Comprehensive identification of transposable element insertions using multiple sequencing technologies

Chong Chu, Rebeca Borges-Monroy, Vinayak V. Viswanadham, Soohyun Lee, Heng Li, Eunjung Alice Lee () and Peter J. Park ()
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Chong Chu: Harvard Medical School
Rebeca Borges-Monroy: Boston Children’s Hospital and Harvard Medical School
Vinayak V. Viswanadham: Harvard Medical School
Soohyun Lee: Harvard Medical School
Heng Li: Harvard Medical School
Eunjung Alice Lee: Boston Children’s Hospital and Harvard Medical School
Peter J. Park: Harvard Medical School

Nature Communications, 2021, vol. 12, issue 1, 1-12

Abstract: Abstract Transposable elements (TEs) help shape the structure and function of the human genome. When inserted into some locations, TEs may disrupt gene regulation and cause diseases. Here, we present xTea (x-Transposable element analyzer), a tool for identifying TE insertions in whole-genome sequencing data. Whereas existing methods are mostly designed for short-read data, xTea can be applied to both short-read and long-read data. Our analysis shows that xTea outperforms other short read-based methods for both germline and somatic TE insertion discovery. With long-read data, we created a catalogue of polymorphic insertions with full assembly and annotation of insertional sequences for various types of retroelements, including pseudogenes and endogenous retroviruses. Notably, we find that individual genomes have an average of nine groups of full-length L1s in centromeres, suggesting that centromeres and other highly repetitive regions such as telomeres are a significant yet unexplored source of active L1s. xTea is available at https://github.com/parklab/xTea .

Date: 2021
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DOI: 10.1038/s41467-021-24041-8

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