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Comprehensive analysis of MHC class I genes from the U-, S-, and Z-lineages in Atlantic salmon

BACKGROUND: We have previously sequenced more than 500 kb of the duplicated MHC class I regions in Atlantic salmon. In the IA region we identified the loci for the MHC class I gene Sasa-UBA in addition to a soluble MHC class I molecule, Sasa-ULA. A pseudolocus for Sasa-UCA was identified in the nonc...

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Autores principales: Lukacs, Morten F, Harstad, Håvard, Bakke, Hege G, Beetz-Sargent, Marianne, McKinnel, Linda, Lubieniecki, Krzysztof P, Koop, Ben F, Grimholt, Unni
Formato: Texto
Lenguaje:English
Publicado: BioMed Central 2010
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2846915/
https://www.ncbi.nlm.nih.gov/pubmed/20205726
http://dx.doi.org/10.1186/1471-2164-11-154
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author Lukacs, Morten F
Harstad, Håvard
Bakke, Hege G
Beetz-Sargent, Marianne
McKinnel, Linda
Lubieniecki, Krzysztof P
Koop, Ben F
Grimholt, Unni
author_facet Lukacs, Morten F
Harstad, Håvard
Bakke, Hege G
Beetz-Sargent, Marianne
McKinnel, Linda
Lubieniecki, Krzysztof P
Koop, Ben F
Grimholt, Unni
author_sort Lukacs, Morten F
collection PubMed
description BACKGROUND: We have previously sequenced more than 500 kb of the duplicated MHC class I regions in Atlantic salmon. In the IA region we identified the loci for the MHC class I gene Sasa-UBA in addition to a soluble MHC class I molecule, Sasa-ULA. A pseudolocus for Sasa-UCA was identified in the nonclassical IB region. Both regions contained genes for antigen presentation, as wells as orthologues to other genes residing in the human MHC region. RESULTS: The genomic localisation of two MHC class I lineages (Z and S) has been resolved. 7 BACs were sequenced using a combination of standard Sanger and 454 sequencing. The new sequence data extended the IA region with 150 kb identifying the location of one Z-lineage locus, ZAA. The IB region was extended with 350 kb including three new Z-lineage loci, ZBA, ZCA and ZDA in addition to a UGA locus. An allelic version of the IB region contained a functional UDA locus in addition to the UCA pseudolocus. Additionally a BAC harbouring two MHC class I genes (UHA) was placed on linkage group 14, while a BAC containing the S-lineage locus SAA (previously known as UAA) was placed on LG10. Gene expression studies showed limited expression range for all class I genes with exception of UBA being dominantly expressed in gut, spleen and gills, and ZAA with high expression in blood. CONCLUSION: Here we describe the genomic organization of MHC class I loci from the U-, Z-, and S-lineages in Atlantic salmon. Nine of the described class I genes are located in the extension of the duplicated IA and IB regions, while three class I genes are found on two separate linkage groups. The gene organization of the two regions indicates that the IB region is evolving at a different pace than the IA region. Expression profiling, polymorphic content, peptide binding properties and phylogenetic relationship show that Atlantic salmon has only one MHC class Ia gene (UBA), in addition to a multitude of nonclassical MHC class I genes from the U-, S- and Z-lineages.
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spelling pubmed-28469152010-03-30 Comprehensive analysis of MHC class I genes from the U-, S-, and Z-lineages in Atlantic salmon Lukacs, Morten F Harstad, Håvard Bakke, Hege G Beetz-Sargent, Marianne McKinnel, Linda Lubieniecki, Krzysztof P Koop, Ben F Grimholt, Unni BMC Genomics Research Article BACKGROUND: We have previously sequenced more than 500 kb of the duplicated MHC class I regions in Atlantic salmon. In the IA region we identified the loci for the MHC class I gene Sasa-UBA in addition to a soluble MHC class I molecule, Sasa-ULA. A pseudolocus for Sasa-UCA was identified in the nonclassical IB region. Both regions contained genes for antigen presentation, as wells as orthologues to other genes residing in the human MHC region. RESULTS: The genomic localisation of two MHC class I lineages (Z and S) has been resolved. 7 BACs were sequenced using a combination of standard Sanger and 454 sequencing. The new sequence data extended the IA region with 150 kb identifying the location of one Z-lineage locus, ZAA. The IB region was extended with 350 kb including three new Z-lineage loci, ZBA, ZCA and ZDA in addition to a UGA locus. An allelic version of the IB region contained a functional UDA locus in addition to the UCA pseudolocus. Additionally a BAC harbouring two MHC class I genes (UHA) was placed on linkage group 14, while a BAC containing the S-lineage locus SAA (previously known as UAA) was placed on LG10. Gene expression studies showed limited expression range for all class I genes with exception of UBA being dominantly expressed in gut, spleen and gills, and ZAA with high expression in blood. CONCLUSION: Here we describe the genomic organization of MHC class I loci from the U-, Z-, and S-lineages in Atlantic salmon. Nine of the described class I genes are located in the extension of the duplicated IA and IB regions, while three class I genes are found on two separate linkage groups. The gene organization of the two regions indicates that the IB region is evolving at a different pace than the IA region. Expression profiling, polymorphic content, peptide binding properties and phylogenetic relationship show that Atlantic salmon has only one MHC class Ia gene (UBA), in addition to a multitude of nonclassical MHC class I genes from the U-, S- and Z-lineages. BioMed Central 2010-03-05 /pmc/articles/PMC2846915/ /pubmed/20205726 http://dx.doi.org/10.1186/1471-2164-11-154 Text en Copyright ©2010 Lukacs et al; licensee BioMed Central Ltd. http://creativecommons.org/licenses/by/2.0 This is an Open Access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/2.0), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
spellingShingle Research Article
Lukacs, Morten F
Harstad, Håvard
Bakke, Hege G
Beetz-Sargent, Marianne
McKinnel, Linda
Lubieniecki, Krzysztof P
Koop, Ben F
Grimholt, Unni
Comprehensive analysis of MHC class I genes from the U-, S-, and Z-lineages in Atlantic salmon
title Comprehensive analysis of MHC class I genes from the U-, S-, and Z-lineages in Atlantic salmon
title_full Comprehensive analysis of MHC class I genes from the U-, S-, and Z-lineages in Atlantic salmon
title_fullStr Comprehensive analysis of MHC class I genes from the U-, S-, and Z-lineages in Atlantic salmon
title_full_unstemmed Comprehensive analysis of MHC class I genes from the U-, S-, and Z-lineages in Atlantic salmon
title_short Comprehensive analysis of MHC class I genes from the U-, S-, and Z-lineages in Atlantic salmon
title_sort comprehensive analysis of mhc class i genes from the u-, s-, and z-lineages in atlantic salmon
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2846915/
https://www.ncbi.nlm.nih.gov/pubmed/20205726
http://dx.doi.org/10.1186/1471-2164-11-154
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