Characterization of a deletion in the Hsp70 cluster in the bovine reference genome

Autores
Suqueli Garcia, M. Florencia; Castellote, Martín Alfredo; Feingold, Sergio Enrique; Corva, Pablo Marcelo
Año de publicación
2017
Idioma
inglés
Tipo de recurso
artículo
Estado
versión publicada
Descripción
The 70 kilodalton heat shock proteins (Hsp70) are highly conserved molecular chaperones which have a crucial role in the stress response of the cell. In mammals, the Hsp70 proteins are encoded by a cluster of three genes: HSPA1A, HSPA1B and HSPA1L. In bovines, this cluster is located on chromosome 23 downstream of the major histocompatibility complex (BoLA). We detected inconsistencies in the location of markers on the Hsp70 genes reported in the literature that pointed to a potential deletion in the bovine reference genome UMD 3.1.1. An in silico analysis of the bovine genomic region of the Hsp70 cluster, using available information from public databases, confirmed the existence of a deletion of 11.1‐kb spanning the HSPA1B gene and the intergenic region between HSPA1B and HSPA1A. Although we originally considered this an assembly error, it is most likely a particular condition of L1 Dominette 01449, the cow sequenced in the Bovine Genome Project. Moreover, we suggest a new classification of bovine Hsp70sequences reported in NCBI and a reassignment of the location of SNPs from dbSNP that map to the deletion on BTA23. We also compared the location of selected transcription factor binding sites on the promoters of HSPA1A and HSPA1B. The results generated in the present work could be helpful to refine the reference genome of an important livestock species and also to understand the role and the regulation of the bovine Hsp70 genes.
EEA Balcarce
Fil: Suqueli García, M.F. Universidad Nacional de Mar del Plata. Facultad de Ciencias Agrarias; Argentina
Fil: Castellote, M.A. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Balcarce; Argentina
Fil: Feingold, Sergio. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Balcarce; Argentina
Fil: Corva, Pablo. Universidad Nacional de Mar del Plata, Facultad de Ciencias Agrarias; Argentina.
Fuente
Animal genetics 48 (4) : 377-385. (2017)
Materia
Ganado bovino
Cattle
Genomes
Genes
Genética Animal
Genomas
Animals Genetics
Nivel de accesibilidad
acceso restringido
Condiciones de uso
Repositorio
INTA Digital (INTA)
Institución
Instituto Nacional de Tecnología Agropecuaria
OAI Identificador
oai:localhost:20.500.12123/3151
Acceder
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oai_identifier_str oai:localhost:20.500.12123/3151
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network_name_str INTA Digital (INTA)
spelling Characterization of a deletion in the Hsp70 cluster in the bovine reference genomeSuqueli Garcia, M. FlorenciaCastellote, Martín AlfredoFeingold, Sergio EnriqueCorva, Pablo MarceloGanado bovinoCattleGenomesGenesGenética AnimalGenomasAnimals GeneticsThe 70 kilodalton heat shock proteins (Hsp70) are highly conserved molecular chaperones which have a crucial role in the stress response of the cell. In mammals, the Hsp70 proteins are encoded by a cluster of three genes: HSPA1A, HSPA1B and HSPA1L. In bovines, this cluster is located on chromosome 23 downstream of the major histocompatibility complex (BoLA). We detected inconsistencies in the location of markers on the Hsp70 genes reported in the literature that pointed to a potential deletion in the bovine reference genome UMD 3.1.1. An in silico analysis of the bovine genomic region of the Hsp70 cluster, using available information from public databases, confirmed the existence of a deletion of 11.1‐kb spanning the HSPA1B gene and the intergenic region between HSPA1B and HSPA1A. Although we originally considered this an assembly error, it is most likely a particular condition of L1 Dominette 01449, the cow sequenced in the Bovine Genome Project. Moreover, we suggest a new classification of bovine Hsp70sequences reported in NCBI and a reassignment of the location of SNPs from dbSNP that map to the deletion on BTA23. We also compared the location of selected transcription factor binding sites on the promoters of HSPA1A and HSPA1B. The results generated in the present work could be helpful to refine the reference genome of an important livestock species and also to understand the role and the regulation of the bovine Hsp70 genes.EEA BalcarceFil: Suqueli García, M.F. Universidad Nacional de Mar del Plata. Facultad de Ciencias Agrarias; ArgentinaFil: Castellote, M.A. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Balcarce; ArgentinaFil: Feingold, Sergio. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Balcarce; ArgentinaFil: Corva, Pablo. Universidad Nacional de Mar del Plata, Facultad de Ciencias Agrarias; Argentina.Wiley Online Library2018-08-22T18:39:54Z2018-08-22T18:39:54Z2017-07-11info:eu-repo/semantics/articleinfo:eu-repo/semantics/publishedVersionhttp://purl.org/coar/resource_type/c_6501info:ar-repo/semantics/articuloapplication/pdfhttps://onlinelibrary.wiley.com/doi/full/10.1111/age.12561http://hdl.handle.net/20.500.12123/31511365-2052https://doi.org/10.1111/age.12561Animal genetics 48 (4) : 377-385. (2017)reponame:INTA Digital (INTA)instname:Instituto Nacional de Tecnología Agropecuariaenginfo:eu-repo/semantics/restrictedAccess2025-09-29T13:44:24Zoai:localhost:20.500.12123/3151instacron:INTAInstitucionalhttp://repositorio.inta.gob.ar/Organismo científico-tecnológicoNo correspondehttp://repositorio.inta.gob.ar/oai/requesttripaldi.nicolas@inta.gob.arArgentinaNo correspondeNo correspondeNo correspondeopendoar:l2025-09-29 13:44:24.718INTA Digital (INTA) - Instituto Nacional de Tecnología Agropecuariafalse
dc.title.none.fl_str_mv Characterization of a deletion in the Hsp70 cluster in the bovine reference genome
title Characterization of a deletion in the Hsp70 cluster in the bovine reference genome
spellingShingle Characterization of a deletion in the Hsp70 cluster in the bovine reference genome
Suqueli Garcia, M. Florencia
Ganado bovino
Cattle
Genomes
Genes
Genética Animal
Genomas
Animals Genetics
title_short Characterization of a deletion in the Hsp70 cluster in the bovine reference genome
title_full Characterization of a deletion in the Hsp70 cluster in the bovine reference genome
title_fullStr Characterization of a deletion in the Hsp70 cluster in the bovine reference genome
title_full_unstemmed Characterization of a deletion in the Hsp70 cluster in the bovine reference genome
title_sort Characterization of a deletion in the Hsp70 cluster in the bovine reference genome
dc.creator.none.fl_str_mv Suqueli Garcia, M. Florencia
Castellote, Martín Alfredo
Feingold, Sergio Enrique
Corva, Pablo Marcelo
author Suqueli Garcia, M. Florencia
author_facet Suqueli Garcia, M. Florencia
Castellote, Martín Alfredo
Feingold, Sergio Enrique
Corva, Pablo Marcelo
author_role author
author2 Castellote, Martín Alfredo
Feingold, Sergio Enrique
Corva, Pablo Marcelo
author2_role author
author
author
dc.subject.none.fl_str_mv Ganado bovino
Cattle
Genomes
Genes
Genética Animal
Genomas
Animals Genetics
topic Ganado bovino
Cattle
Genomes
Genes
Genética Animal
Genomas
Animals Genetics
dc.description.none.fl_txt_mv The 70 kilodalton heat shock proteins (Hsp70) are highly conserved molecular chaperones which have a crucial role in the stress response of the cell. In mammals, the Hsp70 proteins are encoded by a cluster of three genes: HSPA1A, HSPA1B and HSPA1L. In bovines, this cluster is located on chromosome 23 downstream of the major histocompatibility complex (BoLA). We detected inconsistencies in the location of markers on the Hsp70 genes reported in the literature that pointed to a potential deletion in the bovine reference genome UMD 3.1.1. An in silico analysis of the bovine genomic region of the Hsp70 cluster, using available information from public databases, confirmed the existence of a deletion of 11.1‐kb spanning the HSPA1B gene and the intergenic region between HSPA1B and HSPA1A. Although we originally considered this an assembly error, it is most likely a particular condition of L1 Dominette 01449, the cow sequenced in the Bovine Genome Project. Moreover, we suggest a new classification of bovine Hsp70sequences reported in NCBI and a reassignment of the location of SNPs from dbSNP that map to the deletion on BTA23. We also compared the location of selected transcription factor binding sites on the promoters of HSPA1A and HSPA1B. The results generated in the present work could be helpful to refine the reference genome of an important livestock species and also to understand the role and the regulation of the bovine Hsp70 genes.
EEA Balcarce
Fil: Suqueli García, M.F. Universidad Nacional de Mar del Plata. Facultad de Ciencias Agrarias; Argentina
Fil: Castellote, M.A. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Balcarce; Argentina
Fil: Feingold, Sergio. Instituto Nacional de Tecnología Agropecuaria (INTA). Estación Experimental Agropecuaria Balcarce; Argentina
Fil: Corva, Pablo. Universidad Nacional de Mar del Plata, Facultad de Ciencias Agrarias; Argentina.
description The 70 kilodalton heat shock proteins (Hsp70) are highly conserved molecular chaperones which have a crucial role in the stress response of the cell. In mammals, the Hsp70 proteins are encoded by a cluster of three genes: HSPA1A, HSPA1B and HSPA1L. In bovines, this cluster is located on chromosome 23 downstream of the major histocompatibility complex (BoLA). We detected inconsistencies in the location of markers on the Hsp70 genes reported in the literature that pointed to a potential deletion in the bovine reference genome UMD 3.1.1. An in silico analysis of the bovine genomic region of the Hsp70 cluster, using available information from public databases, confirmed the existence of a deletion of 11.1‐kb spanning the HSPA1B gene and the intergenic region between HSPA1B and HSPA1A. Although we originally considered this an assembly error, it is most likely a particular condition of L1 Dominette 01449, the cow sequenced in the Bovine Genome Project. Moreover, we suggest a new classification of bovine Hsp70sequences reported in NCBI and a reassignment of the location of SNPs from dbSNP that map to the deletion on BTA23. We also compared the location of selected transcription factor binding sites on the promoters of HSPA1A and HSPA1B. The results generated in the present work could be helpful to refine the reference genome of an important livestock species and also to understand the role and the regulation of the bovine Hsp70 genes.
publishDate 2017
dc.date.none.fl_str_mv 2017-07-11
2018-08-22T18:39:54Z
2018-08-22T18:39:54Z
dc.type.none.fl_str_mv info:eu-repo/semantics/article
info:eu-repo/semantics/publishedVersion
http://purl.org/coar/resource_type/c_6501
info:ar-repo/semantics/articulo
format article
status_str publishedVersion
dc.identifier.none.fl_str_mv https://onlinelibrary.wiley.com/doi/full/10.1111/age.12561
http://hdl.handle.net/20.500.12123/3151
1365-2052
https://doi.org/10.1111/age.12561
url https://onlinelibrary.wiley.com/doi/full/10.1111/age.12561
http://hdl.handle.net/20.500.12123/3151
https://doi.org/10.1111/age.12561
identifier_str_mv 1365-2052
dc.language.none.fl_str_mv eng
language eng
dc.rights.none.fl_str_mv info:eu-repo/semantics/restrictedAccess
eu_rights_str_mv restrictedAccess
dc.format.none.fl_str_mv application/pdf
dc.publisher.none.fl_str_mv Wiley Online Library
publisher.none.fl_str_mv Wiley Online Library
dc.source.none.fl_str_mv Animal genetics 48 (4) : 377-385. (2017)
reponame:INTA Digital (INTA)
instname:Instituto Nacional de Tecnología Agropecuaria
reponame_str INTA Digital (INTA)
collection INTA Digital (INTA)
instname_str Instituto Nacional de Tecnología Agropecuaria
repository.name.fl_str_mv INTA Digital (INTA) - Instituto Nacional de Tecnología Agropecuaria
repository.mail.fl_str_mv tripaldi.nicolas@inta.gob.ar
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