Data/hora: 23/06/2024 17:54:43

Biblioteca(s): | Embrapa Agricultura Digital; Embrapa Pecuária Sudeste.
Tipo da produção científica: | Artigo em Periódico Indexado
Circulação/Nível: | A - 1
Data corrente: | 04/11/2022
Data da última atualização: | 07/11/2022
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.
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.
Título: | Allele-specific expression reveals functional SNPs affecting muscle-related genes in bovine.
Ano de publicação: | 2022
Fonte/Imprenta: | Biochimica et Biophysica Acta. Gene Regulatory Mechanisms, v. 1865, n. 8, 194886, Nov. 2022.
DOI: | https://doi.org/10.1016/j.bbagrm.2022.194886
Idioma: | Inglês
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 &#8804; 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 &#8804; 0.05). A total of 3333 cis-eQTLs (being 2098 ASE SNPs and 1075 aseQTLs) were associated with the expression of 758 transcripts (FDR &#8804; 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.
Palavras-Chave: | Cis-regulação; Cis-regulation; Data integration; Epigenética; Expressão gênica; Genômica; Integração de dados; Polimorfismos de nucleotídeo único.
Thesagro: | Gado.
Thesaurus Nal: | Cattle; Epigenetics; Genomics; Single nucleotide polymorphism.

Categoria do assunto:

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G Melhoramento Genético

Registro original: | Embrapa Agricultura Digital (CNPTIA)

Exemplares:

CNPTIA - (21462-1) - UPC - AP - DD -  -  -  - DIS
CPPSE - (25768-1) - UPC - AP - DD - PROCI-2022.00106 - BRU - 2022.00182 - DIS