to play an essential role on genome function regulation. We analyzed the spatial arrangement of the three MHC regions (class I, III and II) in macrophages using 3D-FISH. Since this complex presents major differences in humans and pigs with, notably, the presence of the centromere between class III and class II regions in pigs, the analysis was implemented in both species to determine the impact of this organization on the 3D conformation of the MHC. The expression level of the three genes selected to represent each MHC region was assessed by quantitative real-time PCR. Resting and lipopolysaccharide (LPS)-activated states were investigated to ascertain whether a response to a pathogen modifies their expression level and their 3D organization. RESULTS While the three MHC regions occupy an intermediate radial position in porcine macrophages, the class I region was clearly more peripheral in humans. The BAC center-to-center distances allowed us to propose a 3D nuclear organization of the MHC in each species. LPS/IFNγ activation induces a significant decompaction of the chromatin between class I and class III regions in pigs and between class I and class II regions in humans. We detected a strong overexpression of TNFα (class III region) in both species. Moreover, a single nucleus analysis revealed that the two alleles can have either the same or a different compaction pattern. In addition, macrophage activation leads to an increase in alleles that present a decompacted pattern in humans and pigs. CONCLUSIONS The data presented demonstrate that: (i) the MHC harbors a different 3D organization in humans and pigs; (ii) LPS/IFNγ activation induces chromatin decompaction, but it is not the same area affected in the two species. These findings were supported by the application of an original computation method based on the geometrical distribution of the three target genes. Finally, the position of the centromere inside the swine MHC could influence chromatin reorganization during the activation process.
Collapse
Affiliation(s)
- Florence Mompart
- GenPhySE, Université de Toulouse, INRAE, ENVT, 1388 GenPhySE, 24 Chemin de Borde Rouge, 31326 Cedex, Castanet-Tolosan, France
| | - Alain Kamgoué
- Laboratoire de Biologie Moléculaire Eucaryote (LBME), Centre de Biologie Intégrative (CBI), CNRS, UPS, University of Toulouse, 31062, Toulouse, France
| | - Yvette Lahbib-Mansais
- GenPhySE, Université de Toulouse, INRAE, ENVT, 1388 GenPhySE, 24 Chemin de Borde Rouge, 31326 Cedex, Castanet-Tolosan, France
| | - David Robelin
- GenPhySE, Université de Toulouse, INRAE, ENVT, 1388 GenPhySE, 24 Chemin de Borde Rouge, 31326 Cedex, Castanet-Tolosan, France
| | - Agnès Bonnet
- GenPhySE, Université de Toulouse, INRAE, ENVT, 1388 GenPhySE, 24 Chemin de Borde Rouge, 31326 Cedex, Castanet-Tolosan, France
| | | | - Silvia Kocanova
- Laboratoire de Biologie Moléculaire Eucaryote (LBME), Centre de Biologie Intégrative (CBI), CNRS, UPS, University of Toulouse, 31062, Toulouse, France
| | - Martine Yerle-Bouissou
- GenPhySE, Université de Toulouse, INRAE, ENVT, 1388 GenPhySE, 24 Chemin de Borde Rouge, 31326 Cedex, Castanet-Tolosan, France.
| |
Collapse
|
4
|
Lowe JWE. Sequencing through thick and thin: Historiographical and philosophical implications. STUDIES IN HISTORY AND PHILOSOPHY OF BIOLOGICAL AND BIOMEDICAL SCIENCES 2018; 72:10-27. [PMID: 30337139 DOI: 10.1016/j.shpsc.2018.10.007] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/09/2017] [Revised: 07/11/2018] [Accepted: 10/01/2018] [Indexed: 06/08/2023]
Abstract
DNA sequencing has been characterised by scholars and life scientists as an example of 'big', 'fast' and 'automated' science in biology. This paper argues, however, that these characterisations are a product of a particular interpretation of what sequencing is, what I call 'thin sequencing'. The 'thin sequencing' perspective focuses on the determination of the order of bases in a particular stretch of DNA. Based upon my research on the pig genome mapping and sequencing projects, I provide an alternative 'thick sequencing' perspective, which also includes a number of practices that enable the sequence to travel across and be used in wider communities. If we take sequencing in the thin manner to be an event demarcated by the determination of sequences in automated sequencing machines and computers, this has consequences for the historical analysis of sequencing projects, as it focuses attention on those parts of the work of sequencing that are more centralised, fast (and accelerating) and automated. I argue instead that sequencing can be interpreted as a more open-ended process including activities such as the generation of a minimum tile path or annotation, and detail the historiographical and philosophical consequences of this move.
Collapse
Affiliation(s)
- James W E Lowe
- Science, Technology and Innovation Studies, University of Edinburgh, Old Surgeons' Hall, High School Yards, Edinburgh, EH1 1LZ, UK.
| |
Collapse
|
5
|
Mary N, Villagómez DAF, Revay T, Rezaei S, Donaldson B, Pinton A, King WA. Meiotic Synapsis and Gene Expression Altered by a Balanced Y-Autosome Reciprocal Translocation in an Azoospermic Pig. Sex Dev 2018; 12:256-263. [PMID: 30179878 DOI: 10.1159/000491804] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/31/2018] [Indexed: 12/16/2022] Open
Abstract
Meiotic sex chromosome silencing (MSCS) has been argued as a prerequisite for normal meiotic cell division progression during the synaptic prophase I stage. Furthermore, irregular asynapsis of autosomal axes at meiosis may be encompassing the lack of transcriptional activity normally observed for the X and Y sex chromosomes. Therefore, any chromosomal rearrangement compromising the normal mechanism of MSCS and/or the contrary, the normal meiotic transcriptional activity of autosomal chromosomes, may be observed as a meiotic and concomitant spermatogenesis arrest. Previously, we have described a Y-autosome translocation t(Y;13)(p1.3;q3.3) in an azoospermic boar. Its chromosome synapsis behavior by synaptonemal complex immunostaining and FISH analyses is documented here. Histone γH2AX protein foci appeared to be located at unsynapsed chromosomal segments (e.g., X chromosome univalents or unpaired multivalent segments), although interestingly a high proportion of primary spermatocytes showed full paired synaptonemal complex-multivalent configurations which were devoid of a γH2AX focus signal, indicating meiotic chromosome silencing. RT-qPCR analysis of testicular expression showed downregulation of 3 SSC13 genes (MLH1, SOX2, UBE2B) and upregulation of SSCY genes (ZFY, SRY). The irregularity of the normal transcription pattern in case of these genes with proven roles in the testis is in agreement with the cytological observations and could contribute to the observed phenotype.
Collapse
|
6
|
Barasc H, Congras A, Mary N, Trouilh L, Marquet V, Ferchaud S, Raymond-Letron I, Calgaro A, Loustau-Dudez AM, Mouney-Bonnet N, Acloque H, Ducos A, Pinton A. Meiotic pairing and gene expression disturbance in germ cells from an infertile boar with a balanced reciprocal autosome-autosome translocation. Chromosome Res 2016; 24:511-527. [PMID: 27484982 PMCID: PMC5167775 DOI: 10.1007/s10577-016-9533-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2016] [Revised: 07/19/2016] [Accepted: 07/21/2016] [Indexed: 11/07/2022]
Abstract
Individuals carrying balanced constitutional reciprocal translocations generally have a normal phenotype, but often present reproductive disorders. The aim of our research was to analyze the meiotic process in an oligoasthenoteratospermic boar carrying an asymmetric reciprocal translocation involving chromosomes 1 and 14. Different multivalent structures (quadrivalent and trivalent plus univalent) were identified during chromosome pairing analysis. Some of these multivalents were characterized by the presence of unpaired autosomal segments with histone γH2AX accumulation sometimes associated with the XY body. Gene expression in spermatocytes was studied by RNA-DNA-FISH and microarray-based testis transcriptome analysis. Our results revealed a decrease in gene expression for chromosomes 1 and 14 and an up-regulated expression of X-chromosome genes for the translocated boar compared with normal individuals. We hypothesized that the observed meiotic arrest and reproductive failure in this boar might be due to silencing of crucial autosomal genes (MSUC) and disturbance of meiotic sex chromosome inactivation (MSCI). Further analysis revealed abnormal meiotic recombination (frequency and distribution) and the production of a high rate of unbalanced spermatozoa.
Collapse
Affiliation(s)
- Harmonie Barasc
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Toulouse, France.
| | - Annabelle Congras
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Toulouse, France
| | - Nicolas Mary
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Toulouse, France
| | - Lidwine Trouilh
- LISBP, Université de Toulouse, CNRS, INRA, INSA, Toulouse, France
| | - Valentine Marquet
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Toulouse, France
| | - Stéphane Ferchaud
- GenESI Génétique, Expérimentation et Système Innovants, 17700, Saint-Pierre-d'Amilly, France
| | - Isabelle Raymond-Letron
- STROMALab, Université de Toulouse, CNRS ERL 5311, EFS, ENVT, Inserm U1031, UPS, Toulouse, France
| | - Anne Calgaro
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Toulouse, France
| | | | | | - Hervé Acloque
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Toulouse, France
| | - Alain Ducos
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Toulouse, France
| | - Alain Pinton
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, Toulouse, France
| |
Collapse
|
7
|
Mary N, Barasc H, Ferchaud S, Priet A, Calgaro A, Loustau-Dudez AM, Bonnet N, Yerle M, Ducos A, Pinton A. Meiotic Recombination Analyses in Pigs Carrying Different Balanced Structural Chromosomal Rearrangements. PLoS One 2016; 11:e0154635. [PMID: 27124413 PMCID: PMC4849707 DOI: 10.1371/journal.pone.0154635] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2016] [Accepted: 04/15/2016] [Indexed: 01/23/2023] Open
Abstract
Correct pairing, synapsis and recombination between homologous chromosomes are essential for normal meiosis. All these events are strongly regulated, and our knowledge of the mechanisms involved in this regulation is increasing rapidly. Chromosomal rearrangements are known to disturb these processes. In the present paper, synapsis and recombination (number and distribution of MLH1 foci) were studied in three boars (Sus scrofa domestica) carrying different chromosomal rearrangements. One (T34he) was heterozygote for the t(3;4)(p1.3;q1.5) reciprocal translocation, one (T34ho) was homozygote for that translocation, while the third (T34Inv) was heterozygote for both the translocation and a pericentric inversion inv(4)(p1.4;q2.3). All three boars were normal for synapsis and sperm production. This particular situation allowed us to rigorously study the impact of rearrangements on recombination. Overall, the rearrangements induced only minor modifications of the number of MLH1 foci (per spermatocyte or per chromosome) and of the length of synaptonemal complexes for chromosomes 3 and 4. The distribution of MLH1 foci in T34he was comparable to that of the controls. Conversely, the distributions of MLH1 foci on chromosome 4 were strongly modified in boar T34Inv (lack of crossover in the heterosynaptic region of the quadrivalent, and crossover displaced to the chromosome extremities), and also in boar T34ho (two recombination peaks on the q-arms compared with one of higher magnitude in the controls). Analyses of boars T34he and T34Inv showed that the interference was propagated through the breakpoints. A different result was obtained for boar T34ho, in which the breakpoints (transition between SSC3 and SSC4 chromatin on the bivalents) seemed to alter the transmission of the interference signal. Our results suggest that the number of crossovers and crossover interference could be regulated by partially different mechanisms.
Collapse
Affiliation(s)
- Nicolas Mary
- INRA, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse INPT ENSAT, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse INPT ENVT, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Toulouse, France
- * E-mail:
| | - Harmonie Barasc
- INRA, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse INPT ENSAT, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse INPT ENVT, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Toulouse, France
| | - Stéphane Ferchaud
- UE1372 GenESI Génétique, Expérimentation et Système Innovants, Surgères, France
| | - Aurélia Priet
- UE1372 GenESI Génétique, Expérimentation et Système Innovants, Surgères, France
| | - Anne Calgaro
- INRA, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse INPT ENSAT, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse INPT ENVT, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Toulouse, France
| | - Anne-Marie Loustau-Dudez
- INRA, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse INPT ENSAT, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse INPT ENVT, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Toulouse, France
| | - Nathalie Bonnet
- INRA, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse INPT ENSAT, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse INPT ENVT, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Toulouse, France
| | - Martine Yerle
- INRA, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse INPT ENSAT, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse INPT ENVT, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Toulouse, France
| | - Alain Ducos
- INRA, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse INPT ENSAT, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse INPT ENVT, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Toulouse, France
| | - Alain Pinton
- INRA, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse INPT ENSAT, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse INPT ENVT, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Toulouse, France
| |
Collapse
|
8
|
Corominas J, Marchesi JAP, Puig-Oliveras A, Revilla M, Estellé J, Alves E, Folch JM, Ballester M. Epigenetic regulation of the ELOVL6 gene is associated with a major QTL effect on fatty acid composition in pigs. Genet Sel Evol 2015; 47:20. [PMID: 25887840 PMCID: PMC4371617 DOI: 10.1186/s12711-015-0111-y] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2014] [Accepted: 03/04/2015] [Indexed: 11/16/2022] Open
Abstract
Background In previous studies on an Iberian x Landrace cross, we have provided evidence that supported the porcine ELOVL6 gene as the major causative gene of the QTL on pig chromosome 8 for palmitic and palmitoleic acid contents in muscle and backfat. The single nucleotide polymorphism (SNP) ELOVL6:c.-533C > T located in the promoter region of ELOVL6 was found to be highly associated with ELOVL6 expression and, accordingly, with the percentages of palmitic and palmitoleic acids in longissimus dorsi and adipose tissue. The main goal of the current work was to further study the role of ELOVL6 on these traits by analyzing the regulation of the expression of ELOVL6 and the implication of ELOVL6 polymorphisms on meat quality traits in pigs. Results High-throughput sequencing of BAC clones that contain the porcine ELOVL6 gene coupled to RNAseq data re-analysis showed that two isoforms of this gene are expressed in liver and adipose tissue and that they differ in number of exons and 3’UTR length. Although several SNPs in the 3’UTR of ELOVL6 were associated with palmitic and palmitoleic acid contents, this association was lower than that previously observed with SNP ELOVL6:c.-533C > T. This SNP is in full linkage disequilibrium with SNP ELOVL6:c.-394G > A that was identified in the binding site for estrogen receptor alpha (ERα). Interestingly, the ELOVL6:c.-394G allele is associated with an increase in methylation levels of the ELOVL6 promoter and with a decrease of ELOVL6 expression. Therefore, ERα is clearly a good candidate to explain the regulation of ELOVL6 expression through dynamic epigenetic changes in the binding site of known regulators of ELOVL6 gene, such as SREBF1 and SP1. Conclusions Our results strongly suggest the ELOVL6:c.-394G > A polymorphism as the causal mutation for the QTL on pig chromosome 8 that affects fatty acid composition in pigs. Electronic supplementary material The online version of this article (doi:10.1186/s12711-015-0111-y) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Jordi Corominas
- Plant and Animal Genomics, Centre de Recerca en Agrigenòmica (Consorci CSIC-IRTA-UAB-UB), Edifici CRAG, Campus UAB, Bellaterra, Barcelona, 08193, Spain. .,Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Campus UAB, Bellaterra, Barcelona, 08193, Spain.
| | - Jorge A P Marchesi
- Plant and Animal Genomics, Centre de Recerca en Agrigenòmica (Consorci CSIC-IRTA-UAB-UB), Edifici CRAG, Campus UAB, Bellaterra, Barcelona, 08193, Spain.
| | - Anna Puig-Oliveras
- Plant and Animal Genomics, Centre de Recerca en Agrigenòmica (Consorci CSIC-IRTA-UAB-UB), Edifici CRAG, Campus UAB, Bellaterra, Barcelona, 08193, Spain. .,Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Campus UAB, Bellaterra, Barcelona, 08193, Spain.
| | - Manuel Revilla
- Plant and Animal Genomics, Centre de Recerca en Agrigenòmica (Consorci CSIC-IRTA-UAB-UB), Edifici CRAG, Campus UAB, Bellaterra, Barcelona, 08193, Spain. .,Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Campus UAB, Bellaterra, Barcelona, 08193, Spain.
| | - Jordi Estellé
- INRA, UMR 1313, Génétique Animale et Biologie Intégrative, Jouy-en-Josas F, 78352, France. .,AgroParisTech, UMR 1313 Génétique Animale et Biologie Intégrative, Jouy-en-Josas F, 78352, France. .,CEA, DSV/iRCM/SREIT/LREG, Jouy-en-Josas F, 78352, France.
| | - Estefânia Alves
- Departamento de Mejora Genética Animal, INIA, Ctra. de la Coruña km. 7, Madrid, 28040, Spain.
| | - Josep M Folch
- Plant and Animal Genomics, Centre de Recerca en Agrigenòmica (Consorci CSIC-IRTA-UAB-UB), Edifici CRAG, Campus UAB, Bellaterra, Barcelona, 08193, Spain. .,Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Campus UAB, Bellaterra, Barcelona, 08193, Spain.
| | - Maria Ballester
- Plant and Animal Genomics, Centre de Recerca en Agrigenòmica (Consorci CSIC-IRTA-UAB-UB), Edifici CRAG, Campus UAB, Bellaterra, Barcelona, 08193, Spain. .,Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Campus UAB, Bellaterra, Barcelona, 08193, Spain.
| |
Collapse
|
9
|
Lopez-Rios J, Duchesne A, Speziale D, Andrey G, Peterson KA, Germann P, Ünal E, Liu J, Floriot S, Barbey S, Gallard Y, Müller-Gerbl M, Courtney AD, Klopp C, Rodriguez S, Ivanek R, Beisel C, Wicking C, Iber D, Robert B, McMahon AP, Duboule D, Zeller R. Attenuated sensing of SHH by Ptch1 underlies evolution of bovine limbs. Nature 2014; 511:46-51. [DOI: 10.1038/nature13289] [Citation(s) in RCA: 91] [Impact Index Per Article: 9.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/16/2013] [Accepted: 03/27/2014] [Indexed: 11/09/2022]
|
10
|
Mary N, Barasc H, Ferchaud S, Billon Y, Meslier F, Robelin D, Calgaro A, Loustau-Dudez AM, Bonnet N, Yerle M, Acloque H, Ducos A, Pinton A. Meiotic recombination analyses of individual chromosomes in male domestic pigs (Sus scrofa domestica). PLoS One 2014; 9:e99123. [PMID: 24919066 PMCID: PMC4053413 DOI: 10.1371/journal.pone.0099123] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2014] [Accepted: 05/09/2014] [Indexed: 01/05/2023] Open
Abstract
For the first time in the domestic pig, meiotic recombination along the 18 porcine autosomes was directly studied by immunolocalization of MLH1 protein. In total, 7,848 synaptonemal complexes from 436 spermatocytes were analyzed, and 13,969 recombination sites were mapped. Individual chromosomes for 113 of the 436 cells (representing 2,034 synaptonemal complexes) were identified by immunostaining and fluorescence in situ hybridization (FISH). The average total length of autosomal synaptonemal complexes per cell was 190.3 µm, with 32.0 recombination sites (crossovers), on average, per cell. The number of crossovers and the lengths of the autosomal synaptonemal complexes showed significant intra- (i.e. between cells) and inter-individual variations. The distributions of recombination sites within each chromosomal category were similar: crossovers in metacentric and submetacentric chromosomes were concentrated in the telomeric regions of the p- and q-arms, whereas two hotspots were located near the centromere and in the telomeric region of acrocentrics. Lack of MLH1 foci was mainly observed in the smaller chromosomes, particularly chromosome 18 (SSC18) and the sex chromosomes. All autosomes displayed positive interference, with a large variability between the chromosomes.
Collapse
Affiliation(s)
- Nicolas Mary
- INRA, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse INPT ENSAT, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse INPT ENVT, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Toulouse, France
| | - Harmonie Barasc
- INRA, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse INPT ENSAT, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse INPT ENVT, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Toulouse, France
| | - Stéphane Ferchaud
- UE1372 GenESI Génétique, Expérimentation et Système Innovants, Surgères, France
| | - Yvon Billon
- UE1372 GenESI Génétique, Expérimentation et Système Innovants, Surgères, France
| | - Frédéric Meslier
- UE1372 GenESI Génétique, Expérimentation et Système Innovants, Surgères, France
| | - David Robelin
- INRA, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse INPT ENSAT, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse INPT ENVT, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Toulouse, France
| | - Anne Calgaro
- INRA, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse INPT ENSAT, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse INPT ENVT, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Toulouse, France
| | - Anne-Marie Loustau-Dudez
- INRA, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse INPT ENSAT, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse INPT ENVT, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Toulouse, France
| | - Nathalie Bonnet
- INRA, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse INPT ENSAT, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse INPT ENVT, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Toulouse, France
| | - Martine Yerle
- INRA, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse INPT ENSAT, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse INPT ENVT, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Toulouse, France
| | - Hervé Acloque
- INRA, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse INPT ENSAT, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse INPT ENVT, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Toulouse, France
| | - Alain Ducos
- INRA, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse INPT ENSAT, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse INPT ENVT, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Toulouse, France
| | - Alain Pinton
- INRA, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse INPT ENSAT, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Castanet-Tolosan, France
- Université de Toulouse INPT ENVT, UMR1388 Génétique, Physiologie et Systèmes d’Elevage, Toulouse, France
| |
Collapse
|
11
|
Serão NVL, Matika O, Kemp RA, Harding JCS, Bishop SC, Plastow GS, Dekkers JCM. Genetic analysis of reproductive traits and antibody response in a PRRS outbreak herd. J Anim Sci 2014; 92:2905-21. [PMID: 24879764 DOI: 10.2527/jas.2014-7821] [Citation(s) in RCA: 50] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023] Open
Abstract
Porcine reproductive and respiratory syndrome (PRRS) is the most economically significant disease impacting pig production in North America, Europe, and Asia, causing reproductive losses such as increased rates of stillbirth and mummified piglets. The objective of this study was to explore the genetic basis of host response to the PRRS virus (PRRSV) in a commercial multiplier sow herd before and after a PRRS outbreak, using antibody response and reproductive traits. Reproductive data comprising number born alive (NBA), number alive at 24 h (NA24), number stillborn (NSB), number born mummified (NBM), proportion born dead (PBD), number born dead (NBD), number weaned (NW), and number of mortalities through weaning (MW) of 5,227 litters from 1,967 purebred Landrace sows were used along with a pedigree comprising 2,995 pigs. The PRRS outbreak date was estimated from rolling averages of farrowing traits and was used to split the data into a pre-PRRS phase and a PRRS phase. All 641 sows in the herd during the outbreak were blood sampled 46 d after the estimated outbreak date and were tested for anti-PRRSV IgG using ELISA (sample-to-positive [S/P] ratio). Genetic parameters of traits were estimated separately for the pre-PRRS and PRRS phase data sets. Sows were genotyped using the PorcineSNP60 BeadChip, and genome-wide association studies (GWAS) were performed using method Bayes B. Heritability estimates for reproductive traits ranged from 0.01 (NBM) to 0.12 (NSB) and from 0.01 (MW) to 0.12 (NBD) for the pre-PRRS and PRRS phases, respectively. S/P ratio had heritability (0.45) and strong genetic correlations with most traits, ranging from -0.72 (NBM) to 0.73 (NBA). In the pre-PRRS phase, regions associated with NSB and PBD explained 1.6% and 3% of the genetic variance, respectively. In the PRRS phase, regions associated with NBD, NSB, and S/P ratio explained 0.8%, 11%, and 50.6% of the genetic variance, respectively. For S/P ratio, 2 regions on SSC 7 (SSC7) separated by 100 Mb explained 40% of the genetic variation, including a region encompassing the major histocompatibility complex, which explained 25% of the genetic variance. These results indicate a significant genomic component associated with PRRSV antibody response and NSB in this data set. Also, the high heritability and genetic correlation estimates for S/P ratio during the PRRS phase suggest that S/P ratio could be used as an indicator of the impact of PRRS on reproductive traits.
Collapse
Affiliation(s)
- N V L Serão
- Department of Animal Science, Iowa State University, Ames 50011
| | - O Matika
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - R A Kemp
- Genesus, Oakville, MB R0H 0Y0, Canada
| | - J C S Harding
- Department of Large Animal Clinical Sciences, University of Saskatchewan, Saskatoon, SK S7N 5A1, Canada
| | - S C Bishop
- The Roslin Institute and Royal (Dick) School of Veterinary Studies, University of Edinburgh, Easter Bush, Midlothian EH25 9RG, UK
| | - G S Plastow
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2R3, Canada
| | - J C M Dekkers
- Department of Animal Science, Iowa State University, Ames 50011
| |
Collapse
|
12
|
Gahete MD, Durán-Prado M, Delgado-Niebla E, Garrido JJ, Rhodes SJ, García-Navarro S, Gracia-Navarro F, Malagón MM, Luque RM, Castaño JP. Porcine sst1 can physically interact with other somatostatin receptors, and its expression is regulated by metabolic/inflammatory sensors. Am J Physiol Endocrinol Metab 2014; 306:E483-93. [PMID: 24368669 DOI: 10.1152/ajpendo.00587.2013] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The majority of the biological actions attributed to somatostatin (SST) are thought to be mediated by SST receptor 2 (sst2), the most ubiquitous sst, and, to a lesser extent, by sst5. However, a growing body of evidence suggests a relevant role of sst1 in mediating SST actions in (patho)physiological situations (i.e., endometriosis, type 2 diabetes). Moreover, sst1 together with sst2 and sst5 is involved in the well-known actions of SST on pituitary somatotropes in pig and primates. Here, we cloned the porcine sst1 (psst1) and performed a structural and functional characterization using both primary and heterologous models. The psst1 sequence presents the majority of signature motifs shared among G protein-coupled receptors and, specifically, among ssts and exhibits a high homology with other mammalian sst1, with only minor differences in the amino-terminal domain, reinforcing the idea of an early evolutive divergence between mammalian and nonmammalian sst1s. psst1 is functional in terms of decreasing cAMP levels in response to SST when transfected in heterologous models. The psst1 receptor is expressed in several tissues, and analyses of gene cis elements predict regulation by multiple transcription factors and metabolic stimuli. Finally, psst1 is coexpressed with other sst subtypes in various tissues, and in vitro data demonstrate that psst1 can interact with itself forming homodimers and with other ssts forming heterodimers. These data highlight the functional importance of sst1 on the SST-mediated effects and its functional interaction with different ssts, which point out the necessity of exploring the consequences of such interactions.
Collapse
Affiliation(s)
- Manuel D Gahete
- Department of Cell Biology, Physiology and Immunology, University of Córdoba, Instituto Maimónides de Investigación Biomédica de Córdoba, Hospital Universitario Reina Sofia and CIBER Fisiopatología de la Obesidad y Nutrición, Córdoba, Spain
| | | | | | | | | | | | | | | | | | | |
Collapse
|
13
|
Costa MR, Fischer N, Gulich B, Tönjes RR. Comparison of porcine endogenous retroviruses infectious potential in supernatants of producer cells and in cocultures. Xenotransplantation 2014; 21:162-73. [PMID: 24447212 DOI: 10.1111/xen.12081] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/15/2013] [Accepted: 11/25/2013] [Indexed: 11/26/2022]
Abstract
BACKGROUND Porcine endogenous retroviruses (PERV) pose a zoonotic risk potential in pig-to-human xenotransplantation given that PERV capacity to infect different human cell lines in vitro has been clearly shown in the past. However, PERV infectious potential for human peripheral blood mononuclear cells (huPBMC) has been also demonstrated, albeit with controversial results. As productive PERV infection of huPBMC involves immune suppression that may attract opportunistic pathogens as shown for other retroviruses, it is crucial to ascertain unequivocally huPBMC susceptibility for PERV. To address this question, we first investigated in vitro infectivity of PERV for huPBMC using supernatants containing highly infectious PERV-A/C. Second, huPBMC were cocultivated with PERV-A/C producer cells to come a step closer to the in vivo situation of xenotransplantation. In addition, cocultivation of huPBMC with porcine PBMC (poPBMC) isolated from German landrace pigs was performed to distinguish PERV replication competence when they were constitutively produced by immortalized cells or by primary poPBMC. METHODS Supernatants containing recombinant highly infectious PERV-A/C were used to infect PHA-activated huPBMC in the presence or absence of polybrene. Next, PERV-producing cell lines such as human 293/5° and primary mitogenically activated poPBMC of three German landrace pigs were cocultivated with huPBMC as well as with susceptible human and porcine cell lines as controls. PERV infection was monitored by using three test approaches. The presence of provirus DNA in putatively infected cells was detected via sensitive nested PCR. Viral expression was determined by screening for the activity of gammaretroviral reverse transcriptase (RT) in cell-free supernatants of infected cells. Virus release was monitored by counting the number of packaged RNA particles in supernatants via PERV-specific quantitative one-step real-time reverse transcriptase PCR. RESULTS Porcine endogenous retroviruses-A/C in supernatants of human producer 293/5° cells was not able to infect huPBMC. Neither RT activity nor PERV copies were detected. Even provirus could not be detected displaying the inability of PERV-A/C to induce a productive infection in huPBMC. In cocultivation experiments only non-productive infection of huPBMC with PERV derived from 293/5° cell line and from PHA-activated poPBMC was observed by detection of provirus DNA in infected cells. CONCLUSION Recombinant PERV-A/C in supernatants of producer cells failed to infect huPBMC, whereas coculture experiments with producer cell lines lead to non-productive infection of huPBMC. PERV in supernatants seem to have not sufficient infectious potential for huPBMC. However, extensive PERV exposure to huPBMC via cocultivation enabled at least virus cell entry as provirus was detected by nested PCR. Furthermore, results presented support previous data showing German landrace pigs as low producers with negligible infectious potential due to the absence of replication-competent PERV in the genome. The low PERV expression profile and the lack of significant replication competence of German landrace pigs raise hope for considering these animals as putative donor animals in future pig-to-human xenotransplantation. Nonetheless, data imply that PERV still represent a virological risk in the course of xenotransplantation, as the presence of PERV provirus in host cells may lead to a provirus integration resulting in insertional mutagenesis and chromosomal rearrangements.
Collapse
|
14
|
Ren J, Yan X, Ai H, Zhang Z, Huang X, Ouyang J, Yang M, Yang H, Han P, Zeng W, Chen Y, Guo Y, Xiao S, Ding N, Huang L. Susceptibility towards enterotoxigenic Escherichia coli F4ac diarrhea is governed by the MUC13 gene in pigs. PLoS One 2012; 7:e44573. [PMID: 22984528 PMCID: PMC3440394 DOI: 10.1371/journal.pone.0044573] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/05/2012] [Accepted: 08/03/2012] [Indexed: 11/18/2022] Open
Abstract
Enterotoxigenic Escherichia coli (ETEC) F4ac is a major determinant of diarrhea and mortality in neonatal and young pigs. Susceptibility to ETEC F4ac is governed by the intestinal receptor specific for the bacterium and is inherited as a monogenic dominant trait. To identify the receptor gene (F4acR), we first mapped the locus to a 7.8-cM region on pig chromosome 13 using a genome scan with 194 microsatellite markers. A further scan with high density markers on chromosome 13 refined the locus to a 5.7-cM interval. Recombination breakpoint analysis defined the locus within a 2.3-Mb region. Further genome-wide mapping using 39,720 informative SNPs revealed that the most significant markers were proximal to the MUC13 gene in the 2.3-Mb region. Association studies in a collection of diverse outbred populations strongly supported that MUC13 is the most likely responsible gene. We characterized the porcine MUC13 gene that encodes two transcripts: MUC13A and MUC13B. Both transcripts have the characteristic PTS regions of mucins that are enriched in distinct tandem repeats. MUC13B is predicated to be heavily O-glycosylated, forming the binding site of the bacterium; while MUC13A does not have the O-glycosylation binding site. Concordantly, 127 independent pigs homozygous for MUC13A across diverse breeds are all resistant to ETEC F4ac, and all 718 susceptible animals from the broad breed panel carry at least one MUC13B allele. Altogether, we conclude that susceptibility towards ETEC F4ac is governed by the MUC13 gene in pigs. The finding has an immediate translation into breeding practice, as it allows us to establish an efficient and accurate diagnostic test for selecting against susceptible animals. Moreover, the finding improves our understanding of mucins that play crucial roles in defense against enteric pathogens. It revealed, for the first time, the direct interaction between MUC13 and enteric bacteria, which is poorly understood in mammals.
Collapse
Affiliation(s)
- Jun Ren
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, People’s Republic of China
- * E-mail: (LH); (JR)
| | - Xueming Yan
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, People’s Republic of China
- College of Life Science, Jiangxi Science and Technology Normal University, Nanchang, People’s Republic of China
| | - Huashui Ai
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, People’s Republic of China
| | - Zhiyan Zhang
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, People’s Republic of China
| | - Xiang Huang
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, People’s Republic of China
| | - Jing Ouyang
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, People’s Republic of China
| | - Ming Yang
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, People’s Republic of China
| | - Huaigu Yang
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, People’s Republic of China
| | - Pengfei Han
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, People’s Republic of China
| | - Weihong Zeng
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, People’s Republic of China
| | - Yijie Chen
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, People’s Republic of China
| | - Yuanmei Guo
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, People’s Republic of China
| | - Shijun Xiao
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, People’s Republic of China
| | - Nengshui Ding
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, People’s Republic of China
| | - Lusheng Huang
- Key Laboratory for Animal Biotechnology of Jiangxi Province and the Ministry of Agriculture of China, Jiangxi Agricultural University, Nanchang, People’s Republic of China
- * E-mail: (LH); (JR)
| |
Collapse
|
15
|
Stafuzza NB, Abbey CA, Gill CA, Womack JE, Amaral MEJ. Construction and preliminary characterization of a river buffalo bacterial artificial chromosome library. GENETICS AND MOLECULAR RESEARCH 2012; 11:3013-9. [PMID: 22653673 DOI: 10.4238/2012.may.22.6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/03/2022]
Abstract
River buffalo genome analyses have advanced significantly in the last decade, and the genome sequence of Bubalus bubalis will be available shortly. Nonetheless, large-insert DNA library resources such as bacterial artificial chromosomes (BAC) are still required for validation and accurate assembly of the genome sequence. We constructed a river buffalo BAC library containing 52,224 clones with an average insert size of 97 kb, representing 1.7 × coverage of the genome. This genomic resource for river buffalo will facilitate further studies in this economically important species allowing for instance, whole genome physical mapping and isolation of genes and gene clusters, contributing to the elucidation of gene organization and identification of regulatory elements.
Collapse
Affiliation(s)
- N B Stafuzza
- Departamento de Biologia, Instituto de Biociências, Letras e Ciências Exatas, Universidade Estadual de São Paulo "Júlio de Mesquita Filho", São José do Rio Preto, SP, Brazil
| | | | | | | | | |
Collapse
|
16
|
Denner J, Tönjes RR. Infection barriers to successful xenotransplantation focusing on porcine endogenous retroviruses. Clin Microbiol Rev 2012; 25:318-43. [PMID: 22491774 PMCID: PMC3346299 DOI: 10.1128/cmr.05011-11] [Citation(s) in RCA: 136] [Impact Index Per Article: 11.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/03/2023] Open
Abstract
Xenotransplantation may be a solution to overcome the shortage of organs for the treatment of patients with organ failure, but it may be associated with the transmission of porcine microorganisms and the development of xenozoonoses. Whereas most microorganisms may be eliminated by pathogen-free breeding of the donor animals, porcine endogenous retroviruses (PERVs) cannot be eliminated, since these are integrated into the genomes of all pigs. Human-tropic PERV-A and -B are present in all pigs and are able to infect human cells. Infection of ecotropic PERV-C is limited to pig cells. PERVs may adapt to host cells by varying the number of LTR-binding transcription factor binding sites. Like all retroviruses, they may induce tumors and/or immunodeficiencies. To date, all experimental, preclinical, and clinical xenotransplantations using pig cells, tissues, and organs have not shown transmission of PERV. Highly sensitive and specific methods have been developed to analyze the PERV status of donor pigs and to monitor recipients for PERV infection. Strategies have been developed to prevent PERV transmission, including selection of PERV-C-negative, low-producer pigs, generation of an effective vaccine, selection of effective antiretrovirals, and generation of animals transgenic for a PERV-specific short hairpin RNA inhibiting PERV expression by RNA interference.
Collapse
|
17
|
Karniychuk UU, Van Breedam W, Van Roy N, Rogel-Gaillard C, Nauwynck HJ. Demonstration of microchimerism in pregnant sows and effects of congenital PRRSV infection. Vet Res 2012; 43:19. [PMID: 22423651 PMCID: PMC3368719 DOI: 10.1186/1297-9716-43-19] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2011] [Accepted: 03/16/2012] [Indexed: 11/16/2022] Open
Abstract
The presence of foreign cells within the tissue/circulation of an individual is described as microchimerism. The main purpose of the present investigation was to study if microchimerism occurs in healthy sows/fetuses and if porcine reproductive and respiratory syndrome virus (PRRSV) infection influences this phenomenon. Six dams were inoculated intranasally with PRRSV and three non-inoculated dams served as controls. Male DNA was detected in female fetal sera of all dams via PCR. Male DNA was also detected in the maternal circulation. Sex-typing FISH showed the presence of male cells in the female fetal organs and vice versa. PRRSV infection did not influence microchimerism, but might misuse maternal and sibling microchimeric cells to enter fetuses.
Collapse
Affiliation(s)
- Uladzimir U Karniychuk
- Laboratory of Virology, Faculty of Veterinary Medicine, Ghent University, Ghent, Belgium.
| | | | | | | | | |
Collapse
|
18
|
Barasc H, Mary N, Letron R, Calgaro A, Dudez AM, Bonnet N, Lahbib-Mansais Y, Yerle M, Ducos A, Pinton A. Y-autosome translocation interferes with meiotic sex inactivation and expression of autosomal genes: a case study in the pig. Sex Dev 2011; 6:143-50. [PMID: 21921590 DOI: 10.1159/000331477] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022] Open
Abstract
Y-autosome translocations are rare in humans and pigs. In both species, these rearrangements can be responsible for meiotic arrest and subsequent infertility. Chromosome pairing abnormalities on the SSCX, SSCY and SSC1 chromatin domains were identified by analyzing pachytene spermatocytes from a boar carrying a (Y;1) translocation by immunolocalization of specific meiotic protein combined with FISH. Disturbance of the meiotic sex chromosome inactivation (MSCI) was observed by Cot-RNA-FISH and analysis of ZFY gene expression by sequential RNA- and DNA-FISH on spermatocytes. We hypothesized that the meiotic arrest observed in this boar might be due to the silencing of critical autosomal genes and/or the reactivation of some sex chromosome genes.
Collapse
Affiliation(s)
- H Barasc
- Laboratoire de Génétique Cellulaire, UMR 444, Institut National de la Recherche Agronomique, Université de Toulouse, Toulouse, France
| | | | | | | | | | | | | | | | | | | |
Collapse
|
19
|
Characterization of porcine endogenous retrovirus clones from the NIH miniature pig BAC library. J Biomed Biotechnol 2011; 2012:482568. [PMID: 21912484 PMCID: PMC3168785 DOI: 10.1155/2012/482568] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/27/2011] [Revised: 06/08/2011] [Accepted: 06/16/2011] [Indexed: 02/03/2023] Open
Abstract
Pigs have been considered as donors for xenotransplantation in the replacement of human organs and tissues. However, porcine endogenous retroviruses (PERVs) might transmit new infectious disease to humans during xenotransplantation. To investigate PERV integration sites, 45 PERV-positive BAC clones, including 12 PERV-A, 16 PERV-B, and 17 PERV-C clones, were identified from the NIH miniature pig BAC library. The analysis of 12 selected full-length sequences of PERVs, including the long terminal repeat (LTR) region, identified the expected of open reading frame length, an indicative of active PERV, in all five PERV-C clones and one of the four PERV-B clones. Premature stop codons were observed in only three PERV-A clones. Also, eleven PERV integration sites were mapped using a 5000-rad IMpRH panel. The map locations of PERV-C clones have not been reported before, thus they are novel PERV clones identified in this study. The results could provide basic information for the elimination of site-specific PERVs in selection of pigs for xenotransplantation.
Collapse
|
20
|
Gao Y, Wahlberg P, Marthey S, Esquerré D, Jaffrézic F, Lecardonnel J, Hugot K, Rogel-Gaillard C. Analysis of porcine MHC using microarrays. Vet Immunol Immunopathol 2011; 148:78-84. [PMID: 21561666 DOI: 10.1016/j.vetimm.2011.04.007] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2010] [Revised: 03/23/2011] [Accepted: 04/09/2011] [Indexed: 11/26/2022]
Abstract
The major histocompatibility complex (MHC) in Mammals is one of the most gene dense regions of the genome and contains the polymorphic histocompatibility gene families known to be involved in pathogen response and control of auto-immunity. The MHC is a complex genetic system that provides an interesting model system to study genome expression regulation and genetic diversity at the megabase scale. The pig MHC or SLA (Swine Leucocyte Antigen) complex spans 2.4 megabases and 151 loci have been annotated. We will review key results from previous RNA expression studies using microarrays containing probes specific to annotated loci within SLA and in addition present novel data obtained using high-density tiling arrays encompassing the whole SLA complex. We have focused on transcriptome modifications of porcine peripheral blood mononuclear cells stimulated with a mixture of phorbol myristate acetate and ionomycin known to activate B and T cell proliferation. Our results show that numerous loci mapping to the SLA complex are affected by the treatment. A general decreased level of expression for class I and II genes and an up-regulation of genes involved in peptide processing and transport were observed. Tiling array-based experiments contributed to refined gene annotations as presented for one SLA class I gene referred to as SLA-11. In conclusion, high-density tiling arrays can serve as an excellent tool to draw comprehensive transcription maps, and improve genome annotations for the SLA complex. We are currently studying their relevance to characterize SLA genetic diversity in combination with high throughput next generation sequencing.
Collapse
Affiliation(s)
- Yu Gao
- INRA, UMR 1313 de Génétique Animale et Biologie Intégrative, Domaine de Vilvert, 78350 Jouy-en-Josas, France
| | | | | | | | | | | | | | | |
Collapse
|
21
|
Massip K, Yerle M, Billon Y, Ferchaud S, Bonnet N, Calgaro A, Mary N, Dudez AM, Sentenac C, Plard C, Ducos A, Pinton A. Studies of male and female meiosis in inv(4)(p1.4;q2.3) pig carriers. Chromosome Res 2010; 18:925-38. [DOI: 10.1007/s10577-010-9162-7] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2010] [Revised: 10/07/2010] [Accepted: 10/08/2010] [Indexed: 01/30/2023]
|
22
|
Mattiuzzo G, Takeuchi Y. Suboptimal porcine endogenous retrovirus infection in non-human primate cells: implication for preclinical xenotransplantation. PLoS One 2010; 5:e13203. [PMID: 20949092 PMCID: PMC2950858 DOI: 10.1371/journal.pone.0013203] [Citation(s) in RCA: 26] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2010] [Accepted: 09/10/2010] [Indexed: 01/20/2023] Open
Abstract
Background Porcine endogenous retrovirus (PERV) poses a potential risk of zoonotic infection in xenotransplantation. Preclinical transplantation trials using non-human primates (NHP) as recipients of porcine xenografts present the opportunity to assess the zoonosis risk in vivo. However, PERV poorly infects NHP cells for unclear reasons and therefore NHP may represent a suboptimal animal model to assess the risk of PERV zoonoses. We investigated the mechanism responsible for the low efficiency of PERV-A infection in NHP cells. Principal Findings Two steps, cell entry and exit, were inefficient for the replication of high-titer, human-tropic A/C recombinant PERV. A restriction factor, tetherin, is likely to be responsible for the block to matured virion release, supported by the correlation between the levels of inhibition and tetherin expression. In rhesus macaque, cynomolgus macaque and baboon the main receptor for PERV entry, PERV-A receptor 1 (PAR-1), was found to be genetically deficient: PAR-1 genes in these species encode serine at amino acid 109 in place of the leucine in human PAR-1. This genetic defect inevitably impacts in vivo sensitivity to PERV infection of these species. In contrast, African green monkey (AGM) PAR-1 is functional, but PERV infection is still poor. Although the mechanism is unclear, tunicamycin treatment, which removes N-glycosylated sugar chains, increases PERV infection, suggesting a possible role for the glycosylation of the receptors. Conclusions Since cynomolgus macaque and baboon, species often used in pig-to-NHP xenotransplantation experiments, have a defective PAR-1, they hardly represent an ideal animal model to assess the risk of PERV transmission in xenotransplantation. Alternatively, NHP species, like AGM, whose both PARs are functional may represent a better model than baboon and cynomolgus macaque for PERV zoonosis in vivo studies.
Collapse
Affiliation(s)
- Giada Mattiuzzo
- Division of Infection and Immunity, Wohl Virion Centre, University College London, London, United Kingdom
| | - Yasuhiro Takeuchi
- Division of Infection and Immunity, Wohl Virion Centre, University College London, London, United Kingdom
- * E-mail:
| |
Collapse
|
23
|
Schook LB, Beever JE, Rogers J, Humphray S, Archibald A, Chardon P, Milan D, Rohrer G, Eversole K. Swine Genome Sequencing Consortium (SGSC): a strategic roadmap for sequencing the pig genome. Comp Funct Genomics 2010; 6:251-5. [PMID: 18629187 PMCID: PMC2447480 DOI: 10.1002/cfg.479] [Citation(s) in RCA: 76] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2005] [Revised: 03/17/2005] [Accepted: 03/18/2005] [Indexed: 11/08/2022] Open
Abstract
The Swine Genome Sequencing Consortium (SGSC) was formed in September 2003 by academic, government and industry representatives to provide international coordination for sequencing the pig genome. The SGSC's mission is to advance biomedical research for animal production and health by the development of DNAbased tools and products resulting from the sequencing of the swine genome. During the past 2 years, the SGSC has met bi-annually to develop a strategic roadmap for creating the required scientific resources, to integrate existing physical maps, and to create a sequencing strategy that captured international participation and a broad funding base. During the past year, SGSC members have integrated their respective physical mapping data with the goal of creating a minimal tiling path (MTP) that will be used as the sequencing template. During the recent Plant and Animal Genome meeting (January 16, 2005 San Diego, CA), presentations demonstrated that a human-pig comparative map has been completed, BAC fingerprint contigs (FPC) for each of the autosomes and X chromosome have been constructed and that BAC end-sequencing has permitted, through BLAST analysis and RH-mapping, anchoring of the contigs. Thus, significant progress has been made towards the creation of a MTP. In addition, whole-genome (WG) shotgun libraries have been constructed and are currently being sequenced in various laboratories around the globe. Thus, a hybrid sequencing approach in which 3x coverage of BACs comprising the MTP and 3x of the WG-shotgun libraries will be used to develop a draft 6x coverage of the pig genome.
Collapse
Affiliation(s)
- Lawrence B Schook
- Institute for Genomic Biology, University of Illinois, Urbana, IL, USA.
| | | | | | | | | | | | | | | | | |
Collapse
|
24
|
Schoevers EJ, Fink-Gremmels J, Colenbrander B, Roelen BAJ. Porcine oocytes are most vulnerable to the mycotoxin deoxynivalenol during formation of the meiotic spindle. Theriogenology 2010; 74:968-78. [PMID: 20570324 DOI: 10.1016/j.theriogenology.2010.04.026] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/29/2010] [Revised: 04/22/2010] [Accepted: 04/22/2010] [Indexed: 12/24/2022]
Abstract
Deoxynivalenol (DON, vomitoxin) is a secondary metabolite and mycotoxin produced by Fusarium species that occurs with a high prevalence in cereals and grains intended for human and animal consumption. Pigs are considered to be the most sensitive animal species and exposure to DON results in reduced feed intake, reduced performance and cause alterations in the expression of markers of inflammation and cell cycle regulation. The objective of this study was to determine how DON possibly affects the oocyte developmental potential in vitro at concentrations which correspond to those observed in practice. To evaluate DON toxicity during specific stages of oocyte meiosis, cumulus-oocyte complexes were exposed to 0.02, 0.2, or 2 microM DON. Exposure to the highest DON concentration inhibited cumulus expansion and induced cumulus cell death. After exposure for 42 h, DON at all concentrations reduced Metaphase II formation and led to malformations of the meiotic spindle. Despite spindle malformations, exposure to different concentrations of DON did not lead to increased percentages of blastomeres with abnormal ploidy in embryos. Spindle malformation occurred by DON exposure during formation of meiotic spindles at Metaphase I and II, but embryo development was also reduced when oocytes were exposed to DON during Prophase I. Together, these results indicate that exposure to DON via contaminated food or feed can affect oocyte developmental competence by interfering directly with microtubule dynamics during meiosis, and by disturbing oocyte cytoplasmic maturation through other as yet undetermined mechanisms.
Collapse
Affiliation(s)
- E J Schoevers
- Department of Farm Animal Health, Faculty of Veterinary Medicine, Utrecht University, Yalelaan 104, 3584 CM, Utrecht, The Netherlands.
| | | | | | | |
Collapse
|
25
|
Eguchi-Ogawa T, Wertz N, Sun XZ, Puimi F, Uenishi H, Wells K, Chardon P, Tobin GJ, Butler JE. Antibody Repertoire Development in Fetal and Neonatal Piglets. XI. The Relationship of Variable Heavy Chain Gene Usage and the Genomic Organization of the Variable Heavy Chain Locus. THE JOURNAL OF IMMUNOLOGY 2010; 184:3734-42. [DOI: 10.4049/jimmunol.0903616] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
|
26
|
Liu L, Yin J, Li W, Liu K, Peng Y, Tan P, Ma RZ. Construction of a bacterial artificial chromosome library for the Rongchang pig breed and its use for the identification of genes involved in intramuscular fat deposition. Biochem Biophys Res Commun 2009; 391:1280-4. [PMID: 20018173 DOI: 10.1016/j.bbrc.2009.12.060] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2009] [Accepted: 12/10/2009] [Indexed: 11/28/2022]
Abstract
In a search for genes affecting intramuscular fat deposition, we constructed a bacterial artificial chromosome (BAC) library for the whole genome of Rongchang pig, a domestic Chinese swine breed. The library consisted of approximately 192,000 clones, with an averaged insert size of 116 kb. Frequency of non-insert clone of the BAC library was no higher than 1.8%, based on estimation of 220 BAC clones randomly selected. We estimated the coverage of the library to be more than seven porcine genome equivalents. Subsequent screening of the BAC library with a three-step PCR procedure resulted in identification of seven candidate genes that were potentially involved in intramuscular fat deposition. The number of positive BAC clones ranged from 2 to 4 for each of the seven genes. One positive clone, containing the lipin1 gene, was fully sequenced by shotgun method to generate 118,041 bp porcine genomic sequences. The BAC clone contained complete DNA sequence of porcine lipin1 gene including all the exons and introns. Our results indicate that this BAC library is a useful tool for gene identification and help to serve as an important resource for future porcine genomic study.
Collapse
Affiliation(s)
- Ling Liu
- College of Animal Science & Technology, State Key Laboratory of Animal Nutrition, China Agricultural University, Beijing 100193, China
| | | | | | | | | | | | | |
Collapse
|
27
|
Jung WY, Kim JE, Jung KC, Jin DI, Moran C, Park EW, Jeon JT, Lee JH. Comparison of PERV genomic locations between Asian and European pigs. Anim Genet 2009; 41:89-92. [PMID: 19781037 DOI: 10.1111/j.1365-2052.2009.01953.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
Xenotransplantation from pigs provides a possible solution to the shortage of human organs for allotransplantation. Porcine endogenous retroviruses (PERVs) are a possible obstacle to using porcine organs in addition to the immunological barriers. Three main types of PERVs (A, B and C) have been previously investigated in diverse pig breeds. To examine the copy numbers of PERVs and their genomic locations in the Korean native pig genome, we screened a BAC (Bacterial Artificial Chromosome) library with PERV-specific protease primers for initial recognition of PERV-positive clones and three sets of envelope-specific primers for the identification of PERV types. A total of 45 PERV-positive clones, nine PERV-A and 36 PERV-B, have been identified from the library screening and the BAC contigs were constructed using the primers designed from BAC end sequences (BESs). These primers were also used for SCH (Somatic Cell Hybrid) and RH (Radiation Hybrid) mapping of the PERV-positive clones. The results indicate that 45 PERV-positive BAC clones belong to nine contigs and a singleton. SCH and IMpRH (INRA-Minnesota Porcine Radiation Hybrid) mapping results indicated that there are at least eight separate PERV genomic locations, consisting of three PERV-A and five PERV-B. One contig could not be mapped, and two contigs are closely located on SSC7. Southern blotting indicates there may be up to 15 additional sites. Further investigation of these clones will contribute to a general strategy to generate PERV-free lines of pigs suitable for xenotransplantation.
Collapse
Affiliation(s)
- W Y Jung
- Chungnam National University, Daejeon, Korea
| | | | | | | | | | | | | | | |
Collapse
|
28
|
Massip K, Berland H, Bonnet N, Calgaro A, Billoux S, Baquié V, Mary N, Bonnet-Garnier A, Ducos A, Yerle M, Pinton A. Study of inter- and intra-individual variation of meiotic segregation patterns in t(3;15)(q27;q13) boars. Theriogenology 2008; 70:655-61. [DOI: 10.1016/j.theriogenology.2008.04.026] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2008] [Revised: 04/10/2008] [Accepted: 04/11/2008] [Indexed: 10/22/2022]
|
29
|
Humphray SJ, Scott CE, Clark R, Marron B, Bender C, Camm N, Davis J, Jenks A, Noon A, Patel M, Sehra H, Yang F, Rogatcheva MB, Milan D, Chardon P, Rohrer G, Nonneman D, de Jong P, Meyers SN, Archibald A, Beever JE, Schook LB, Rogers J. A high utility integrated map of the pig genome. Genome Biol 2008; 8:R139. [PMID: 17625002 PMCID: PMC2323232 DOI: 10.1186/gb-2007-8-7-r139] [Citation(s) in RCA: 110] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2007] [Revised: 06/21/2007] [Accepted: 07/11/2007] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The domestic pig is being increasingly exploited as a system for modeling human disease. It also has substantial economic importance for meat-based protein production. Physical clone maps have underpinned large-scale genomic sequencing and enabled focused cloning efforts for many genomes. Comparative genetic maps indicate that there is more structural similarity between pig and human than, for example, mouse and human, and we have used this close relationship between human and pig as a way of facilitating map construction. RESULTS Here we report the construction of the most highly continuous bacterial artificial chromosome (BAC) map of any mammalian genome, for the pig (Sus scrofa domestica) genome. The map provides a template for the generation and assembly of high-quality anchored sequence across the genome. The physical map integrates previous landmark maps with restriction fingerprints and BAC end sequences from over 260,000 BACs derived from 4 BAC libraries and takes advantage of alignments to the human genome to improve the continuity and local ordering of the clone contigs. We estimate that over 98% of the euchromatin of the 18 pig autosomes and the X chromosome along with localized coverage on Y is represented in 172 contigs, with chromosome 13 (218 Mb) represented by a single contig. The map is accessible through pre-Ensembl, where links to marker and sequence data can be found. CONCLUSION The map will enable immediate electronic positional cloning of genes, benefiting the pig research community and further facilitating use of the pig as an alternative animal model for human disease. The clone map and BAC end sequence data can also help to support the assembly of maps and genome sequences of other artiodactyls.
Collapse
Affiliation(s)
- Sean J Humphray
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA UK
| | - Carol E Scott
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA UK
| | - Richard Clark
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA UK
| | - Brandy Marron
- College of Agriculture, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801 USA
| | - Clare Bender
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA UK
| | - Nick Camm
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA UK
| | - Jayne Davis
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA UK
| | - Andrew Jenks
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA UK
| | - Angela Noon
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA UK
| | - Manish Patel
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA UK
| | - Harminder Sehra
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA UK
| | - Fengtang Yang
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA UK
| | - Margarita B Rogatcheva
- College of Agriculture, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801 USA
| | - Denis Milan
- Laboratoire de Génétique Cellulaire, INRA, 31326 Castanet-Tolosan, France
| | - Patrick Chardon
- INRA-CEA, Domaine de Vilvert, 78352, Jouy en Josas cedex, France
| | - Gary Rohrer
- US Department of Agriculture, Agricultural Research Service, US Meat Animal Research Center, Clay Center, NE 68933-0166, USA
| | - Dan Nonneman
- US Department of Agriculture, Agricultural Research Service, US Meat Animal Research Center, Clay Center, NE 68933-0166, USA
| | - Pieter de Jong
- Children's Hospital Oakland-BACPAC Resources, Oakland, California 94609, USA
| | - Stacey N Meyers
- College of Agriculture, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801 USA
| | | | - Jonathan E Beever
- College of Agriculture, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801 USA
| | - Lawrence B Schook
- College of Agriculture, Consumer and Environmental Sciences, University of Illinois at Urbana-Champaign, Urbana, Illinois 61801 USA
| | - Jane Rogers
- The Wellcome Trust Sanger Institute, Wellcome Trust Genome Campus, Hinxton, Cambridge CB10 1SA UK
| |
Collapse
|
30
|
Rogatcheva MB, Chen K, Larkin DM, Meyers SN, Marron BM, He W, Schook LB, Beever JE. Piggy-BACing the Human Genome I: Constructing a Porcine BAC Physical Map Through Comparative Genomics. Anim Biotechnol 2008; 19:28-42. [DOI: 10.1080/10495390701807634] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
|
31
|
Malekinejad H, Schoevers EJ, Daemen IJJM, Zijlstra C, Colenbrander B, Fink-Gremmels J, Roelen BAJ. Exposure of Oocytes to the Fusarium Toxins Zearalenone and Deoxynivalenol Causes Aneuploidy and Abnormal Embryo Development in Pigs1. Biol Reprod 2007; 77:840-7. [PMID: 17652666 DOI: 10.1095/biolreprod.107.062711] [Citation(s) in RCA: 91] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/26/2022] Open
Abstract
Fungi of the Fusarium species can infect food and feed commodities and produce the mycotoxins zearalenone (ZEA) and deoxynivalenol (DON). Since both toxins have been reported to reduce fertility, the mechanisms of ZEA and DON on inhibition of oocyte maturation were examined. Pig oocytes were matured in the presence of ZEA (a mycotoxin with estrogenlike activity), 17beta-estradiol, and DON (all 3.12 micromol/L). Zearalenone, 17beta-estradiol, and DON inhibited oocyte maturation and caused approximately 34% of the oocytes to form an aberrant spindle. Different ratios of ZEA:DON did not lead to a more severe inhibition of oocyte maturation. Both mycotoxins caused abnormal formation of the meiotic spindle. The developmental competence of oocytes matured in the presence of mycotoxins was further investigated after in vitro fertilization. Presence of ZEA (3.12 micromol/L) during maturation reduced the percentages of oocytes that cleaved and formed a blastocyst to about 12%, compared with 25% of control oocytes. Maturation in the presence of equimolar concentrations of DON was not compatible with development. The ploidy of blastomeres from blastocysts derived from mycotoxin-exposed oocytes was analyzed with fluorescent in situ hybridization. All blastocysts, even those from the control group, contained at least one blastomere with abnormal ploidy, but the variation in the percentages of aneuploid blastomeres was significantly larger in embryos from oocytes exposed to mycotoxins. It is concluded that ZEA and DON can lead to abnormal spindle formation, leading to less fertile oocytes and embryos with abnormal ploidy, and that the effects of ZEA and DON are not synergistic.
Collapse
Affiliation(s)
- Hassan Malekinejad
- Department of Veterinary Pharmacology, Utrecht University, 3584 CM Utrecht, The Netherlands
| | | | | | | | | | | | | |
Collapse
|
32
|
|
33
|
Tennant LM, Renard C, Chardon P, Powell PP. Regulation of porcine classical and nonclassical MHC class I expression. Immunogenetics 2007; 59:377-89. [PMID: 17351769 DOI: 10.1007/s00251-007-0206-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2007] [Accepted: 02/22/2007] [Indexed: 11/28/2022]
Abstract
Major histocompatibility complex (MHC) class I molecules comprise a family of polymorphic cell surface receptors consisting of classical 1 a molecules that present antigenic peptides and nonclassical 1 b molecules. Gene expression for human classical and nonclassical MHC class I molecules has been shown to be differentially regulated by interferon, with variation in the nucleotide sequence of promoter regions, resulting in differences in interferon inducibility and basal levels of gene transcription. In this study on porcine classical and nonclassical swine leukocyte Ag (SLA) class I molecules, we show alignments of putative regulatory elements in the promoters of the three functional classical class I genes, SLA-1, SLA-2, and SLA-3; two nonclassical 1 b genes, SLA-6 and SLA-7; and a MIC-2 gene. Promoter elements were cloned upstream from a luciferase reporter gene, and the basal and inducible activities of each were characterized by expression in Max cells, an immortalized pig cell line that responds to interferon and tumor necrosis factor alpha (TNF-alpha). All three classical class I but not nonclassical promoters responded to interferon. This was confirmed by the transactivation of SLA-1, but not SLA-7, after the co expression with interferon regulatory factors (IRFs), IRF-1, IRF-2, IRF-3, IRF-7, and IRF-9. Classical class I genes were activated by cotransfection with nuclear factor kappa B (NF-kappaB) p65 and by treatment of cells with TNF-alpha, although, unlike human promoter there was no synergistic effect with interferon. The greatest effect on classical class I promoters was coexpression with the class II transactivator (CIITA), important for constitutive transactivation. These results determine the differential regulation of porcine classical and nonclassical MHC class I and reflects their importance in antigen presentation during infection.
Collapse
Affiliation(s)
- Laura M Tennant
- Department of Immunology, Institute for Animal Health, Ash Road, Pirbright, Surrey, GU24 0NF, UK
| | | | | | | |
Collapse
|
34
|
Chen K, Baxter T, Muir WM, Groenen MA, Schook LB. Genetic resources, genome mapping and evolutionary genomics of the pig (Sus scrofa). Int J Biol Sci 2007; 3:153-65. [PMID: 17384734 PMCID: PMC1802013 DOI: 10.7150/ijbs.3.153] [Citation(s) in RCA: 73] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/16/2006] [Accepted: 01/09/2007] [Indexed: 02/01/2023] Open
Abstract
The pig, a representative of the artiodactyla clade, is one of the first animals domesticated, and has become an important agriculture animal as one of the major human nutritional sources of animal based protein. The pig is also a valuable biomedical model organism for human health. The pig's importance to human health and nutrition is reflected in the decision to sequence its genome (3X). As an animal species with its wild ancestors present in the world, the pig provides a unique opportunity for tracing mammalian evolutionary history and defining signatures of selection resulting from both domestication and natural selection. Completion of the pig genome sequencing project will have significant impacts on both agriculture and human health. Following the pig whole genome sequence drafts, along with large-scale polymorphism data, it will be possible to conduct genome sweeps using association mapping, and identify signatures of selection. Here, we provide a description of the pig genome sequencing project and perspectives on utilizing genomic technologies to exploit pig genome evolution and the molecular basis for phenotypic traits for improving pig production and health.
Collapse
Affiliation(s)
- Kefei Chen
- 1. Department of Animal Sciences, University of Illinois at Urbana-Champaign, 1201 W. Gregory Dr., Urbana, IL 61801, USA
| | - Tara Baxter
- 1. Department of Animal Sciences, University of Illinois at Urbana-Champaign, 1201 W. Gregory Dr., Urbana, IL 61801, USA
| | - William M. Muir
- 2. Department of Animal Science, Purdue University, West Lafayette, Indiana 47907-1151, USA
| | - Martien A. Groenen
- 3. Animal Breeding and Genetics Group, Wageningen University, PO Box 9101, Wageningen, 6701 BH, The Netherlands
| | - Lawrence B. Schook
- 1. Department of Animal Sciences, University of Illinois at Urbana-Champaign, 1201 W. Gregory Dr., Urbana, IL 61801, USA
- 4. Institute for Genomic Biology, University of Illinois at Urbana-Champaign, 1206 W. Gregory Dr., Urbana, IL 61801, USA
| |
Collapse
|
35
|
Sanz G, Pérez E, Jiménez-Marín A, Mompart F, Morera L, Barbancho M, Llanes D, Garrido JJ. Molecular cloning, chromosomal location, and expression analysis of porcine CD14. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2007; 31:738-47. [PMID: 17169425 DOI: 10.1016/j.dci.2006.10.006] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/11/2006] [Revised: 10/31/2006] [Accepted: 10/31/2006] [Indexed: 05/13/2023]
Abstract
CD14 is a membrane-associated glycosylphosphatidylinositol (GPI)-anchored protein that binds lipopolysaccharide (LPS) of Gram-negative bacteria and enables LPS-dependent responses in a variety of cells. In this study a cDNA containing the porcine CD14 coding sequence has been cloned and its complete sequence determined. The amino acid sequence deduced from pig CD14 cDNA encodes a 373 amino acid polypeptide that exhibits 75%, 72%, 69%, 66%, 57% and 56% similarity to CD14 from cow, horse, human, rabbit, mouse and rat, respectively. Structural analysis showed that the porcine CD14 is a membrane glycoprotein with a GPI-anchor site and an extracellular domain containing 11 leucine-rich repeats. In addition, the LPS-binding regions identified in the human CD14 are highly conserved in the N-terminal domain of the porcine sequence. Fluorescence in situ hybridization was used to locate the CD14 gene on the pig chromosome 2, band q28. Expression analysis revealed that porcine CD14 transcripts were detected in all tissues and cells examined, suggesting that the expression of porcine CD14 gene is not restricted to myeloid cell lineage. Finally, we report that LPS stimulation significantly up-regulated CD14 gene expression in porcine alveolar macrophages.
Collapse
Affiliation(s)
- Gema Sanz
- Unidad de Marcadores Genéticos Moleculares, Departamento de Genética, Universidad de Córdoba, Campus de Rabanales, 14071 Córdoba, Spain
| | | | | | | | | | | | | | | |
Collapse
|
36
|
Liu W, Zhao Y, Liu Z, Zhang Y, Lian Z, Li N. Construction of a 7-fold BAC library and cytogenetic mapping of 10 genes in the giant panda (Ailuropoda melanoleuca). BMC Genomics 2006; 7:294. [PMID: 17109760 PMCID: PMC1664575 DOI: 10.1186/1471-2164-7-294] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2006] [Accepted: 11/17/2006] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The giant panda, one of the most primitive carnivores, is an endangered animal. Although it has been the subject of many interesting studies during recent years, little is known about its genome. In order to promote research on this genome, a bacterial artificial chromosome (BAC) library of the giant panda was constructed in this study. RESULTS This BAC library contains 198,844 clones with an average insert size of 108 kb, which represents approximately seven equivalents of the giant panda haploid genome. Screening the library with 15 genes and 8 microsatellite markers demonstrates that it is representative and has good genome coverage. Furthermore, ten BAC clones harbouring AGXT, GHR, FSHR, IRBP, SOX14, TTR, BDNF, NT-4, LH and ZFX1 were mapped to 8 pairs of giant panda chromosomes by fluorescence in situ hybridization (FISH). CONCLUSION This is the first large-insert genomic DNA library for the giant panda, and will contribute to understanding this endangered species in the areas of genome sequencing, physical mapping, gene cloning and comparative genomic studies. We also identified the physical locations of ten genes on their relative chromosomes by FISH, providing a preliminary framework for further development of a high resolution cytogenetic map of the giant panda.
Collapse
Affiliation(s)
- Wei Liu
- State Key Laboratory for Agro-Biotechnology, China Agricultural University, Beijing 100094, China
| | - Yonghui Zhao
- State Key Laboratory for Agro-Biotechnology, China Agricultural University, Beijing 100094, China
| | - Zhaoliang Liu
- State Key Laboratory for Agro-Biotechnology, China Agricultural University, Beijing 100094, China
| | - Ying Zhang
- State Key Laboratory for Agro-Biotechnology, China Agricultural University, Beijing 100094, China
| | - Zhengxing Lian
- College of Animal Science and Technology, China Agricultural University, Beijing 100094, China
| | - Ning Li
- State Key Laboratory for Agro-Biotechnology, China Agricultural University, Beijing 100094, China
| |
Collapse
|
37
|
Zhang K, Demeure O, Belliard A, Goujon JM, Favreau F, Desurmont T, Mauco G, Barrière M, Carretier M, Milan D, Papadopoulos V, Hauet T. Cloning, sequencing, and chromosomal localization of pig peripheral benzodiazepine receptor: three different forms produced by alternative splicing. Mamm Genome 2006; 17:1050-62. [PMID: 17019653 DOI: 10.1007/s00335-006-0022-x] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/05/2006] [Accepted: 06/02/2006] [Indexed: 10/25/2022]
Abstract
We report the molecular cloning of the cDNA sequence for pig peripheral benzodiazepine receptor (PBR) by using RT-PCR and 5'/3' terminal extension. Three different transcripts (long, middle, and short) are identified. The open reading frame (ORF) of the longest PBR mRNA encodes a deduced polypeptide of 169 amino acids with a calculated molecular weight of 18,609 Da and an estimated pI of 9.70, which corresponds to the authentic PBR of other mammalian species. The middle transcript (PBR-M) contains a 141-codon ORF, which is consistent with that of the authentic PBR, but lacks a region of 84 bp so that its encoded polypeptide lacks a region of 28 amino acids from 35 to 62 of the authentic PBR polypeptide. The short transcript (PBR-S) contains a 104-codon ORF, which overlaps that of the authentic PBR, but lacks a region of 211 bp so that its encoded polypeptide lacks a region of 65 amino acids of the N-terminal of the authentic PBR. The pig PBR gene was mapped to the telomeric end of SSC5p. In addition, PBR mRNA was the more abundant detected form in pig tissues and in warm kidney that underwent ischemia suggesting functional implications of PBR during the renal repair process.
Collapse
Affiliation(s)
- Keqiang Zhang
- Institut national de la santé de la recherche médicale (INSERM), ERM 324, CHU de Poitiers, rue de la Milétrie, 86021, Poitiers, France
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
38
|
Lahbib-Mansais Y, Mompart F, Milan D, Leroux S, Faraut T, Delcros C, Yerle M. Evolutionary breakpoints through a high-resolution comparative map between porcine chromosomes 2 and 16 and human chromosomes. Genomics 2006; 88:504-12. [PMID: 16765019 DOI: 10.1016/j.ygeno.2006.04.010] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2006] [Revised: 04/11/2006] [Accepted: 04/20/2006] [Indexed: 11/20/2022]
Abstract
This study reports a high-resolution comparative map between human chromosomes and porcine chromosomes 2 (SSC2) and 16 (SSC16), pointing out new homologies and evolutionary breakpoints. SSC2 is of particular interest because of the presence of several important QTLs. Among 226 porcine ESTs selected according to their expected localization, 151 were RH mapped and ordered on SSC2. This study confirmed the extensive conservation between SSC2 and HSA11 and HSA19 and refined the homology with HSA5 (three blocks defined). Furthermore the SSC2q pericentromeric region was shown to be homologous to another human chromosome (HSA1). A complex organization of these syntenies was demonstrated on SSC2q. Our strategy led us to improve also the SSC16 RH map by adding 45 markers. Two-color fluorescence in situ hybridization of markers representative of each synteny confirmed block order. Finally, 29 breakpoints were identified in both species, and porcine BACs containing two breakpoints were isolated.
Collapse
Affiliation(s)
- Yvette Lahbib-Mansais
- Institut National de la Recherche Agronomique, Laboratoire de Génétique Cellulaire, BP52627, 31326 Castanet-Tolosan, France.
| | | | | | | | | | | | | |
Collapse
|
39
|
Stratil A, Van Poucke M, Bartenschlager H, Knoll A, Yerle M, Peelman LJ, Kopecný M, Geldermann H. Porcine OGN and ASPN: mapping, polymorphisms and use for quantitative trait loci identification for growth and carcass traits in a Meishan × Pietrain intercross. Anim Genet 2006; 37:415-8. [PMID: 16879361 DOI: 10.1111/j.1365-2052.2006.01480.x] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
The porcine orthologues of human chromosome HSA9q22.31 genes osteoglycin (OGN) and asporin (ASPN) were mapped to porcine chromosome SSC3 using linkage analysis and a somatic cell hybrid panel. This mapping was refined to SSC3q11 using fluorescence in situ hybridization. These results confirm the existence of a small conserved synteny group between SSC3 and HSA9. Polymorphisms were revealed in both genes, including a pentanucleotide microsatellite (SCZ003) in OGN and two single nucleotide polymorphisms (AM181682.1:g.780G>T and AM181682.1:g.825T>C) in ASPN. The two genes were included in a set of markers for quantitative trait loci (QTL) mapping on SSC3 in the Hohenheim Meishan x Piétrain F2 family. Major QTL for growth and carcass traits were centred in the ASPN-SW902 region.
Collapse
Affiliation(s)
- A Stratil
- Institute of Animal Physiology and Genetics, Academy of Sciences of the Czech Republic, 277 21 Libechov, Czech Republic.
| | | | | | | | | | | | | | | |
Collapse
|
40
|
|
41
|
Uzbekova S, Roy-Sabau M, Dalbiès-Tran R, Perreau C, Papillier P, Mompart F, Thelie A, Pennetier S, Cognie J, Cadoret V, Royere D, Monget P, Mermillod P. Zygote arrest 1 gene in pig, cattle and human: evidence of different transcript variants in male and female germ cells. Reprod Biol Endocrinol 2006; 4:12. [PMID: 16551357 PMCID: PMC1435755 DOI: 10.1186/1477-7827-4-12] [Citation(s) in RCA: 54] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 12/06/2005] [Accepted: 03/21/2006] [Indexed: 12/02/2022] Open
Abstract
BACKGROUND Zygote arrest 1 (ZAR1) is one of the few known oocyte-specific maternal-effect genes essential for the beginning of embryo development discovered in mice. This gene is evolutionary conserved in vertebrates and ZAR1 protein is characterized by the presence of atypical plant homeobox zing finger domain, suggesting its role in transcription regulation. This work was aimed at the study of this gene, which could be one of the key regulators of successful preimplantation development of domestic animals, in pig and cattle, as compared with human. METHODS Screenings of somatic cell hybrid panels and in silico research were performed to characterize ZAR1 chromosome localization and sequences. Rapid amplification of cDNA ends was used to obtain full-length cDNAs. Spatio-temporal mRNA expression patterns were studied using Northern blot, reverse transcription coupled to polymerase chain reaction and in situ hybridization. RESULTS We demonstrated that ZAR1 is a single copy gene, positioned on chromosome 8 in pig and 6 in cattle, and several variants of correspondent cDNA were cloned from oocytes. Sequence analysis of ZAR1 cDNAs evidenced numerous short inverted repeats within the coding sequences and putative Pumilio-binding and embryo-deadenylation elements within the 3'-untranslated regions, indicating the potential regulation ways. We showed that ZAR1 expressed exclusively in oocytes in pig ovary, persisted during first cleavages in embryos developed in vivo and declined sharply in morulae and blastocysts. ZAR1 mRNA was also detected in testis, and, at lower level, in hypothalamus and pituitary in both species. For the first time, ZAR1 was localized in testicular germ cells, notably in round spermatids. In addition, in pig, cattle and human only shorter ZAR1 transcript variants resulting from alternative splicing were found in testis as compared to oocyte. CONCLUSION Our data suggest that in addition to its role in early embryo development highlighted by expression pattern of full-length transcript in oocytes and early embryos, ZAR1 could also be implicated in the regulation of meiosis and post meiotic differentiation of male and female germ cells through expression of shorter splicing variants. Species conservation of ZAR1 expression and regulation underlines the central role of this gene in early reproductive processes.
Collapse
Affiliation(s)
- Svetlana Uzbekova
- Physiologie de la Reproduction et des Comportements, UMR 6175 Institut National de la Recherche Agronomique/Centre National de la Recherche Scientifique, Université François Rabelais de Tours, Haras Nationaux, 37380 Nouzilly, France
| | - Monica Roy-Sabau
- Physiologie de la Reproduction et des Comportements, UMR 6175 Institut National de la Recherche Agronomique/Centre National de la Recherche Scientifique, Université François Rabelais de Tours, Haras Nationaux, 37380 Nouzilly, France
| | - Rozenn Dalbiès-Tran
- Physiologie de la Reproduction et des Comportements, UMR 6175 Institut National de la Recherche Agronomique/Centre National de la Recherche Scientifique, Université François Rabelais de Tours, Haras Nationaux, 37380 Nouzilly, France
| | - Christine Perreau
- Physiologie de la Reproduction et des Comportements, UMR 6175 Institut National de la Recherche Agronomique/Centre National de la Recherche Scientifique, Université François Rabelais de Tours, Haras Nationaux, 37380 Nouzilly, France
| | - Pascal Papillier
- Physiologie de la Reproduction et des Comportements, UMR 6175 Institut National de la Recherche Agronomique/Centre National de la Recherche Scientifique, Université François Rabelais de Tours, Haras Nationaux, 37380 Nouzilly, France
| | - Florence Mompart
- Laboratoire de Génétique Cellulaire, INRA, Chemin de Borde-Rouge – Auzeville, BP 52627 31326 Castanet-Tolosan Cedex, France
| | - Aurore Thelie
- Physiologie de la Reproduction et des Comportements, UMR 6175 Institut National de la Recherche Agronomique/Centre National de la Recherche Scientifique, Université François Rabelais de Tours, Haras Nationaux, 37380 Nouzilly, France
| | - Sophie Pennetier
- Physiologie de la Reproduction et des Comportements, UMR 6175 Institut National de la Recherche Agronomique/Centre National de la Recherche Scientifique, Université François Rabelais de Tours, Haras Nationaux, 37380 Nouzilly, France
| | - Juliette Cognie
- Physiologie de la Reproduction et des Comportements, UMR 6175 Institut National de la Recherche Agronomique/Centre National de la Recherche Scientifique, Université François Rabelais de Tours, Haras Nationaux, 37380 Nouzilly, France
| | - Veronique Cadoret
- Physiologie de la Reproduction et des Comportements, UMR 6175 Institut National de la Recherche Agronomique/Centre National de la Recherche Scientifique, Université François Rabelais de Tours, Haras Nationaux, 37380 Nouzilly, France
- Service de Médecine et Biologie de la Reproduction, UMR 6175, Centre Hospitalier Universitaire Bretonneau, 37044 Tours, France
| | - Dominique Royere
- Service de Médecine et Biologie de la Reproduction, UMR 6175, Centre Hospitalier Universitaire Bretonneau, 37044 Tours, France
| | - Philippe Monget
- Physiologie de la Reproduction et des Comportements, UMR 6175 Institut National de la Recherche Agronomique/Centre National de la Recherche Scientifique, Université François Rabelais de Tours, Haras Nationaux, 37380 Nouzilly, France
| | - Pascal Mermillod
- Physiologie de la Reproduction et des Comportements, UMR 6175 Institut National de la Recherche Agronomique/Centre National de la Recherche Scientifique, Université François Rabelais de Tours, Haras Nationaux, 37380 Nouzilly, France
| |
Collapse
|
42
|
Renard C, Hart E, Sehra H, Beasley H, Coggill P, Howe K, Harrow J, Gilbert J, Sims S, Rogers J, Ando A, Shigenari A, Shiina T, Inoko H, Chardon P, Beck S. The genomic sequence and analysis of the swine major histocompatibility complex. Genomics 2006; 88:96-110. [PMID: 16515853 DOI: 10.1016/j.ygeno.2006.01.004] [Citation(s) in RCA: 89] [Impact Index Per Article: 4.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/07/2005] [Revised: 01/18/2006] [Accepted: 01/18/2006] [Indexed: 10/25/2022]
Abstract
We describe the generation and analysis of an integrated sequence map of a 2.4-Mb region of pig chromosome 7, comprising the classical class I region, the extended and classical class II regions, and the class III region of the major histocompatibility complex (MHC), also known as swine leukocyte antigen (SLA) complex. We have identified and manually annotated 151 loci, of which 121 are known genes (predicted to be functional), 18 are pseudogenes, 8 are novel CDS loci, 3 are novel transcripts, and 1 is a putative gene. Nearly all of these loci have homologues in other mammalian genomes but orthologues could be identified with confidence for only 123 genes. The 28 genes (including all the SLA class I genes) for which unambiguous orthology to genes within the human reference MHC could not be established are of particular interest with respect to porcine-specific MHC function and evolution. We have compared the porcine MHC to other mammalian MHC regions and identified the differences between them. In comparison to the human MHC, the main differences include the absence of HLA-A and other class I-like loci, the absence of HLA-DP-like loci, and the separation of the extended and classical class II regions from the rest of the MHC by insertion of the centromere. We show that the centromere insertion has occurred within a cluster of BTNL genes located at the boundary of the class II and III regions, which might have resulted in the loss of an orthologue to human C6orf10 from this region.
Collapse
Affiliation(s)
- C Renard
- LREG INRA CEA, Jouy en Josas, France
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
43
|
Jacobs K, Rohrer G, Van Poucke M, Piumi F, Yerle M, Barthenschlager H, Mattheeuws M, Van Zeveren A, Peelman LJ. Porcine PPARGC1A (peroxisome proliferative activated receptor gamma coactivator 1A): coding sequence, genomic organization, polymorphisms and mapping. Cytogenet Genome Res 2006; 112:106-13. [PMID: 16276098 DOI: 10.1159/000087521] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2004] [Accepted: 02/25/2005] [Indexed: 01/12/2023] Open
Abstract
We report here the characterisation of porcine PPARGC1A. Primers based on human PPARGC1A were used to isolate two porcine BAC clones. Porcine coding sequences of PPARGC1A were sequenced together with the splice site regions and the 5' and 3' regions. Using direct sequencing nine SNPs were found. Allele frequencies were determined in unrelated animals of five different pig breeds. In the MARC Meishan-White Composite resource population, the polymorphism in exon 9 was significantly associated with leaf fat weight. PPARGC1A has been mapped by FISH to SSC8p21. A (CA)n microsatellite (SGU0001) has been localised near marker SWR1101 on chromosome 8 by RH mapping and at the same position as marker KS195 (32.5 cM) by linkage mapping. The AseI (nt857, Asn/Asn489) polymorphism in exon 8 was used to perform linkage analysis in the Hohenheim pedigrees and located the gene in the same genomic region. Transcription of the gene was detected in adipose, muscle, kidney, liver, brain, heart and adrenal gland tissues, which is in agreement with the function of PPARGC1A in adaptive thermogenesis.
Collapse
Affiliation(s)
- K Jacobs
- Department of Animal Nutrition, Genetics, Breeding and Ethology, Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | | | | | | | | | | | | | | | | |
Collapse
|
44
|
Demars J, Riquet J, Feve K, Gautier M, Morisson M, Demeure O, Renard C, Chardon P, Milan D. High resolution physical map of porcine chromosome 7 QTL region and comparative mapping of this region among vertebrate genomes. BMC Genomics 2006; 7:13. [PMID: 16433907 PMCID: PMC1420295 DOI: 10.1186/1471-2164-7-13] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2005] [Accepted: 01/24/2006] [Indexed: 11/10/2022] Open
Abstract
Background On porcine chromosome 7, the region surrounding the Major Histocompatibility Complex (MHC) contains several Quantitative Trait Loci (QTL) influencing many traits including growth, back fat thickness and carcass composition. Previous studies highlighted that a fragment of ~3.7 Mb is located within the Swine Leucocyte Antigen (SLA) complex. Internal rearrangements of this fragment were suggested, and partial contigs had been built, but further characterization of this region and identification of all human chromosomal fragments orthologous to this porcine fragment had to be carried out. Results A whole physical map of the region was constructed by integrating Radiation Hybrid (RH) mapping, BAC fingerprinting data of the INRA BAC library and anchoring BAC end sequences on the human genome. 17 genes and 2 reference microsatellites were ordered on the high resolution IMNpRH212000rad Radiation Hybrid panel. A 1000:1 framework map covering 550 cR12000 was established and a complete contig of the region was developed. New micro rearrangements were highlighted between the porcine and human genomes. A bovine RH map was also developed in this region by mapping 16 genes. Comparison of the organization of this region in pig, cattle, human, mouse, dog and chicken genomes revealed that 1) the translocation of the fragment described previously is observed only on the bovine and porcine genomes and 2) the new internal micro rearrangements are specific of the porcine genome. Conclusion We estimate that the region contains several rearrangements and covers 5.2 Mb of the porcine genome. The study of this complete BAC contig showed that human chromosomal fragments homologs of this heavily rearranged QTL region are all located in the region of HSA6 that surrounds the centromere. This work allows us to define a list of all candidate genes that could explain these QTL effects.
Collapse
Affiliation(s)
- Julie Demars
- Laboratoire de Génétique Cellulaire, INRA, BP52627, 31326 Castanet-Tolosan, France
| | - Juliette Riquet
- Laboratoire de Génétique Cellulaire, INRA, BP52627, 31326 Castanet-Tolosan, France
| | - Katia Feve
- Laboratoire de Génétique Cellulaire, INRA, BP52627, 31326 Castanet-Tolosan, France
| | - Mathieu Gautier
- Laboratoire de Génétique Biochimique et de Cytogénétique, INRA, 78352 Jouy en Josas, France
| | - Mireille Morisson
- Laboratoire de Génétique Cellulaire, INRA, BP52627, 31326 Castanet-Tolosan, France
| | - Olivier Demeure
- Laboratoire de Génétique animale, INRA, 35042 Rennes, France
| | - Christine Renard
- Laboratoire de Radiobiologie et d'Etude du Génome, INRA-CEA, 78352 Jouy en Josas, France
| | - Patrick Chardon
- Laboratoire de Radiobiologie et d'Etude du Génome, INRA-CEA, 78352 Jouy en Josas, France
| | - Denis Milan
- Laboratoire de Génétique Cellulaire, INRA, BP52627, 31326 Castanet-Tolosan, France
| |
Collapse
|
45
|
Lahbib-Mansais Y, Karlskov-Mortensen P, Mompart F, Milan D, Jørgensen CB, Cirera S, Gorodkin J, Faraut T, Yerle M, Fredholm M. A high-resolution comparative map between pig chromosome 17 and human chromosomes 4, 8, and 20: identification of synteny breakpoints. Genomics 2006; 86:405-13. [PMID: 16111857 DOI: 10.1016/j.ygeno.2005.07.002] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2005] [Revised: 07/04/2005] [Accepted: 07/05/2005] [Indexed: 11/22/2022]
Abstract
We report on the construction of a high-resolution comparative map of porcine chromosome 17 (SSC17) focusing on evolutionary breakpoints with human chromosomes. The comparative map shows high homology with human chromosome 20 but suggests more limited homologies with other human chromosomes. SSC17 is of particular interest in studies of chromosomal organization due to the presence of QTLs that affect meat quality and carcass composition. A total of 158 pig ESTs available in databases or developed by the Sino-Danish Pig Genome Sequencing Consortium were mapped using the INRA-University of Minnesota porcine radiation hybrid panel. The high-resolution map was further anchored by fluorescence in situ hybridization. This study confirmed the extensive conservation between SSC17 and HSA20 and enabled the gene order to be determined. The homology of the SSC17 pericentromeric region was extended to other human chromosomes (HSA4, HSA8) and the chromosomal breakpoint boundaries were accurately defined. In total 15 breakpoints were identified.
Collapse
MESH Headings
- Animals
- Chromosome Breakage/genetics
- Chromosomes, Artificial, Bacterial/genetics
- Chromosomes, Human, Pair 20
- Chromosomes, Human, Pair 4
- Chromosomes, Human, Pair 8
- Chromosomes, Mammalian
- Cytogenetics
- Expressed Sequence Tags
- Genetic Markers
- Genome, Human
- Humans
- In Situ Hybridization, Fluorescence
- Radiation Hybrid Mapping
- Swine/genetics
- Synteny/genetics
Collapse
Affiliation(s)
- Yvette Lahbib-Mansais
- Institut National de la Recherche Agronomique, Laboratoire de Génétique Cellulaire, BP 52627, 31326 Castanet-Tolosan, France.
| | | | | | | | | | | | | | | | | | | |
Collapse
|
46
|
Ando A, Shigenari A, Kulski JK, Renard C, Chardon P, Shiina T, Inoko H. Genomic sequence analysis of the 238-kb swine segment with a cluster of TRIM and olfactory receptor genes located, but with no class I genes, at the distal end of the SLA class I region. Immunogenetics 2005; 57:864-73. [PMID: 16328468 DOI: 10.1007/s00251-005-0053-6] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2005] [Accepted: 09/20/2005] [Indexed: 10/25/2022]
Abstract
Continuous genomic sequence has been previously determined for the swine leukocyte antigen (SLA) class I region from the TNF gene cluster at the border between the major histocompatibility complex (MHC) class III and class I regions to the UBD gene at the telomeric end of the classical class I gene cluster (SLA-1 to SLA-5, SLA-9, SLA-11). To complete the genomic sequence of the entire SLA class I genomic region, we have analyzed the genomic sequences of two BAC clones carrying a continuous 237,633-bp-long segment spanning from the TRIM15 gene to the UBD gene located on the telomeric side of the classical SLA class I gene cluster. Fifteen non-class I genes, including the zinc finger and the tripartite motif (TRIM) ring-finger-related family genes and olfactory receptor genes, were identified in the 238-kilobase (kb) segment, and their location in the segment was similar to their apparent human homologs. In contrast, a human segment (alpha block) spanning about 375 kb from the gene ETF1P1 and from the HLA-J to HLA-F genes was absent from the 238-kb swine segment. We conclude that the gene organization of the MHC non-class I genes located in the telomeric side of the classical SLA class I gene cluster is remarkably similar between the swine and the human segments, although the swine lacks a 375-kb segment corresponding to the human alpha block.
Collapse
Affiliation(s)
- Asako Ando
- Department of Molecular Life Science, Division of Basic Medical Science and Molecular Medicine, Tokai University School of Medicine, Bohseidai, Isehara, Kanagawa, Japan
| | | | | | | | | | | | | |
Collapse
|
47
|
Butler JE, Wertz N, Sun J, Wang H, Lemke C, Chardon P, Piumi F, Wells K. The pre-immune variable kappa repertoire of swine is selectively generated from certain subfamilies of Vkappa2 and one Jkappa gene. Vet Immunol Immunopathol 2005; 108:127-37. [PMID: 16112743 DOI: 10.1016/j.vetimm.2005.07.016] [Citation(s) in RCA: 14] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Combinatorial diversity is highly restricted during formation of the pre-immune heavy chain repertoire of swine, raising the question of whether the same is true for the pre-immune light chain repertoire. Before addressing this question, we first used competitive PCR to show that kappa and lambda light chains in swine are equally expressed in mature B cells similar to the situation in humans but alike that in other studied Ungulates. This justified efforts to examine the repertoire of both light chain types. These studies also revealed that lambda is preferentially expressed at sites of B cells lymphogenesis, perhaps because of the use of a surrogate light chain containing lambda5. Data are presented here on >100 VkappaJkappa-containing transcripts and approximately 180 genomic Vkappa genes to show that >90% of the pre-immune repertoire is generated from three subfamilies of IGKV2 genes and one of five Jkappa segments. The kappa locus contains >or=50 IGKV2 genes belonging to at least five subfamilies and an undetermined but perhaps equal number of IGKV1 genes. The porcine IGKV1 and IGKV2 genes share 87% sequence similarity with their human counterparts and Jkappa1 through Jkappa5 share sequence and organizational homology with those in sheep, horse, human and mouse. Swine have a single Ckappa gene. These findings contrast with those from rodents and primates but are reminiscent of those on the pre-immune heavy chain repertoire of swine in that it is generated using a relatively restricted number of gene segments. These restricted pre-immune repertoires may reflect the minimal exposure of the fetus to maternal factors and environmental antigens. The significance for swine immunology of characterizing the pre-immune repertoire is discussed.
Collapse
Affiliation(s)
- J E Butler
- The University of Iowa, Department of Microbiology and Interdisciplinary Immunology Program, Iowa City, IA 52242, USA.
| | | | | | | | | | | | | | | |
Collapse
|
48
|
Meyers SN, Rogatcheva MB, Larkin DM, Yerle M, Milan D, Hawken RJ, Schook LB, Beever JE. Piggy-BACing the human genome. Genomics 2005; 86:739-52. [PMID: 16246521 DOI: 10.1016/j.ygeno.2005.04.010] [Citation(s) in RCA: 87] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2005] [Revised: 04/15/2005] [Accepted: 04/19/2005] [Indexed: 11/17/2022]
Abstract
Using the INRA-Minnesota porcine radiation hybrid panel, we have constructed a human-pig comparative map composed of 2274 loci, including 206 ESTs and 2068 BAC-end sequences, assigned to 34 linkage groups. The average spacing between comparative anchor loci is 1.15 Mb based on human genome sequence coordinates. A total of 51 conserved synteny groups that include 173 conserved segments were identified. This radiation hybrid map has the highest resolution of any porcine map to date and its integration with the porcine linkage map (reported here) will greatly facilitate the positional cloning of genes influencing complex traits of both agricultural and biomedical interest. Additionally, this map will provide a framework for anchoring contigs generated through BAC fingerprinting efforts and assist in the selection of a BAC minimal tiling path and assembly of the first sequence-ready map of the porcine genome.
Collapse
Affiliation(s)
- Stacey N Meyers
- University of Illinois at Urbana-Champaign, 220 Edward R. Madigan Laboratory, MC-051, 1201 West Gregory Drive, Urbana, IL 61801, USA
| | | | | | | | | | | | | | | |
Collapse
|
49
|
Van Poucke M, Bourry D, Piumi F, Mattheeuws M, Van Zeveren A, Chardon P, Peelman LJ. Comparative analysis of a BAC contig of porcine chromosome 13q31-q32 and human chromosome 3q21-q22. BMC Genomics 2005; 6:133. [PMID: 16176575 PMCID: PMC1249572 DOI: 10.1186/1471-2164-6-133] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2005] [Accepted: 09/21/2005] [Indexed: 12/03/2022] Open
Abstract
Background The gene(s) encoding the ETEC F4ab/ac receptors, involved in neonatal diarrhoea in pigs (a disease not yet described in humans), is located close to the TF locus on Sscr13. In order to reveal and characterize possible candidate genes encoding these receptors, a porcine physical map of the TF region is indispensable. Results A contig of 33 BAC clones, covering approximately 1.35 Mb surrounding the TF locus on Sscr13q31-q32, was built by chromosome walking. A total of 22,552 bp from the BAC contig were sequenced and compared with database sequences to identify genes, ESTs and repeat sequences, and to anchor the contig to the syntenic region of the human genome sequence (Hsap3q21-q22). The contig was further annotated based on this human/porcine comparative map, and was also anchored to the Sanger porcine framework map and the integrated map of Sscr13 by RH mapping. Conclusion The annotated contig, containing 10 genes and 2 ESTs, showed a complete conservation of linkage (gene order and orientation) with the human genome sequence, based on 46 anchor points. This underlines the importance of the human/porcine comparative map for the identification of porcine genes associated with genetic defects and economically important traits, and for assembly of the porcine genome sequence.
Collapse
Affiliation(s)
- Mario Van Poucke
- Department of Animal Genetics and Breeding, Faculty of Veterinary Medicine, Ghent University, Heidestraat 19, B-9820 Merelbeke, Belgium
| | - David Bourry
- Department of Animal Genetics and Breeding, Faculty of Veterinary Medicine, Ghent University, Heidestraat 19, B-9820 Merelbeke, Belgium
- Department of Organic Chemistry, Faculty of Sciences, Ghent University, Krijgslaan 281 S4, B-9000 Ghent, Belgium
| | - François Piumi
- Laboratoire de Radiobiologie et d'Etude du Génome, UMR INRA-CEA, F-78352 Jouy en Josas cedex, France
| | - Marc Mattheeuws
- Department of Animal Genetics and Breeding, Faculty of Veterinary Medicine, Ghent University, Heidestraat 19, B-9820 Merelbeke, Belgium
| | - Alex Van Zeveren
- Department of Animal Genetics and Breeding, Faculty of Veterinary Medicine, Ghent University, Heidestraat 19, B-9820 Merelbeke, Belgium
| | - Patrick Chardon
- Laboratoire de Radiobiologie et d'Etude du Génome, UMR INRA-CEA, F-78352 Jouy en Josas cedex, France
| | - Luc J Peelman
- Department of Animal Genetics and Breeding, Faculty of Veterinary Medicine, Ghent University, Heidestraat 19, B-9820 Merelbeke, Belgium
| |
Collapse
|
50
|
Barbosa A, Demeure O, Urien C, Milan D, Chardon P, Renard C. A physical map of large segments of pig chromosome 7q11-q14: comparative analysis with human chromosome 6p21. Mamm Genome 2005; 15:982-95. [PMID: 15599557 DOI: 10.1007/s00335-004-3008-6] [Citation(s) in RCA: 20] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2004] [Accepted: 07/20/2004] [Indexed: 11/29/2022]
Abstract
The aim of this study was to establish a porcine physical map along the chromosome SSC7q by construction of BAC contigs between microsatellites Sw1409 and S0102. The SLA class II contig, located on SSC7q, was lengthened. Four major BAC contigs and 10 short contigs span a region equivalent to 800 cR measured by IMpRH7000 mapping. The BAC contigs were initiated by PCR screening with primers derived from human orthologous segments, extended by chromosome walking, and controlled and oriented by RH mapping with the two available panels, IMpRH7000Rad and IMNpRH12000Rad. The location of 43 genes was revealed by sequenced segments, either from BAC ends or PCR products from BAC clones. The 220 BAC end sequences (BES) were also used to analyze the different marks of evolution. Comparative mapping analysis between pigs and humans demonstrated that the gene organization on HSA6p21 and on SSC7p11 and q11-q14 segments was conserved during evolution, with the exception of long fragments of HSA6p12 which shuffled and spliced the SLA extended class II region. Additional punctual variations (unique gene insertion/deletion) were observed, even within conserved segments, revealing the evolutionary complexity of this region. In addition, 18 new polymorphic microsatellites have been selected in order to cover the entire SSC7p11-q14 region.
Collapse
Affiliation(s)
- Angela Barbosa
- Laboratoire mixte de Radiobiologie et d'Etude du Génome, Institut National de la Recherche Agronomigue et Center d'Energie Atomique, Domaine de Vilvert, 78352, Jouy en Josas cedex, France
| | | | | | | | | | | |
Collapse
|