Mirele Poleti

Universidade de São Paulo

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Luiz Lehmann Coutinho

Universidade de São Paulo

101

Aline Cesar

Universidade de São Paulo

Luciana Correia de Almeida Regitano

Brazilian Agricultural Research Corporation

James M. Reecy

Iowa State University

James E. Koltes

Iowa State University

Gérson Barreto Mourão

Universidade de São Paulo

Andrezza Felício

Universidade de São Paulo

Júlio César de Carvalho Balieiro

Universidade de São Paulo

Gabriel Costa Monteiro Moreira

University of Liège

Heidge Fukumasu

Universidade de São Paulo

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Universidade de São Paulo

242

Universidade Estadual Paulista (Unesp)

Universidade Brasil

Fundação Oswaldo Cruz

Instituto Butantan

Secretaria de Agricultura e Abastecimento

Universidade Federal de Minas Gerais

Hospital Universitário da Universidade de São Paulo

Brazilian Agricultural Research Corporation

Clinics Hospital of Ribeirão Preto

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451 Identification and characterization of euchromatic regions associated with gene expression and intramuscular fat in Nelore cattle.

Journal of Animal Science (2018)

Luiz Lehmann Coutinho Natalia S. Morosini Aline Cesar Mirele Poleti Luciana Correia de Almeida Regitano

In eukaryotes, DNA is organized along with histones in nucleoprotein complexes known as chromatin, which has nucleosomes as their fundamental unit. Chromatin exists in two forms: euchromatin, corresponding to a lightly condensed structure and an easily transcribed region, and heterochromatin, a highly condensed and transcriptionally silent region. Therefore, the chromatin compaction degree interferes with regulation of gene expression, and nucleosomes act as gene silencers. In this context, using Assay for Transposase-Accessible Chromatin technique (ATAC-seq), the aims of the present study were to identify, map and characterize euchromatin regions in Longissimus dorsi muscle of Nellore cattle to understand if these regions are associated with gene expression and intramuscular fat content. Different transposase-treated nuclei concentrations were tested: 50 thousand, 75 thousand and 100 thousand, and their nucleosomal periodicity was analyzed to check the efficiency of ATAC-seq enzymatic activity. From these, 6,811, 11,121, and 11,473 euchromatin peaks were respectively found by using Model-based Analysis of ChIP-Seq (MACS2). A total of 6,212 open chromatin regions were coincident among the three nuclei concentrations, and this data was used in subsequent analyzes. Enrichment analysis performed using package RegioneR in R, considering significance of p < 0.05, revealed over-representation of peaks in 1) transcription start sites of genes expressed in skeletal muscle; 2) differentially expressed genes (GDE) associated with intramuscular fat content; 3) expression quantitative trait loci (eQTL) identified in skeletal muscle tissue. Our results indicate that skeletal muscle regulatory regions identified by ATAC-seq are involved in the control of gene expression and intramuscular fat content in cattle.

Euchromatin

Intramuscular fat

10.1093/jas/sky404.509

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PSV-24 Effect of pre-weaning, post-weaning and fattening growth rate on carcass and meat traits in feedlot Nellore cattle

Journal of Animal Science (2019)

Tamyres Rodrigues de Amorim Jéssica Luana Gemelli I. H. S. Fuzikawa Taiane da Silva Martins Gabriella Moura

Abstract The goal of this study was to evaluate the effect of contrasting growth rate in pre and post-weaning period on carcass traits and meat quality of feedlot Nellore cattle. To high weight gain, in pre and post-weaning period, were be considered management groups with mean weight gain above the third quartile of pre-weaning (PREW) or post-weaning (PROW) weight gain distribution of population to group of moderate gain were be considered management lots with daily average gains between the first and third quartiles of PREW or PROW weight gain distribution of population. In the low gain group will be considered management lots with daily average gains lower than the first quartile of PREW or PROW weight gain distribution of population. We used a total of 500 bulls, registered in the National Association of Breeders and Researchers, fed during 90 days with the same diet, confined and slaughtered. The PREW presented a weight gain rate (WGR) of 57.1, 67.3, and 77.7 kg for low, moderate and high WGR, respectively; and the PROW of 110.3, 113.4, and 119.4 kg for low, moderate and high WGR, respectively. The hot carcass weight influenced WGR in pre-weaning (297.56±11.80, 323.53±10.09, and 364.31±18.88 kg) for low, moderate and high, respectively (P = 0.03). The carcass dressing was affected by weaning period in WGR (pre-weaning: 54.18, 54.33, and 57.88 %; P = 0.034, and post-weaning 55.52, 56.23, and 54.66%; P = 0.471) for low, moderate and high WGR, respectively. The contrasting weight gain groups did not influence the marbling score in PREW (P = 0.128) and PROW (P = 0.772), back fat thickness in PREW (P = 0.719) and PROW (P = 0.833), ribeye area in PREW (P = 0.472) and PROW (P = 0.833), tenderness in PREW (P = 0.936) and PROW (P = 0.911). In general, the gain rate did not improve the carcass traits and meat quality of feedlot Nellore cattle.

Feedlot

Quartile

10.1093/jas/skz258.669

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Additional file 3: Table S3. of Integrative analysis of microRNAs and mRNAs revealed regulation of composition and metabolism in Nelore cattle

Figshare (2018)

Gabriella Oliveira Luciana Correia de Almeida Regitano Aline Cesar James M. Reecy Karina Degaki

List of most relevant canonical pathways enriched by IPA using the miRNA’s target genes list. The table contains the name of pathway and the target genes that are present in each pathway. (XLSX 19 kb)

Table (database)

10.6084/m9.figshare.5867322

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Additional file 17: Tables S22, S23, S24 and S25. of Integrative analysis of microRNAs and mRNAs revealed regulation of composition and metabolism in Nelore cattle

Figshare (2018)

Gabriella Oliveira Luciana Correia de Almeida Regitano Aline Cesar James M. Reecy Karina Degaki

Gene ontology (GO) enrichment analysis by Cytoscape of genes in mRNA modules correlated with the intramuscular fat (IMF) trait: enrichment of genes from mRNA modules correlated with High IMF (Table S22) and Low IMF groups (Table S23). Gene ontology enrichment analysis by Cytoscape of target genes of hub miRNAs in modules correlated with the IMF trait: enrichment of target genes of miRNA modules correlated with High intramuscular fat (Table S24) and Low IMF groups (Table S25). The table contains module’s name, gene ontology ID, p-value and adjusted p-value of GO, the description of them and the genes present in each biological process enriched. (XLSX 98 kb)

10.6084/m9.figshare.5867244

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MOESM5 of MiRNAs differentially expressed in skeletal muscle of animals with divergent estimated breeding values for beef tenderness

Figshare (2019)

Berna Kappeler Luciana Correia de Almeida Regitano Mirele Poleti Aline Cesar Gabriel Costa Monteiro Moreira

Additional file 5. Significative (p < 0.1) canonical pathways from the list of target genes of bta-mir-182 (Sheet 1), bta-mir-183 (Sheet 2) and bta-mir-338 (Sheet 3).

Beef Cattle

10.6084/m9.figshare.7542524

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Additional file 14: Tables S18, S19, S20 and S21. of Integrative analysis of microRNAs and mRNAs revealed regulation of composition and metabolism in Nelore cattle

Figshare (2018)

Gabriella Oliveira Luciana Correia de Almeida Regitano Aline Cesar James M. Reecy Karina Degaki

Gene ontology (GO) enrichment analysis by Cytoscape of genes in mRNA modules negatively correlated with miRNA modules: enrichment of genes from mRNA modules constructed in the High intramuscular fat (IMF) group (Table S18) and in the Low IMF group (Table S19). Gene ontology enrichment analysis by Cytoscape of target genes of hub miRNAs in modules negatively correlated with mRNA modules: enrichment of target genes of miRNA modules constructed in the High IMF group (Table S20) and in the Low IMF group (Table S21). The table contains the module’s name, gene ontology ID, p-value and adjusted p-value of GO, the description of them and the genes present in each biological process enriched. (XLSX 71 kb)

10.6084/m9.figshare.5867181

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MOESM4 of MiRNAs differentially expressed in skeletal muscle of animals with divergent estimated breeding values for beef tenderness

Figshare (2019)

Berna Kappeler Luciana Correia de Almeida Regitano Mirele Poleti Aline Cesar Gabriel Costa Monteiro Moreira

Additional file 4. List of Longissimus thoracis muscle expressed genes in Nelore.

Beef Cattle

10.6084/m9.figshare.7542515

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Additional file 3: Table S3. of Comparative muscle transcriptome associated with carcass traits of Nellore cattle

Figshare (2017)

BĂĄrbara Silva-Vignato Luiz Lehmann Coutinho Aline Cesar Mirele Poleti Luciana Correia de Almeida Regitano

Differentially expressed genes obtained between high and low genomic breeding value groups for backfat thickness in Nellore steers with FDR 10%. The table contains the Ensembl gene identification, gene symbol, mean normalized counts, Log2 fold Change from low to high group, p value and p value adjusted for a false discovery rate of 10%. (XLS 31Â kb)

Table (database)

10.6084/m9.figshare.c.3817633_d3

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Avaliação de antígenos de cisticercos de Taenia solium e Taenia crassiceps para o sorodiagnóstico da cisticercose suína

Revista Brasileira de Parasitologia Veterinária/Brazilian Journal of Veterinary Parasitology (2004)

Killarney Ataíde Soares M. R. M. Silva Mirele Poleti Cibele N.S. Uyhara Antônio Augusto Mendes Maia

Taenia crassiceps

Taenia solium

Taenia

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Comparative muscle transcriptome associated with carcass traits of Nellore cattle

BMC Genomics (2017)

Bárbara Silva-Vignato Luiz Lehmann Coutinho Aline Cesar Mirele Poleti Luciana Correia de Almeida Regitano

Commercial cuts yield is an important trait for beef production, which affects the final value of the products, but its direct determination is a challenging procedure to be implemented in practice. The measurement of ribeye area (REA) and backfat thickness (BFT) can be used as indirect measures of meat yield. REA and BFT are important traits studied in beef cattle due to their strong implication in technological (carcass yield) and nutritional characteristics of meat products, like the degree of muscularity and total body fat. Thus, the aim of this work was to study the Longissimus dorsi muscle transcriptome of Nellore cattle, associated with REA and BFT, to find differentially expressed (DE) genes, metabolic pathways, and biological processes that may regulate these traits. By comparing the gene expression level between groups with extreme genomic estimated breeding values (GEBV), 101 DE genes for REA and 18 for BFT (false discovery rate, FDR 10%) were identified. Functional enrichment analysis for REA identified two KEGG pathways, MAPK (Mitogen-Activated Protein Kinase) signaling pathway and endocytosis pathway, and three biological processes, response to endoplasmic reticulum stress, cellular protein modification process, and macromolecule modification. The MAPK pathway is responsible for fundamental cellular processes, such as growth, differentiation, and hypertrophy. For BFT, 18 biological processes were found to be altered and grouped into 8 clusters of semantically similar terms. The DE genes identified in the biological processes for BFT were ACHE, SRD5A1, RSAD2 and RSPO3. RSAD2 has been previously shown to be associated with lipid droplet content and lipid biosynthesis. In this study, we identified genes, metabolic pathways, and biological processes, involved in differentiation, proliferation, protein turnover, hypertrophy, as well as adipogenesis and lipid biosynthesis related to REA and BFT. These results enlighten some of the molecular processes involved in muscle and fat deposition, which are economically important carcass traits for beef production.

KEGG

Beef Cattle

Metabolic pathway

10.1186/s12864-017-3897-x

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Citations (58)