HLA-F displays highly divergent and frequent haplotype lineages associated with different mRNA expression levels
Autor(a) principal: | |
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Data de Publicação: | 2019 |
Outros Autores: | , , , , , |
Tipo de documento: | Artigo |
Idioma: | eng |
Título da fonte: | Repositório Institucional da UNESP |
Texto Completo: | http://dx.doi.org/10.1016/j.humimm.2018.10.016 http://hdl.handle.net/11449/187017 |
Resumo: | HLA-F is one of the most conserved loci among the HLA gene family. The exact function of HLA-F is still under investigation. HLA-F might present tolerogenic features, participate in the stabilization of HLA molecules in open conformation, and also participate in the recycling of HLA molecules. Here we evaluate the variability and haplotype structure of the HLA-F distal promoter segment (from −1893 to −943) and how this segment is correlated with the coding region. Variability at the promoter segment was surveyed in 196 Brazilian samples using second-generation sequencing. The HLA-F promoter region presents two major haplotype lineages. Most of the variable sites are in perfect linkage and associated with a single promoter haplotype, here named F ∗ distal-C. This haplotype is associated with F ∗ 01:01:02 alleles, while alleles from the F ∗ 01:01:01 or F ∗ 01:03 groups present closely related promoter sequences. F ∗ distal-C is quite frequent in Brazil and in worldwide populations, with frequencies ranging from 8.41% at the Iberian Population in Spain to 34.34% in Vietnam. F ∗ distal-C is also present in Neanderthal and Denisovan samples. In silico analyses demonstrated that F ∗ distal-C presents a different transcription factor binding profile compared with other HLA-F promoters. Moreover, individuals carrying this haplotype present higher HLA-F mRNA expression levels. Functional studies are required to define the exact mechanism underlying this higher HLA-F mRNA expression level associated with F ∗ distal-C and F ∗ 01:01:02 alleles. |
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HLA-F displays highly divergent and frequent haplotype lineages associated with different mRNA expression levelsBrazilExpression regulationGene expressionHaplotypesHLA-FNext Generation Sequencing (NGS)PolymorphismsPromoterRNA-SeqVariabilityHLA-F is one of the most conserved loci among the HLA gene family. The exact function of HLA-F is still under investigation. HLA-F might present tolerogenic features, participate in the stabilization of HLA molecules in open conformation, and also participate in the recycling of HLA molecules. Here we evaluate the variability and haplotype structure of the HLA-F distal promoter segment (from −1893 to −943) and how this segment is correlated with the coding region. Variability at the promoter segment was surveyed in 196 Brazilian samples using second-generation sequencing. The HLA-F promoter region presents two major haplotype lineages. Most of the variable sites are in perfect linkage and associated with a single promoter haplotype, here named F ∗ distal-C. This haplotype is associated with F ∗ 01:01:02 alleles, while alleles from the F ∗ 01:01:01 or F ∗ 01:03 groups present closely related promoter sequences. F ∗ distal-C is quite frequent in Brazil and in worldwide populations, with frequencies ranging from 8.41% at the Iberian Population in Spain to 34.34% in Vietnam. F ∗ distal-C is also present in Neanderthal and Denisovan samples. In silico analyses demonstrated that F ∗ distal-C presents a different transcription factor binding profile compared with other HLA-F promoters. Moreover, individuals carrying this haplotype present higher HLA-F mRNA expression levels. Functional studies are required to define the exact mechanism underlying this higher HLA-F mRNA expression level associated with F ∗ distal-C and F ∗ 01:01:02 alleles.Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES)Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)Conselho Nacional de Desenvolvimento Científico e Tecnológico (CNPq)São Paulo State University (UNESP) Molecular Genetics and Bioinformatics Laboratory Experimental Research Unit (UNIPEX) School of MedicineSchool of Medicine of Ribeirão Preto University of São PauloDepartamento de Química Faculdade de Filosofia Ciências e Letras de Ribeirão Preto Universidade de São PauloSão Paulo State University (UNESP) Pathology Department School of MedicineSão Paulo State University (UNESP) Molecular Genetics and Bioinformatics Laboratory Experimental Research Unit (UNIPEX) School of MedicineSão Paulo State University (UNESP) Pathology Department School of MedicineFAPESP: 2013/17084-2CNPq: 302590/2016-1CNPq: 309572/2014-2Universidade Estadual Paulista (Unesp)Universidade de São Paulo (USP)Buttura, Renato V. [UNESP]Ramalho, Jaqueline [UNESP]Lima, Thálitta H.A. [UNESP]Donadi, Eduardo A.Veiga-Castelli, Luciana C.Mendes-Junior, Celso T.Castelli, Erick C. [UNESP]2019-10-06T15:22:53Z2019-10-06T15:22:53Z2019-02-01info:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/article112-119http://dx.doi.org/10.1016/j.humimm.2018.10.016Human Immunology, v. 80, n. 2, p. 112-119, 2019.1879-11660198-8859http://hdl.handle.net/11449/18701710.1016/j.humimm.2018.10.0162-s2.0-85055737689Scopusreponame:Repositório Institucional da UNESPinstname:Universidade Estadual Paulista (UNESP)instacron:UNESPengHuman Immunologyinfo:eu-repo/semantics/openAccess2021-10-22T21:54:17Zoai:repositorio.unesp.br:11449/187017Repositório InstitucionalPUBhttp://repositorio.unesp.br/oai/requestopendoar:29462021-10-22T21:54:17Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP)false |
dc.title.none.fl_str_mv |
HLA-F displays highly divergent and frequent haplotype lineages associated with different mRNA expression levels |
title |
HLA-F displays highly divergent and frequent haplotype lineages associated with different mRNA expression levels |
spellingShingle |
HLA-F displays highly divergent and frequent haplotype lineages associated with different mRNA expression levels Buttura, Renato V. [UNESP] Brazil Expression regulation Gene expression Haplotypes HLA-F Next Generation Sequencing (NGS) Polymorphisms Promoter RNA-Seq Variability |
title_short |
HLA-F displays highly divergent and frequent haplotype lineages associated with different mRNA expression levels |
title_full |
HLA-F displays highly divergent and frequent haplotype lineages associated with different mRNA expression levels |
title_fullStr |
HLA-F displays highly divergent and frequent haplotype lineages associated with different mRNA expression levels |
title_full_unstemmed |
HLA-F displays highly divergent and frequent haplotype lineages associated with different mRNA expression levels |
title_sort |
HLA-F displays highly divergent and frequent haplotype lineages associated with different mRNA expression levels |
author |
Buttura, Renato V. [UNESP] |
author_facet |
Buttura, Renato V. [UNESP] Ramalho, Jaqueline [UNESP] Lima, Thálitta H.A. [UNESP] Donadi, Eduardo A. Veiga-Castelli, Luciana C. Mendes-Junior, Celso T. Castelli, Erick C. [UNESP] |
author_role |
author |
author2 |
Ramalho, Jaqueline [UNESP] Lima, Thálitta H.A. [UNESP] Donadi, Eduardo A. Veiga-Castelli, Luciana C. Mendes-Junior, Celso T. Castelli, Erick C. [UNESP] |
author2_role |
author author author author author author |
dc.contributor.none.fl_str_mv |
Universidade Estadual Paulista (Unesp) Universidade de São Paulo (USP) |
dc.contributor.author.fl_str_mv |
Buttura, Renato V. [UNESP] Ramalho, Jaqueline [UNESP] Lima, Thálitta H.A. [UNESP] Donadi, Eduardo A. Veiga-Castelli, Luciana C. Mendes-Junior, Celso T. Castelli, Erick C. [UNESP] |
dc.subject.por.fl_str_mv |
Brazil Expression regulation Gene expression Haplotypes HLA-F Next Generation Sequencing (NGS) Polymorphisms Promoter RNA-Seq Variability |
topic |
Brazil Expression regulation Gene expression Haplotypes HLA-F Next Generation Sequencing (NGS) Polymorphisms Promoter RNA-Seq Variability |
description |
HLA-F is one of the most conserved loci among the HLA gene family. The exact function of HLA-F is still under investigation. HLA-F might present tolerogenic features, participate in the stabilization of HLA molecules in open conformation, and also participate in the recycling of HLA molecules. Here we evaluate the variability and haplotype structure of the HLA-F distal promoter segment (from −1893 to −943) and how this segment is correlated with the coding region. Variability at the promoter segment was surveyed in 196 Brazilian samples using second-generation sequencing. The HLA-F promoter region presents two major haplotype lineages. Most of the variable sites are in perfect linkage and associated with a single promoter haplotype, here named F ∗ distal-C. This haplotype is associated with F ∗ 01:01:02 alleles, while alleles from the F ∗ 01:01:01 or F ∗ 01:03 groups present closely related promoter sequences. F ∗ distal-C is quite frequent in Brazil and in worldwide populations, with frequencies ranging from 8.41% at the Iberian Population in Spain to 34.34% in Vietnam. F ∗ distal-C is also present in Neanderthal and Denisovan samples. In silico analyses demonstrated that F ∗ distal-C presents a different transcription factor binding profile compared with other HLA-F promoters. Moreover, individuals carrying this haplotype present higher HLA-F mRNA expression levels. Functional studies are required to define the exact mechanism underlying this higher HLA-F mRNA expression level associated with F ∗ distal-C and F ∗ 01:01:02 alleles. |
publishDate |
2019 |
dc.date.none.fl_str_mv |
2019-10-06T15:22:53Z 2019-10-06T15:22:53Z 2019-02-01 |
dc.type.status.fl_str_mv |
info:eu-repo/semantics/publishedVersion |
dc.type.driver.fl_str_mv |
info:eu-repo/semantics/article |
format |
article |
status_str |
publishedVersion |
dc.identifier.uri.fl_str_mv |
http://dx.doi.org/10.1016/j.humimm.2018.10.016 Human Immunology, v. 80, n. 2, p. 112-119, 2019. 1879-1166 0198-8859 http://hdl.handle.net/11449/187017 10.1016/j.humimm.2018.10.016 2-s2.0-85055737689 |
url |
http://dx.doi.org/10.1016/j.humimm.2018.10.016 http://hdl.handle.net/11449/187017 |
identifier_str_mv |
Human Immunology, v. 80, n. 2, p. 112-119, 2019. 1879-1166 0198-8859 10.1016/j.humimm.2018.10.016 2-s2.0-85055737689 |
dc.language.iso.fl_str_mv |
eng |
language |
eng |
dc.relation.none.fl_str_mv |
Human Immunology |
dc.rights.driver.fl_str_mv |
info:eu-repo/semantics/openAccess |
eu_rights_str_mv |
openAccess |
dc.format.none.fl_str_mv |
112-119 |
dc.source.none.fl_str_mv |
Scopus reponame:Repositório Institucional da UNESP instname:Universidade Estadual Paulista (UNESP) instacron:UNESP |
instname_str |
Universidade Estadual Paulista (UNESP) |
instacron_str |
UNESP |
institution |
UNESP |
reponame_str |
Repositório Institucional da UNESP |
collection |
Repositório Institucional da UNESP |
repository.name.fl_str_mv |
Repositório Institucional da UNESP - Universidade Estadual Paulista (UNESP) |
repository.mail.fl_str_mv |
|
_version_ |
1799964414790598656 |