Identification of long non-coding RNA in the horse transcriptome

Area of Science:

• Genomics
• Transcriptomics
• Molecular Biology

Background:

• Equine genome research has primarily focused on protein-coding RNA.
• Intergenic regions in the horse genome, detected by RNA-seq, remain largely uncharacterized.
• Previous equine transcriptome studies provide a basis for lncRNA discovery.

Purpose of the Study:

• To create the deepest and most expansive equine long non-coding RNA (lncRNA) database.
• To characterize transcribed sequences within equine intergenic regions.
• To annotate novel lncRNA candidates using established human annotation approaches.

Main Methods:

• RNA sequencing (RNA-seq) data from eight equine tissues were analyzed.
• Intergenic reads and novel gene categories were utilized for lncRNA identification.
• A filtering approach based on size, expression, protein-coding potential, and proximity to protein-coding genes was applied.

Main Results:

• A comprehensive equine lncRNA database containing 20,800 candidate transcripts was established.
• Identified lncRNA candidates exhibit characteristic features such as low expression, low exon diversity, and low sequence conservation.
• This represents the most extensive catalog of equine lncRNAs to date.

Conclusions:

• The developed equine lncRNA database serves as a foundational resource for understanding non-coding RNA in horses.
• This study begins to characterize the vast RNA-seq reads originating from equine intergenic regions.
• The findings pave the way for deeper investigations into the functional roles of lncRNAs in the equine genome.