Integrative transcriptome sequencing reveals extensive alternative trans-splicing and cis-backsplicing in human cells

Area of Science:

• Molecular Biology
• Genomics
• Transcriptomics

Background:

• Non-co-linear (NCL) transcripts arise from trans-splicing (tsRNA) or cis-backsplicing (circRNA).
• CircRNAs are well-studied, but tsRNAs remain largely uninvestigated.
• Understanding NCL RNA biogenesis is crucial for deciphering transcriptome complexity.

Purpose of the Study:

• To comprehensively analyze and differentiate tsRNAs and circRNAs in the human transcriptome.
• To investigate the prevalence and characteristics of both trans-splicing and cis-backsplicing events.
• To explore the regulatory implications of distinct tsRNA and circRNA expression patterns.

Main Methods:

• Integrative transcriptome sequencing using poly(A)- and non-poly(A)-selected RNA-seq data from human cell lines.
• Bioinformatic analysis to identify and distinguish NCL events originating from tsRNAs and circRNAs.
• Comparative analysis of expression patterns, stability, and localization of tsRNAs and circRNAs.

Main Results:

• Identification of 24,498 NCL events, with 20-35% attributed to both tsRNAs and circRNAs.
• Discovery of shared sequence features between tsRNAs and circRNAs, with inverted Alu repeats promoting both.
• Demonstration of distinct expression profiles for tsRNAs and circRNAs relative to their linear counterparts, abundance, stability, and localization.

Conclusions:

• Trans-splicing and cis-backsplicing are widespread in human cells, contributing significantly to NCL transcripts.
• tsRNAs and circRNAs, despite shared formation mechanisms, possess distinct regulatory functions.
• Future analyses of NCL events must consider the interplay between different splicing types and multiple NCL events.