Evaluation of RNA quality and functional transcriptome of beef longissimus thoracis et lumborum muscle tissue over time post-mortem

ABSTRACT: Evaluating RNA quality and transcriptomic profile of beef muscle tissue over time post-mortem may provide insight on RNA degradation and underlying biological and functional mechanisms influencing the biochemical changes occurring post-mortem that transform muscle tissue to meat. RNA-sequencing was performed on longissimus thoracis et lumborum (LTL) muscle samples collected at 5 time points [0 h (45 min post-mortem), 6 h, 24 h, 48 h, and 72 h (drip cooler)] post-mortem from British Continental crossbred beef heifers (n=7). Processed mRNA reads were aligned to the ARS-UCD1.2 bovine genome assembly. 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 of both up and downregulated genes increasing over time . Gene ontology and KEGG pathway term enrichment analyses revealed significant enrichment of biological and molecular functions relating to cellular energy, oxidative stress and NADH activity specific to early time points, as well as cellular signaling and transport and ribosome activity at specific to late time points. This study also revealed that LTL muscle tissue samples, collected as late as 72 h post-mortem remained at a high RNA integrity, suggesting opportunities for late sampling regimes for RNA-Seq analysis of post-mortem muscle tissue and the potential for larger studies to associate desirable meat quality traits with post-mortem transcriptome activity. Additionally, this study highlights the need to evaluate non-coding genetic features involved with epigenetic regulation in post-mortem muscle tissue, as indicated by non-coding RNA transcripts detected post-mortem, including small nucleolar RNA, mitochondrial DNA genes, and long non-coding RNA.

ORGANISM(S): Bos taurus

PROVIDER: GSE163766 | GEO | 2021/06/02

REPOSITORIES: GEO