Identification of large intergenic non-coding RNAs in bovine muscle using next-generation transcriptomic sequencing.

Area of Science:

• Genomics
• Molecular Biology
• Livestock Science

Background:

• Thousands of non-coding transcripts exist in eukaryotic cells, with long non-coding RNAs (lncRNAs) emerging as key regulators.
• The function and significance of lncRNAs, particularly long intergenic non-coding RNAs (lincRNAs), in bovine muscle remain largely unexplored.

Purpose of the Study:

• To conduct the first comprehensive survey of lincRNAs in bovine Longissimus thoraci muscle.
• To characterize identified bovine lincRNAs and analyze their expression variability.

Main Methods:

• Paired-end RNA sequencing (RNA-Seq) was employed on nine Limousin bull calf Longissimus thoraci muscle samples.
• A computational pipeline was used to identify and define lincRNAs, followed by RT-PCR validation for selected candidates.

Main Results:

• A total of 30,548 transcripts were identified, leading to the definition of 584 unique lincRNAs, with 418 found in all samples.
• Bovine lincRNAs exhibit characteristics similar to mammalian counterparts, including shorter lengths and lower expression levels compared to protein-encoding genes.
• Significant differences in expression variation were observed between lincRNAs and protein-encoding genes, and 2,083 lincRNA/protein-encoding gene pairs showed correlated expression.

Conclusions:

• This study provides a foundational catalog of lincRNAs in bovine muscle, facilitating future functional studies.
• Identified lincRNAs may play a role in the genetic variability of meat quality traits.
• The findings contribute to a better annotation of the bovine genome and complement existing cattle lncRNA databases.