Meta-Analysis Suggests That Intron Retention Can Affect Quantification of Transposable Elements from RNA-Seq Data

Area of Science:

• Genomics
• Molecular Biology
• Bioinformatics

Background:

• Transposable elements (TEs) are mobile genetic sequences crucial in biological processes, but their accurate expression quantification is challenging due to repetitive sequences.
• Intron retention (IR), the persistence of introns in mature RNA, is a common regulatory mechanism with cell-type-specific patterns.
• The overlap of TEs within introns raises the possibility that IR could bias TE expression quantification in RNA sequencing (RNA-seq).

Purpose of the Study:

• To investigate whether intron retention (IR) introduces bias in the quantification of transposable element (TE) expression using RNA-seq data.
• To determine if reads from retained introns affect the accurate detection of independent TE transcription.
• To assess the impact of IR on TE quantification tools and the potential confusion between differential IR and differential TE expression.

Main Methods:

• Performed a meta-analysis of public RNA-seq data from lymphoblastoid cell lines.
• Utilized established quantification tools with default parameters to analyze TE expression.
• Confirmed findings using additional independent datasets with varying levels of IR.

Main Results:

• Demonstrated that intron retention (IR) significantly impacts TE quantification in RNA-seq data.
• Showed that reads mapping to intronic TEs are associated with TE expression, leading to over-quantification.
• Confirmed that the observed bias is absent in samples lacking IR and that differential TE expression does not affect IR quantification.

Conclusions:

• Intron retention (IR) is a significant source of bias, causing the over-quantification of intronic transposable elements (TEs).
• Differential IR can be mistakenly interpreted as differential TE expression, highlighting the need for careful analysis.
• Accurate TE quantification from RNA-seq data requires consideration of IR, especially in samples with abundant retained introns.