ORCID Profile
0000-0001-7512-5893
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Publisher: Cold Spring Harbor Laboratory
Date: 15-10-2019
DOI: 10.1101/804419
Abstract: Mineral amount in bovine muscle affect meat quality, growth, health and reproductive traits in beef cattle. To better understand the genetic basis of this phenotype, we implemented new applications of use for two complementary algorithms: the partial correlation and information theory (PCIT) and the regulatory impact factor (RIF), by including GEBVs as part of the input. We used PCIT to determine putative regulatory relationships based on significant associations between gene expression and mineral amount. Then, RIF was used to determine the regulatory impact of genes and miRNA expression over mineral amount. We also investigated over-represented pathways, as well as evidences from previous studies carried in the same population, to determine regulatory genes for mineral amount e.g. NOX1 , whose expression was positively correlated to Zn and was described as regulated by this mineral in humans. With this methodology, we were able to identify genes, miRNAs and pathways not yet described as important for mineral amount. The results support the hypothesis that extracellular matrix interactions are the core regulator of mineral amount in muscle cells. Putative regulators described here add information to this hypothesis, expanding the molecular relationships between gene expression and minerals.
Publisher: Springer Science and Business Media LLC
Date: 13-09-2018
DOI: 10.1038/S41598-018-32146-2
Abstract: Transcription factors (TFs) are pivotal regulatory proteins that control gene expression in a context-dependent and tissue-specific manner. In contrast to human, where comprehensive curated TF collections exist, bovine TFs are only rudimentary recorded and characterized. In this article, we present a manually-curated compendium of 865 sequence-specific DNA-binding bovines TFs, which we analyzed for domain family distribution, evolutionary conservation, and tissue-specific expression. In addition, we provide a list of putative transcription cofactors derived from known interactions with the identified TFs. Since there is a general lack of knowledge concerning the regulation of gene expression in cattle, the curated list of TF should provide a basis for an improved comprehension of regulatory mechanisms that are specific to the species.
Publisher: Springer Science and Business Media LLC
Date: 21-05-2020
DOI: 10.1038/S41598-020-65454-7
Abstract: Mineral contents in bovine muscle can affect meat quality, growth, health, and reproductive traits. To better understand the genetic basis of this phenotype in Nelore ( Bos indicus) cattle, we analysed genome-wide mRNA and miRNA expression data from 114 muscle s les. The analysis implemented a new application for two complementary algorithms: the partial correlation and information theory (PCIT) and the regulatory impact factor (RIF), in which we included the estimated genomic breeding values (GEBVs) for the phenotypes additionally to the expression levels, originally proposed for these methods. We used PCIT to determine putative regulatory relationships based on significant associations between gene expression and GEBVs for each mineral amount. Then, RIF was adopted to determine the regulatory impact of genes and miRNAs expression over the GEBVs for the mineral amounts. We also investigated over-represented pathways, as well as pieces of evidences from previous studies carried in the same population and in the literature, to determine regulatory genes for the mineral amounts. For ex le, NOX1 expression level was positively correlated to Zinc and has been described as Zinc-regulated in humans. Based on our approach, we were able to identify genes, miRNAs and pathways not yet described as underlying mineral amount. The results support the hypothesis that extracellular matrix interactions are the core regulator of mineral amount in muscle cells. Putative regulators described here add information to this hypothesis, expanding the knowledge on molecular relationships between gene expression and minerals.
Location: Brazil
No related grants have been discovered for Marcela Maria de Souza.