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1.
Genes (Basel) ; 13(12)2022 12 11.
Artigo em Inglês | MEDLINE | ID: mdl-36553605

RESUMO

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.


Assuntos
Carne , Músculo Esquelético , Bovinos/genética , Animais , Alelos , Fenótipo , Genótipo , Músculo Esquelético/metabolismo
2.
Biochim Biophys Acta Gene Regul Mech ; 1865(8): 194886, 2022 11.
Artigo em Inglês | MEDLINE | ID: mdl-36265837

RESUMO

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.


Assuntos
Polimorfismo de Nucleotídeo Único , Locos de Características Quantitativas , Bovinos/genética , Animais , Alelos , Reprodutibilidade dos Testes , Músculos
3.
Epigenetics Chromatin ; 15(1): 15, 2022 05 13.
Artigo em Inglês | MEDLINE | ID: mdl-35562812

RESUMO

BACKGROUND: Beef tenderness is a complex trait of economic importance for the beef industry. Understanding the epigenetic mechanisms underlying this trait may help improve the accuracy of breeding programs. However, little is known about epigenetic effects on Bos taurus muscle and their implications in tenderness, and no studies have been conducted in Bos indicus. RESULTS: Comparing methylation profile of Bos indicus skeletal muscle with contrasting beef tenderness at 14 days after slaughter, we identified differentially methylated cytosines and regions associated with this trait. Interestingly, muscle that became tender beef had higher levels of hypermethylation compared to the tough group. Enrichment analysis of predicted target genes suggested that differences in methylation between tender and tough beef may affect signal transduction pathways, among which G protein signaling was a key pathway. In addition, different methylation levels were found associated with expression levels of GNAS, PDE4B, EPCAM and EBF3 genes. The differentially methylated elements correlated with EBF3 and GNAS genes overlapped CpG islands and regulatory elements. GNAS, a complex imprinted gene, has a key role on G protein signaling pathways. Moreover, both G protein signaling pathway and the EBF3 gene regulate muscle homeostasis, relaxation, and muscle cell-specificity. CONCLUSIONS: We present differentially methylated loci that may be of interest to decipher the epigenetic mechanisms affecting tenderness. Supported by the previous knowledge about regulatory elements and gene function, the methylation data suggests EBF3 and GNAS as potential candidate genes and G protein signaling as potential candidate pathway associated with beef tenderness via methylation.


Assuntos
Metilação de DNA , Carne , Animais , Bovinos , Ilhas de CpG , Carne/análise , Músculo Esquelético/metabolismo , Transdução de Sinais
4.
Front Genet ; 12: 709937, 2021.
Artigo em Inglês | MEDLINE | ID: mdl-34646299

RESUMO

Animals with muscle hypertrophy phenotype are targeted by the broiler industry to increase the meat production and the quality of the final product. Studies characterizing the molecular machinery involved with these processes, such as quantitative trait loci studies, have been carried out identifying several candidate genes related to this trait; however, validation studies of these candidate genes in cell culture is scarce. The aim of this study was to evaluate SAP30 as a candidate gene for muscle development and to validate its function in cell culture in vitro. The SAP30 gene was downregulated in C2C12 muscle cell culture using siRNA technology to evaluate its impact on morphometric traits and gene expression by RNA-seq analysis. Modulation of SAP30 expression increased C2C12 myotube area, indicating a role in muscle hypertrophy. RNA-seq analysis identified several upregulated genes annotated in muscle development in treated cells (SAP30-knockdown), corroborating the role of SAP30 gene in muscle development regulation. Here, we provide experimental evidence of the involvement of SAP30 gene as a regulator of muscle cell hypertrophy.

5.
Sci Rep ; 11(1): 7321, 2021 04 01.
Artigo em Inglês | MEDLINE | ID: mdl-33795794

RESUMO

Single nucleotide polymorphisms (SNPs) located in transcript sequences showing allele-specific expression (ASE SNPs) were previously identified in the Longissimus thoracis muscle of a Nelore (Bos indicus) population consisting of 190 steers. Given that the allele-specific expression pattern may result from cis-regulatory SNPs, called allele-specific expression quantitative trait loci (aseQTLs), in this study, we searched for aseQTLs in a window of 1 Mb upstream and downstream from each ASE SNP. After this initial analysis, aiming to investigate variants with a potential regulatory role, we further screened our aseQTL data for sequence similarity with transcription factor binding sites and microRNA (miRNA) binding sites. These aseQTLs were overlapped with methylation data from reduced representation bisulfite sequencing (RRBS) obtained from 12 animals of the same population. We identified 1134 aseQTLs associated with 126 different ASE SNPs. For 215 aseQTLs, one allele potentially affected the affinity of a muscle-expressed transcription factor to its binding site. 162 aseQTLs were predicted to affect 149 miRNA binding sites, from which 114 miRNAs were expressed in muscle. Also, 16 aseQTLs were methylated in our population. Integration of aseQTL with GWAS data revealed enrichment for traits such as meat tenderness, ribeye area, and intramuscular fat . To our knowledge, this is the first report of aseQTLs identification in bovine muscle. Our findings indicate that various cis-regulatory and epigenetic mechanisms can affect multiple variants to modulate the allelic expression. Some of the potential regulatory variants described here were associated with the expression pattern of genes related to interesting phenotypes for livestock. Thus, these variants might be useful for the comprehension of the genetic control of these phenotypes.


Assuntos
Alelos , Carne , Músculo Esquelético/metabolismo , Animais , Sítios de Ligação , Biotecnologia/métodos , Bovinos , Metilação de DNA , Expressão Gênica , Regulação da Expressão Gênica , Marcadores Genéticos , Genoma , Estudo de Associação Genômica Ampla , Genótipo , Heterozigoto , Desequilíbrio de Ligação , Metilação , MicroRNAs/metabolismo , Fenótipo , Polimorfismo de Nucleotídeo Único , Locos de Características Quantitativas
6.
Sci Rep ; 10(1): 10204, 2020 06 23.
Artigo em Inglês | MEDLINE | ID: mdl-32576896

RESUMO

Differences between the expression of the two alleles of a gene are known as allele-specific expression (ASE), a common event in the transcriptome of mammals. Despite ASE being a source of phenotypic variation, its occurrence and effects on genetic prediction of economically relevant traits are still unexplored in bovines. Furthermore, as ASE events are likely driven by cis-regulatory mutations, scanning them throughout the bovine genome represents a significant step to elucidate the mechanisms underlying gene expression regulation. To address this question in a Bos indicus population, we built the ASE profile of the skeletal muscle tissue of 190 Nelore steers, using RNA sequencing data and SNPs genotypes from the Illumina BovineHD BeadChip (770 K bp). After quality control, 820 SNPs showed at least one sample with ASE. These SNPs were widespread among all autosomal chromosomes, being 32.01% found in 3'UTR and 31.41% in coding regions. We observed a considerable variation of ASE profile among individuals, which highlighted the need for biological replicates in ASE studies. Functional analysis revealed that ASE genes play critical biological functions in the development and maintenance of muscle tissue. Additionally, some of these genes were previously reported as associated with beef production and quality traits in livestock, thus indicating a possible source of bias on genomic predictions for these traits.


Assuntos
Bovinos/genética , Regulação da Expressão Gênica/genética , Músculo Esquelético/fisiologia , Alelos , Animais , Genoma/genética , Genômica/métodos , Genótipo , Carne , Fenótipo , Polimorfismo de Nucleotídeo Único/genética , Locos de Características Quantitativas/genética , Análise de Sequência de RNA , Transcriptoma/genética
7.
Meat Sci ; 96(1): 436-40, 2014 Jan.
Artigo em Inglês | MEDLINE | ID: mdl-23995697

RESUMO

Calcium (Ca) and potassium (K) are essential nutrients in animal nutrition. Furthermore, the Ca content can influence meat tenderness because it is needed by the proteolytic system of calpains and calpastatins, major factors in postmortem tenderization of skeletal muscles. K content, which is needed for muscle contraction, can also affect meat tenderness. This study showed that K positively affects the Warner-Bratzler shear force (WBSF), measured at 14days of meat aging, which means that higher levels of K are related to lower meat tenderness. Additionally, a significant effect (P≤0.015) of a SNP in the calcium-activated neutral protease 1 (CAPN1) gene on Ca content was observed. Metal content in beef can affect not only nutritional values but also meat quality traits. Part of this effect may be related to variation in specific genes.


Assuntos
Cálcio/análise , Carne/análise , Potássio/análise , Fenômenos Fisiológicos da Nutrição Animal , Animais , Biomarcadores , Proteínas de Ligação ao Cálcio/genética , Proteínas de Ligação ao Cálcio/metabolismo , Calpaína/genética , Calpaína/metabolismo , Bovinos , Manipulação de Alimentos , Variação Genética , Genótipo , Proteínas Musculares/genética , Proteínas Musculares/metabolismo , Músculo Esquelético/química , Fenótipo , Polimorfismo de Nucleotídeo Único
8.
Zygote ; 21(1): 59-63, 2013 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-21867598

RESUMO

Trichostatin A (TSA) is a histone deacetylase inhibitor that induces histone hyperacetylation and increases gene expression levels. The aim of the present study was to establish a suitable condition for the use of TSA in in vitro cultures of bovine embryos, and to determine whether TSA would increase blastocyst rates by improvement of chromatin remodelling during embryonic genome activation and by increasing the expression of crucial genes during early development. To test this hypothesis, 8-cell embryos were exposed to four concentrations of TSA for different periods of time to establish adequate protocols. In a second experiment, three experimental groups were selected for the evaluation of embryo quality based on the following parameters: apoptosis, total cell number and blastocyst hatching. TSA promoted embryonic arrest and degeneration at concentrations of 15, 25 and 50 nM. All treated groups presented lower blastocyst rates. Exposure of embryos to 5 nM for 144 h and to 15 nM for 48 h decreased blastocyst hatching. However, the terminal deoxynucleotidyl transferase-mediated dUTP nick-end labeling assay (TUNEL) assay revealed similar apoptosis rates and total cell numbers in all groups studied. Although, in the present study, TSA treatment did not improve the parameters studied, the results provided background information on TSA supplementation during in vitro culture of bovine embryos and showed that embryo quality was apparently not affected, despite a decrease in blastocyst rate after exposure to TSA.


Assuntos
Blastocisto/efeitos dos fármacos , Bovinos/embriologia , Inibidores de Histona Desacetilases/farmacologia , Ácidos Hidroxâmicos/farmacologia , Animais , Apoptose/efeitos dos fármacos , Blastocisto/citologia , Blastocisto/fisiologia , Montagem e Desmontagem da Cromatina/efeitos dos fármacos , Relação Dose-Resposta a Droga , Técnicas de Cultura Embrionária , Embrião de Mamíferos/citologia , Feminino , Fertilização in vitro , Regulação da Expressão Gênica no Desenvolvimento/efeitos dos fármacos , Masculino
9.
Meat Sci ; 90(2): 507-10, 2012 Feb.
Artigo em Inglês | MEDLINE | ID: mdl-21899958

RESUMO

This study aimed to investigate differential allele expression (DAE) and polymorphism and parent-of-origin effects on expression of genes related to beef traits. CAST, related to meat tenderness, and DGAT1 and leptin, related to fat deposition, were evaluated. In bovine fetal tissues CAST was expressed twice as much (P < 0.05) in muscle of homozygous GG than in heterozygous AG. Leptin was expressed about one-tenth as much (P < 0.05) in heterozygous TpCm (allele T of paternal origin and allele C of maternal origin) than in homozygous CC. No DAE was observed. The evidence of polymorphism effect on expression of CAST and parent-of-origin effect on leptin contributes to a better understanding of events controlling the expression of genes of economic interest in cattle. Furthermore, if the parent-of-origin effects observed in fetal tissues are confirmed in adult tissues and associated to phenotypic variation, this parental origin criterion may be considered in marker-assisted selection of beef traits.


Assuntos
Proteínas de Ligação ao Cálcio/genética , Bovinos/genética , Diacilglicerol O-Aciltransferase/genética , Leptina/genética , Carne , Polimorfismo de Nucleotídeo Único , Alelos , Animais , Composição Corporal/genética , Proteínas de Ligação ao Cálcio/metabolismo , Diacilglicerol O-Aciltransferase/metabolismo , Regulação da Expressão Gênica , Heterozigoto , Homozigoto , Padrões de Herança , Leptina/metabolismo
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