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| Registros recuperados : 82 | |
| 10. |  | MELO, A. L. de; SOUZA, M. M. de; REGITANO, L. C. de A. Identificação de possíveis causas de expressão alelo-específica em músculo de novilhos da raça Nelore. In: JORNADA CIENTÍFICA DA EMBRAPA SÃO CARLOS, 10., 2018, São Carlos, SP. Anais... São Carlos, SP: Embrapa Instrumentação; Embrapa Pecuária Sudeste, 2018. p. 43. (Embrapa Instrumentação. Documentos, 68). Editores técnicos: Daniel Souza Corrêa, Elaine Cristina Paris, Maria Alice Martins, Paulino Ribeiro Villas Boas, Wilson Tadeu Lopes da Silva.| Biblioteca(s): Embrapa Pecuária Sudeste. |
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| 13. | | SOUZA, G. F. J. P. de; OLIVEIRA, A. L. P. C. de; SOUZA, M. M. de. Contribuição ao conhecimento do lenho de Laguncularia racemosa (L.). Silvicultura em São Paulo, São Paulo, v. 16-A, pt. 1, p. 280-292, 1982. Edição dos Anais do Congresso Nacional sobre Essências Nativas, 1982, Campos do Jordão.| Biblioteca(s): Embrapa Florestas. |
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| 19. | | SOUZA, M. M. de; PEREIRA, T. N. S.; AMARAL JUNIOR, A. T.; RODRIGUES, R.; DUTRA, G. A.; SUDRE, C. P. Polimorfismo polinico em acessos de pimenta com base em microscopia eletronica de varredura e analise multivariada. Horticultura Brasileira, Brasilia, v.18, p.749-750, jul. 2000.| Biblioteca(s): Embrapa Hortaliças. |
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| 20. | | SILVA, A. F. da; SILVA, C. da; SOUZA, M. M. de; TARDIN, F. D.; BEHLING, M.; MAY, A. Comportamento produtivo de sorgo sacarino em função do arranjo de plantas, no município de Sinop-MT. In: CONGRESSO NACIONAL DE MILHO E SORGO, 30.; SIMPÓSIO SOBRE LEPDÓPTEROS COMUNS A MILHO, SOJA E ALGODÃO, 1., 2014, Salvador. Eficiência nas cadeias produtivas e o abastecimento global: resumos expandidos. Sete Lagoas: Associação Brasileira de Milho e Sorgo, 2014. 1 CD-ROM.| Biblioteca(s): Embrapa Agrossilvipastoril; Embrapa Milho e Sorgo. |
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 | Acesso ao texto completo restrito à biblioteca da Embrapa Agricultura Digital. Para informações adicionais entre em contato com cnptia.biblioteca@embrapa.br. |
Registro Completo
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Biblioteca(s): |
Embrapa Agricultura Digital; Embrapa Pecuária Sudeste. |
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Data corrente: |
04/11/2022 |
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Data da última atualização: |
07/11/2022 |
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Tipo da produção científica: |
Artigo em Periódico Indexado |
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Circulação/Nível: |
A - 1 |
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Autoria: |
BRUSCADIN, J. J.; CARDOSO, T. F.; DINIZ, W. J. da S.; AFONSO, J.; SOUZA, M. M. de; PETRINI, J.; ANDRADE, B. G. N.; SILVA, V. H. da; FERRAZ, J. B. S.; ZERLOTINI NETO, A.; MOURÃO, G. B.; COUTINHO, L. L.; REGITANO, L. C. de A. |
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Afiliação: |
JENNIFER JESSICA BRUSCADIN, UNIVERSIDADE FEDERAL DE SÃO CARLOS; TAINÃ FIGUEIREDO CARDOSO; WELLISON JARLES DA SILVA DINIZ, AUBURN UNIVERSITY; JULIANA AFONSO; MARCELA MARIA DE SOUZA, IOWA STATE UNIVERSITY; JULIANA PETRINI, AUBURN UNIVERSITY; BRUNO GABRIEL NASCIMENTO ANDRADE, MUNSTER TECHNOLOGICAL UNIVERSITY; VINICIUS HENRIQUE DA SILVA, UNIVERSIDADE DE SÃO PAULO; JOSÉ BENTO STERMAN FERRAZ, UNIVERSIDADE DE SÃO PAULO; ADHEMAR ZERLOTINI NETO, CNPTIA; GERSON BARRETO MOURÃO, UNIVERSIDADE DE SÃO PAULO; LUIZ LEHMANN COUTINHO, UNIVERSIDADE DE SÃO PAULO; LUCIANA CORREIA DE ALMEIDA REGITANO, CPPSE. |
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Título: |
Allele-specific expression reveals functional SNPs affecting muscle-related genes in bovine. |
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Ano de publicação: |
2022 |
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Fonte/Imprenta: |
Biochimica et Biophysica Acta. Gene Regulatory Mechanisms, v. 1865, n. 8, 194886, Nov. 2022. |
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DOI: |
https://doi.org/10.1016/j.bbagrm.2022.194886 |
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Idioma: |
Inglês |
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Conteúdo: |
Single nucleotide polymorphisms showing allele-specific expression (ASE SNPs) are useful for cis-regulatory variants discovery. Despite this potential, there are expensive costs involved in genome-level ASE analysis for large sample sizes. If different data resolutions are available, genotype imputation can be used to mitigate this limitation. Aiming to increase the power to detect regulatory variants, we used a large dataset (>4 million) of imputed SNP genotypes and RNA-Seq data from 190 Nelore steers. Differences between major and minor allele expressions in muscle were tested with a Binomial Test. We identified 38,177 ASE SNPs (FDR ≤ 0.05) within 7304 linkage disequilibrium blocks. After that, we searched for aseQTLs (i.e., neighboring SNPs potentially regulating the ASE SNPs' allelic expression) by comparing the ASE of heterozygous to homozygous sample groups under a Wilcoxon Rank Sum test. We identified 21,543 aseQTLs potentially regulating 430 ASE SNPs (FDR ≤ 0.05). A total of 3333 cis-eQTLs (being 2098 ASE SNPs and 1075 aseQTLs) were associated with the expression of 758 transcripts (FDR ≤ 0.05), demonstrating the cis-regulatory effect of these ASE SNPs and aseQTLs. Data integration showed reproducibility with previous studies in bovine ASE and genomic imprinting. Furthermore, we identified 36,756 novel ASE regions due to the imputation approach. Comparisons with epigenetics data from Functional Annotation of Animal Genomes (FAANG) suggest a regulatory potential of the ASE-related SNPs. The affected genes were enriched in metabolic pathways essential for muscle homeostasis. These findings reinforce the potential of using ASE for discovering cis-regulatory SNPs that may affect muscle-related traits. MenosSingle nucleotide polymorphisms showing allele-specific expression (ASE SNPs) are useful for cis-regulatory variants discovery. Despite this potential, there are expensive costs involved in genome-level ASE analysis for large sample sizes. If different data resolutions are available, genotype imputation can be used to mitigate this limitation. Aiming to increase the power to detect regulatory variants, we used a large dataset (>4 million) of imputed SNP genotypes and RNA-Seq data from 190 Nelore steers. Differences between major and minor allele expressions in muscle were tested with a Binomial Test. We identified 38,177 ASE SNPs (FDR ≤ 0.05) within 7304 linkage disequilibrium blocks. After that, we searched for aseQTLs (i.e., neighboring SNPs potentially regulating the ASE SNPs' allelic expression) by comparing the ASE of heterozygous to homozygous sample groups under a Wilcoxon Rank Sum test. We identified 21,543 aseQTLs potentially regulating 430 ASE SNPs (FDR ≤ 0.05). A total of 3333 cis-eQTLs (being 2098 ASE SNPs and 1075 aseQTLs) were associated with the expression of 758 transcripts (FDR ≤ 0.05), demonstrating the cis-regulatory effect of these ASE SNPs and aseQTLs. Data integration showed reproducibility with previous studies in bovine ASE and genomic imprinting. Furthermore, we identified 36,756 novel ASE regions due to the imputation approach. Comparisons with epigenetics data from Functional Annotation of Animal Genomes (FAANG) suggest a regulato... Mostrar Tudo |
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Palavras-Chave: |
Cis-regulação; Cis-regulation; Data integration; Epigenética; Expressão gênica; Genômica; Integração de dados; Polimorfismos de nucleotídeo único. |
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Thesagro: |
Gado. |
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Thesaurus NAL: |
Cattle; Epigenetics; Genomics; Single nucleotide polymorphism. |
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Categoria do assunto: |
--
G Melhoramento Genético |
|
Marc: |
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100 1 $aBRUSCADIN, J. J.
245 $aAllele-specific expression reveals functional SNPs affecting muscle-related genes in bovine.$h[electronic resource]
260 $c2022
520 $aSingle nucleotide polymorphisms showing allele-specific expression (ASE SNPs) are useful for cis-regulatory variants discovery. Despite this potential, there are expensive costs involved in genome-level ASE analysis for large sample sizes. If different data resolutions are available, genotype imputation can be used to mitigate this limitation. Aiming to increase the power to detect regulatory variants, we used a large dataset (>4 million) of imputed SNP genotypes and RNA-Seq data from 190 Nelore steers. Differences between major and minor allele expressions in muscle were tested with a Binomial Test. We identified 38,177 ASE SNPs (FDR ≤ 0.05) within 7304 linkage disequilibrium blocks. After that, we searched for aseQTLs (i.e., neighboring SNPs potentially regulating the ASE SNPs' allelic expression) by comparing the ASE of heterozygous to homozygous sample groups under a Wilcoxon Rank Sum test. We identified 21,543 aseQTLs potentially regulating 430 ASE SNPs (FDR ≤ 0.05). A total of 3333 cis-eQTLs (being 2098 ASE SNPs and 1075 aseQTLs) were associated with the expression of 758 transcripts (FDR ≤ 0.05), demonstrating the cis-regulatory effect of these ASE SNPs and aseQTLs. Data integration showed reproducibility with previous studies in bovine ASE and genomic imprinting. Furthermore, we identified 36,756 novel ASE regions due to the imputation approach. Comparisons with epigenetics data from Functional Annotation of Animal Genomes (FAANG) suggest a regulatory potential of the ASE-related SNPs. The affected genes were enriched in metabolic pathways essential for muscle homeostasis. These findings reinforce the potential of using ASE for discovering cis-regulatory SNPs that may affect muscle-related traits.
650 $aCattle
650 $aEpigenetics
650 $aGenomics
650 $aSingle nucleotide polymorphism
650 $aGado
653 $aCis-regulação
653 $aCis-regulation
653 $aData integration
653 $aEpigenética
653 $aExpressão gênica
653 $aGenômica
653 $aIntegração de dados
653 $aPolimorfismos de nucleotídeo único
700 1 $aCARDOSO, T. F.
700 1 $aDINIZ, W. J. da S.
700 1 $aAFONSO, J.
700 1 $aSOUZA, M. M. de
700 1 $aPETRINI, J.
700 1 $aANDRADE, B. G. N.
700 1 $aSILVA, V. H. da
700 1 $aFERRAZ, J. B. S.
700 1 $aZERLOTINI NETO, A.
700 1 $aMOURÃO, G. B.
700 1 $aCOUTINHO, L. L.
700 1 $aREGITANO, L. C. de A.
773 $tBiochimica et Biophysica Acta. Gene Regulatory Mechanisms$gv. 1865, n. 8, 194886, Nov. 2022.
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