Comprehensive identification of transposable element insertions using multiple sequencing technologies.

Area of Science:

• Genomics
• Molecular Biology
• Bioinformatics

Background:

• Transposable elements (TEs) are mobile DNA sequences that influence genome evolution and function.
• TE insertions can disrupt gene regulation, leading to various diseases.
• Accurate identification of TE insertions is crucial for understanding genome dynamics and disease mechanisms.

Purpose of the Study:

• To introduce xTea, a novel computational tool for detecting transposable element insertions in whole-genome sequencing data.
• To develop a method applicable to both short-read and long-read sequencing technologies.
• To analyze the landscape of TE insertions, particularly in challenging genomic regions.

Main Methods:

• Development and application of xTea, a tool for transposable element insertion analysis.
• Utilizing both short-read and long-read whole-genome sequencing data.
• Comparative analysis of xTea against existing short-read based TE detection methods.

Main Results:

• xTea demonstrates superior performance in identifying germline and somatic TE insertions compared to existing short-read methods.
• Long-read data analysis with xTea enabled the cataloging of polymorphic retroelement insertions, including pseudogenes and endogenous retroviruses.
• An average of nine groups of full-length L1 elements were identified in centromeres per individual genome.

Conclusions:

• xTea provides a robust and versatile platform for transposable element insertion discovery across different sequencing data types.
• Centromeres and telomeres represent significant, previously underestimated reservoirs of active L1 elements.
• The findings highlight the ongoing impact of TEs on human genome structure and potential disease associations.