Allele-specific expression reveals functional SNPs affecting muscle-related genes in bovine

Bruscadin, Jennifer Jessica; Cardoso, Tainã Figueiredo; Diniz, W. J. da S.; Afonso, Juliana; Souza, Marcela Maria de; Petrini, Juliana; Andrade, Bruno Gabriel de; Silva, Vinícius da; Ferraz, José Bento Sterman; Zerlotini, Adhemar; Mourão, Gérson Barreto; Coutinho, Luiz Lehmann; Regitano, L. C. de A.

doi:10.1016/j.bbagrm.2022.194886

Cited by 2 publications

(15 citation statements)

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“…As our research group [ 8 , 9 ] and others reported, ASE is widespread in bovine [ 4 , 6 , 8 , 10 , 11 ]. Previously, we described a high coverage list of single nucleotide polymorphisms (SNPs) located in transcripts with ASE (ASE SNPs) distributed in Nelore ( Bos indicus ) muscle and the candidate cis -regulatory variants potentially affecting the allelic expression.…”

Section: Introductionmentioning

confidence: 82%

“…Blood samples and collected in vacuum tubes containing potassium EDTA (K3) and muscle samples were immediately collected between the 11th and 13th ribs of the Longissimus thoracis muscle [ 14 , 15 , 16 ]. Here, we used the data of 190 steers from this experimental population for which phenotype, genotype, and RNA-Seq data were available, being the same samples used in previous studies of our group [ 8 , 9 ], to ensure comparability.…”

Section: Methodsmentioning

confidence: 99%

“…We conducted data integration analysis to examine if the SNPs found in this work were previously related to ASE and bovine phenotypes in other studies. First, we retrieved ASE data from the same Nelore population, regardless of the phenotypes [ 8 , 9 ]. After that, to compare the potential effect on the phenotypes, we downloaded all GWAS data obtained in the muscle of Nelore from previously published manuscripts related to meat quality [ 15 ], fatty acid content [ 16 ], and mineral concentration traits [ 37 ].…”

Section: Methodsmentioning

confidence: 99%

“…To identify SNPs potentially regulating the expression pattern, we considered a window of 200 kb upstream and downstream of each DASE SNP to search for aseQTLs [ 9 ], cis -eQTLs [ 9 ] and differentially methylated SNPs (DM) [ 38 ]. This 200 kb window was chosen based on our previous study [ 23 ] where the aseQTLs were mostly located until 200 kb of the regulated ASE SNP, and based on the high LD with the DASE SNPs expected to be present in that genomic distance.…”

Section: Methodsmentioning

confidence: 99%

“…Previously, we described a high coverage list of single nucleotide polymorphisms (SNPs) located in transcripts with ASE (ASE SNPs) distributed in Nelore ( Bos indicus ) muscle and the candidate cis -regulatory variants potentially affecting the allelic expression. Additionally, we have shown evidence that the ASE SNPs can regulate transcription, as they are located in functional regions [ 9 ]. ASE analysis benefits the search for functional variants affecting important economic traits, since genes containing ASE SNPs (ASE genes) may play a role in muscle maintenance and are related to meat quality traits [ 8 , 10 ].…”

Section: Introductionmentioning

confidence: 99%

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Differential Allele-Specific Expression Revealed Functional Variants and Candidate Genes Related to Meat Quality Traits in B. indicus Muscle

Bruscadin

Cardoso

Diniz

et al. 2022

Genes

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Traditional transcriptomics approaches have been used to identify candidate genes affecting economically important livestock traits. Regulatory variants affecting these traits, however, remain under covered. Genomic regions showing allele-specific expression (ASE) are under the effect of cis-regulatory variants, being useful for improving the accuracy of genomic selection models. Taking advantage of the better of these two methods, we investigated single nucleotide polymorphisms (SNPs) in regions showing differential ASE (DASE SNPs) between contrasting groups for beef quality traits. For these analyses, we used RNA sequencing data, imputed genotypes and genomic estimated breeding values of muscle-related traits from 190 Nelore (Bos indicus) steers. We selected 40 contrasting unrelated samples for the analysis (N = 20 animals per contrasting group) and used a beta-binomial model to identify ASE SNPs in only one group (i.e., DASE SNPs). We found 1479 DASE SNPs (FDR ≤ 0.05) associated with 55 beef-quality traits. Most DASE genes were involved with tenderness and muscle homeostasis, presenting a co-expression module enriched for the protein ubiquitination process. The results overlapped with epigenetics and phenotype-associated data, suggesting that DASE SNPs are potentially linked to cis-regulatory variants affecting simultaneously the transcription and phenotype through chromatin state modulation.

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Section: Introductionmentioning

confidence: 82%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 99%

See 3 more Smart Citations

Differential Allele-Specific Expression Revealed Functional Variants and Candidate Genes Related to Meat Quality Traits in B. indicus Muscle

Bruscadin

Cardoso

Diniz

et al. 2022

Genes

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Livestock species as emerging models for genomic imprinting

Hubert,

Perret,

Riquet

et al. 2024

Front. Cell Dev. Biol.

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Genomic imprinting is an epigenetically-regulated process of central importance in mammalian development and evolution. It involves multiple levels of regulation, with spatio-temporal heterogeneity, leading to the context-dependent and parent-of-origin specific expression of a small fraction of the genome. Genomic imprinting studies have therefore been essential to increase basic knowledge in functional genomics, evolution biology and developmental biology, as well as with regard to potential clinical and agrigenomic perspectives. Here we offer an overview on the contribution of livestock research, which features attractive resources in several respects, for better understanding genomic imprinting and its functional impacts. Given the related broad implications and complexity, we promote the use of such resources for studying genomic imprinting in a holistic and integrative view. We hope this mini-review will draw attention to the relevance of livestock genomic imprinting studies and stimulate research in this area.

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Allele-specific expression reveals functional SNPs affecting muscle-related genes in bovine

Cited by 2 publications

References 67 publications

Differential Allele-Specific Expression Revealed Functional Variants and Candidate Genes Related to Meat Quality Traits in B. indicus Muscle

Differential Allele-Specific Expression Revealed Functional Variants and Candidate Genes Related to Meat Quality Traits in B. indicus Muscle

Livestock species as emerging models for genomic imprinting

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