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| Registros recuperados : 17 | |
| 2. |  | SILVA, V. H.; GIACHETTO, P. F.; TIZIOTO, P. L.; GONÇALVES, T. M.; REGITANO, L. C. A.; COUTINHO, L. L. A network landscape from CNVs to Nellore cattle beef tenderness. In: INTERNATIONAL SYMPOSIUM ON ANIMAL FUNCTIONAL GENOMICS, 5., 2013, Guarujá. Programme and abstract book... [S.l.: s.n.], 2013. p. 8. ISAFG 2013. AB.01.| Biblioteca(s): Embrapa Agricultura Digital; Embrapa Pecuária Sudeste. |
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| 3. | | GODOY, T. F.; SILVA, V. H. da; MOREIRA, G. C. M.; BOSCHIERO, C.; LEDUR, M. C.; CROOIJAMANS, R. P.; GROENEN, M. A. M.; COUTINHO, L. L. Inherited CNVs in regions related to breast muscle development in a broiler population. In: PLANT AND ANIMAL GENOME CONFERENCE, 26., 2018, San Diego. Abstracts... [S.l. : s.n.], 2018. Paper 29816. Organizers: Sébastien Praud and Kellye Eversole. PAG XXVI.| Biblioteca(s): Embrapa Suínos e Aves. |
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| 4. | | GODOY, T. F.; SILVA, V. H.; TESSMANN, A. L.; PANDOLFI, J. R. C.; PEIXOTO, J. de O.; COUTINHO, L. L.; LEDUR, M. C. Adiponectin receptor 2 gene associated with bone traits in broiler chickens. In: CONGRESSO BRASILEIRO DE GENÉTICA, 60., 2014, Guarujá. Resumos... Ribeirão Preto: Sociedade Brasileira de Genética, 2014. p. 39.| Biblioteca(s): Embrapa Suínos e Aves. |
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| 5. | | CARVALHO JUNIOR, P. S.; DINIZ, L. F.; SILVA, G. T. S. T. da; COUTINHO, N. D.; SANTOS, P. G. dos; CARVALHO-SILVA, V. H.; RIBEIRO, C.; ELLENA, J. Amino - imino tautomerism in the salt formation of Albendazole: Hydrobromide and nitrate salts. Crystal Growth & Design, v. 21, 2021. 1122?1135| Biblioteca(s): Embrapa Instrumentação. |
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| 6. | | FERNANDES, L. T.; GODOY, T. F.; SILVA, V. H.; PANDOLFI, J. R. C.; CANTAO, M. E.; PEIXOTO, J. de O.; COUTINHO, L. L.; LEDUR, M. C. Sex-specific association of a SNP in the ADIPOR2 gene with carcass traits in a paternal broiler line. In: WORLD CONGRESS OF GENETICS APPLIED TO LIVESTOCK PRODUCTION, 10., 2014, Vancouver. Proceedings... Vancouver: WCGALP: American Society of Animal Science, 2014.| Biblioteca(s): Embrapa Suínos e Aves. |
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| 7. | | GONÇALVES, T. M.; ANDRADE, S. C. S.; GASPARIN, G.; SILVA, V. H. da; REGITANO, L. C. de A.; COUTINHO, L. L. Glutathione pathway could be associated with meat tenderness in Nellore. In: INTERNATIONAL SYMPOSIUM ON ANIMAL FUNCTIONAL GENOMICS, 5., 2013, Guarujá. Abstract... Guarujá:[ s.n.], 2013. AB.40.| Biblioteca(s): Embrapa Pecuária Sudeste. |
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| 8. | | GODOY, T. F.; MOREIRA, G. C. M.; SILVA, V. H.; BOSCHIERO, C.; LEDUR, M. C.; MOURA, A. S. A. M. T.; COUTINHO, L. L. Identification of CNVs on the genome of Brazilian chicken lines. In: PLANT & ANIMAL GENOME CONFERENCE, 24., 2016, San Diego, CA. [Abstracts...]. San Diego: [s.n.], 2016. Pôster P0646.| Biblioteca(s): Embrapa Suínos e Aves. |
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| 9. | | SILVA, V. H.; PANDOLFI, J. R. C.; GODOY, T. F.; PEIXOTO, J. de O.; TESSMANN, A. L.; CANTAO, M. E.; LEDUR, M. C. Hepatocyte nuclear factor 4 gene associated with bone traits and birth weight in male chickens. In: CONGRESSO BRASILEIRO DE GENÉTICA, 59., 2013, Águas de Lindóia. Resumos... Ribeirão Preto: SBG, 2013. p. 27.| Biblioteca(s): Embrapa Suínos e Aves. |
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| 10. | | PÉRTILLE, F.; BOSAGNA, C. G.; SILVA, V. H. da; BOSCHIERO, C.; NUNES, J. de R. da S.; LEDUR, M. C.; JENSEN, P.; COUTINHO, L. L. High-throughput and cost-effective chicken genotyping using next-generation sequencing. Scientific Reports, v. 6, n. 26929, 2016.| Biblioteca(s): Embrapa Suínos e Aves. |
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| 11. | | SILVA, V. H. da; REGITANO, L. C. de A.; GEISTLINGER, L.; PÉRTILLE, F.; GIACHETTO, P. F.; BRASSALOTI, R. A.; MOROSINI, N. S.; ZIMMER, R.; COUTINHO, L. L. Genome-wide detection of CNVs and their association with meat tenderness in Nelore cattle. Plos One, june 2016.| Biblioteca(s): Embrapa Pecuária Sudeste. |
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| 12. | | PÉRTILLE, F.; FELÍCIO, A. M.; ROSÁRIO, M. F. do; SILVA, V. H.; MANGUETTI, T.; SILVA, N. A.; LEDUR, M. C.; COUTINHO, L. L. PPARGC1A indel polymorphism is associated with performance and carcass traits in chickens. In: CONGRESSO BRASILEIRO DE GENÉTICA, 58., 2012, Foz do Iguaçu. Resumos... Foz do Iguaçú: SBG, 2012. p. 72| Biblioteca(s): Embrapa Suínos e Aves. |
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| 13. | | GEISTLINGER, L.; SILVA, V. H. da; CESAR, A. S. M.; TIZIOTO, P. C.; WALDRON, L.; ZIMMER, R.; REGITANO, L. C. de A.; COUTINHO, L. L. Widespread modulation of gene expression by copy number variation in skeletal muscle. Scientific Reports, v. 8, n. 1399, p. 1-11, jan. 2018.| Biblioteca(s): Embrapa Pecuária Sudeste. |
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| 14. | | RAMOS, B.; VAZ, W. F.; DINIZ, L. F.; SANCHES NETO, F. O.; RIBEIRO, J. C. O.; CARVALHO-SILVA, V. H.; TEIXEIRA, A. C. S. C.; RIBEIRO, C.; NAPOLITANO, H. B.; CARVALHO JR, P. S. Kinetics, mechanism, and tautomerism in ametryn acid hydrolysis: From molecular structure to environmental impacts. Chemosphere, v. 324, 138278, 2023. 1 - 10| Biblioteca(s): Embrapa Instrumentação. |
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| 15. | | MOREIRA, G. C. M.; GODOY, T. F.; BOSCHIERO, C.; CESAR, A. S. M.; REECY, J. M.; LEDUR, M. C.; GARRICK, D.; SILVA, V. H. da; CROOIJAMANS, R. P.; GROENEN, M. A. M.; COUTINHO, L. L. Integration of GWAS, CNV and sele ction signature reveals candidate genes for abdominal fat regulation in chickens. In: WORLD CONGRESS ON GENETICS APPLIED TO LIVESTOCK PRODUCTION, 11., 2018, Auckland, New Zealand. Proceedings... Massey University, 2018. Digital Archive.| Biblioteca(s): Embrapa Suínos e Aves. |
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| 16. | | FERNANDES, A. C.; SILVA, V. H. da; GOES, C. P.; MOREIRA, G. C. M.; GODOY, T. F.; IBELLI, A. M. G.; PEIXOTO, J. de O.; CANTAO, M. E.; LEDUR, M. C.; REZENDE, F. M. de; COUTINHO, L. L. Genome-wide detection of CNVs and their association with performance traits in broilers. BMC Genomics, v. 22, n. 354, 2021.| Biblioteca(s): Embrapa Suínos e Aves. |
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| 17. | | 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. Allele-specific expression reveals functional SNPs affecting muscle-related genes in bovine. Biochimica et Biophysica Acta. Gene Regulatory Mechanisms, v. 1865, n. 8, 194886, Nov. 2022.| Biblioteca(s): Embrapa Agricultura Digital; Embrapa Pecuária Sudeste. |
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| Registros recuperados : 17 | |
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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 |
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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.
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700 1 $aAFONSO, J.
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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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