TEspeX: consensus-specific quantification of transposable element expression preventing biases from exonized...

Area of Science:

• Genomics
• Molecular Biology
• Bioinformatics

Background:

• Transposable elements (TEs) are vital genetic components influencing biological processes.
• Accurate quantification of TE expression is crucial for understanding their roles.
• Existing tools struggle to differentiate active TE transcription from TE fragments in other transcripts.

Purpose of the Study:

• To develop a computational pipeline, TEspeX, for precise quantification of transposable element expression at the consensus level.
• To address the limitation of existing tools in distinguishing autonomous TE transcription from TE sequences within canonical transcripts.

Main Methods:

• TEspeX pipeline utilizes Illumina RNA-seq short reads.
• The method quantifies TE expression by specifically excluding reads from inactive TE fragments embedded in canonical transcripts.
• Implementation in Python 3.

Main Results:

• TEspeX enables accurate quantification of transposable element expression.
• The pipeline effectively distinguishes transcription from autonomous TEs versus TE fragments within other transcripts.
• Avoids misinterpretation of expression changes due to TE-containing non-TE transcripts.

Conclusions:

• TEspeX provides a robust solution for accurate transposable element expression analysis.
• This tool enhances the study of TE functions in biological pathways.
• Facilitates more reliable research on the impact of transposable elements in genomics and transcriptomics.