Profiling long noncoding RNA of multi-tissue transcriptome enhances porcine noncoding genome annotation

Area of Science:

• Genomics
• Transcriptomics
• Bioinformatics

Background:

• The porcine genome requires enhanced annotation, particularly for noncoding regions.
• Long noncoding RNAs (lncRNAs) play crucial roles in gene regulation but are underrepresented in current annotations.

Purpose of the Study:

• To construct a comprehensive pig noncoding transcriptome.
• To enhance porcine noncoding genome annotation.
• To explore the relationship between lncRNAs and protein-coding genes.

Main Methods:

• Tissue-based long noncoding RNA (lncRNA) profiling using high-throughput sequencing across 34 normal pig tissues.
• Identification of 32,212 nonredundant lncRNA isoforms from 18,676 lncRNA loci.
• Computational assessment of potential lncRNA-protein-coding gene interactions.

Main Results:

• A comprehensive catalog of porcine lncRNAs was generated.
• Ubiquitously expressed lncRNAs were found at higher levels than tissue-specific ones.
• A genome-wide lncRNA-targeted genome draft was developed.

Conclusions:

• The study provides extensive knowledge of porcine noncoding RNAs.
• Enhanced pig noncoding genome annotation was achieved.
• High-confidence lncRNAs were deposited in the NONCODE database, creating a valuable resource for pig genomic studies.