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Comprehensive identification of transposable element insertions using multiple sequencing technologies

Author

Listed:
  • Chong Chu

    (Harvard Medical School)

  • Rebeca Borges-Monroy

    (Boston Children’s Hospital and Harvard Medical School
    Broad Institute of MIT and Harvard)

  • Vinayak V. Viswanadham

    (Harvard Medical School)

  • Soohyun Lee

    (Harvard Medical School)

  • Heng Li

    (Harvard Medical School
    Dana-Farber Cancer Institute)

  • Eunjung Alice Lee

    (Boston Children’s Hospital and Harvard Medical School
    Broad Institute of MIT and Harvard)

  • Peter J. Park

    (Harvard Medical School)

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 .

Suggested Citation

  • Chong Chu & Rebeca Borges-Monroy & Vinayak V. Viswanadham & Soohyun Lee & Heng Li & Eunjung Alice Lee & Peter J. Park, 2021. "Comprehensive identification of transposable element insertions using multiple sequencing technologies," Nature Communications, Nature, vol. 12(1), pages 1-12, December.
    • Handle: RePEc:nat:natcom:v:12:y:2021:i:1:d:10.1038_s41467-021-24041-8
    DOI: 10.1038/s41467-021-24041-8
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    Cited by:

    1. Arthur S. Lee & Lauren J. Ayers & Michael Kosicki & Wai-Man Chan & Lydia N. Fozo & Brandon M. Pratt & Thomas E. Collins & Boxun Zhao & Matthew F. Rose & Alba Sanchis-Juan & Jack M. Fu & Isaac Wong & X, 2024. "A cell type-aware framework for nominating non-coding variants in Mendelian regulatory disorders," Nature Communications, Nature, vol. 15(1), pages 1-26, December.
    2. Cristian Groza & Xun Chen & Travis J. Wheeler & Guillaume Bourque & Clément Goubert, 2024. "A unified framework to analyze transposable element insertion polymorphisms using graph genomes," Nature Communications, Nature, vol. 15(1), pages 1-17, December.
    3. Alexander S. Leonard & Danang Crysnanto & Zih-Hua Fang & Michael P. Heaton & Brian L. Vander Ley & Carolina Herrera & Heinrich Bollwein & Derek M. Bickhart & Kristen L. Kuhn & Timothy P. L. Smith & Be, 2022. "Structural variant-based pangenome construction has low sensitivity to variability of haplotype-resolved bovine assemblies," Nature Communications, Nature, vol. 13(1), pages 1-13, December.

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