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Evaluation of RNA quality and functional transcriptome of beef longissimus thoracis over time post-mortem

Evaluating RNA quality and transcriptomic profile of beef muscle over time post-mortem may provide insight into RNA degradation and underlying biological and functional mechanisms that accompany biochemical changes occurring post-mortem during transformation of muscle to meat. RNA was extracted from...

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Autores principales: Lam, Stephanie, Kommadath, Arun, López-Campos, Óscar, Prieto, Nuria, Aalhus, Jennifer, Juárez, Manuel, Dugan, Michael E. R., Vahmani, Payam
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2021
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8148330/
https://www.ncbi.nlm.nih.gov/pubmed/34033656
http://dx.doi.org/10.1371/journal.pone.0251868
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author Lam, Stephanie
Kommadath, Arun
López-Campos, Óscar
Prieto, Nuria
Aalhus, Jennifer
Juárez, Manuel
Dugan, Michael E. R.
Vahmani, Payam
author_facet Lam, Stephanie
Kommadath, Arun
López-Campos, Óscar
Prieto, Nuria
Aalhus, Jennifer
Juárez, Manuel
Dugan, Michael E. R.
Vahmani, Payam
author_sort Lam, Stephanie
collection PubMed
description Evaluating RNA quality and transcriptomic profile of beef muscle over time post-mortem may provide insight into RNA degradation and underlying biological and functional mechanisms that accompany biochemical changes occurring post-mortem during transformation of muscle to meat. RNA was extracted from longissimus thoracis (LT) sampled from British Continental crossbred heifer carcasses (n = 7) stored at 4°C in an abattoir drip cooler at 5 time points post-mortem, i.e., 45 min (0 h), 6 h, 24 h, 48 h, and 72 h. Following RNA-Sequencing, processed reads were aligned to the ARS-UCD1.2 bovine genome assembly. Subsequent differential expression (DE) analysis identified from 51 to 1434 upregulated and 27 to 2256 downregulated DE genes at individual time points compared to time 0 h, showing a trend for increasing counts of both upregulated and downregulated genes over time. Gene ontology and biological pathway term enrichment analyses on sets of DE genes revealed several processes and their timelines of activation/deactivation that accompanied or were involved with muscle transformation to meat. Although the quality of RNA in refrigerated LT remained high for several days post-mortem, the expression levels of several known biomarker genes for meat quality began to change from 24 h onwards. Therefore, to ensure accuracy of predictions on meat quality traits based on the expression levels of those biomarker genes in refrigerated beef muscle tissue, it is crucial that those expression measurements be made on RNA sampled within 24 h post-mortem. The present study also highlighted the need for more research on the roles of mitochondrial genes and non-coding genes in orchestrating muscle tissue processes after death, and how pre-mortem immune status might influence post-mortem meat quality.
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spelling pubmed-81483302021-06-07 Evaluation of RNA quality and functional transcriptome of beef longissimus thoracis over time post-mortem Lam, Stephanie Kommadath, Arun López-Campos, Óscar Prieto, Nuria Aalhus, Jennifer Juárez, Manuel Dugan, Michael E. R. Vahmani, Payam PLoS One Research Article Evaluating RNA quality and transcriptomic profile of beef muscle over time post-mortem may provide insight into RNA degradation and underlying biological and functional mechanisms that accompany biochemical changes occurring post-mortem during transformation of muscle to meat. RNA was extracted from longissimus thoracis (LT) sampled from British Continental crossbred heifer carcasses (n = 7) stored at 4°C in an abattoir drip cooler at 5 time points post-mortem, i.e., 45 min (0 h), 6 h, 24 h, 48 h, and 72 h. Following RNA-Sequencing, processed reads were aligned to the ARS-UCD1.2 bovine genome assembly. Subsequent differential expression (DE) analysis identified from 51 to 1434 upregulated and 27 to 2256 downregulated DE genes at individual time points compared to time 0 h, showing a trend for increasing counts of both upregulated and downregulated genes over time. Gene ontology and biological pathway term enrichment analyses on sets of DE genes revealed several processes and their timelines of activation/deactivation that accompanied or were involved with muscle transformation to meat. Although the quality of RNA in refrigerated LT remained high for several days post-mortem, the expression levels of several known biomarker genes for meat quality began to change from 24 h onwards. Therefore, to ensure accuracy of predictions on meat quality traits based on the expression levels of those biomarker genes in refrigerated beef muscle tissue, it is crucial that those expression measurements be made on RNA sampled within 24 h post-mortem. The present study also highlighted the need for more research on the roles of mitochondrial genes and non-coding genes in orchestrating muscle tissue processes after death, and how pre-mortem immune status might influence post-mortem meat quality. Public Library of Science 2021-05-25 /pmc/articles/PMC8148330/ /pubmed/34033656 http://dx.doi.org/10.1371/journal.pone.0251868 Text en © 2021 Lam et al https://creativecommons.org/licenses/by/4.0/This is an open access article distributed under the terms of the Creative Commons Attribution License (https://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Lam, Stephanie
Kommadath, Arun
López-Campos, Óscar
Prieto, Nuria
Aalhus, Jennifer
Juárez, Manuel
Dugan, Michael E. R.
Vahmani, Payam
Evaluation of RNA quality and functional transcriptome of beef longissimus thoracis over time post-mortem
title Evaluation of RNA quality and functional transcriptome of beef longissimus thoracis over time post-mortem
title_full Evaluation of RNA quality and functional transcriptome of beef longissimus thoracis over time post-mortem
title_fullStr Evaluation of RNA quality and functional transcriptome of beef longissimus thoracis over time post-mortem
title_full_unstemmed Evaluation of RNA quality and functional transcriptome of beef longissimus thoracis over time post-mortem
title_short Evaluation of RNA quality and functional transcriptome of beef longissimus thoracis over time post-mortem
title_sort evaluation of rna quality and functional transcriptome of beef longissimus thoracis over time post-mortem
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC8148330/
https://www.ncbi.nlm.nih.gov/pubmed/34033656
http://dx.doi.org/10.1371/journal.pone.0251868
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