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A Role for Retrotransposons in Chromothripsis

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Chromothripsis

Part of the book series: Methods in Molecular Biology ((MIMB,volume 1769))

Abstract

Chromothripsis is a mutational event driven by tens to hundreds of double-stranded DNA breaks which occur in a single event between a limited number of chromosomes. Following chromosomal shattering, DNA fragments are stitched together in a seemingly random manner resulting in complex genomic rearrangements including sequence shuffling, deletions, and inversions of varying size. This genomic catastrophe has been observed in cancer genomes and the genomes of patients harboring developmental and congenital defects. The mechanisms catalyzing DNA breakage and coordinating the “random” assembly of genomic fragments are actively being investigated. Recently, retrotransposons—a type of “jumping gene”—have been implicated as one means to generate double-stranded DNA breaks during chromothripsis and as sequences which can contribute to the final configuration of the derived chromosomes. In this methods chapter, I discuss how to apply available bioinformatic tools and the hallmarks of retrotransposon mobilization to breakpoint junctions to assess the role for active and inactive retrotransposon sequences in chromothriptic events.

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Acknowledgments

D.C.H. is funded by a K99/R00 Pathway to Independence Award from the National Institutes of Health (USA, NIGMS) and the Cancer Prevention & Research Institute of Texas (CPRIT).

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Authors and Affiliations

  1. Eccles Institute of Human Genetics, School of Medicine, University of Utah, Salt Lake City, UT, USA

    Dustin C. Hancks

  2. Department of Immunology, UT Southwestern Medical Center, Dallas, TX, USA

    Dustin C. Hancks

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  1. Dustin C. Hancks
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Correspondence to Dustin C. Hancks .

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Editors and Affiliations

  1. Unit of Chromosomal Genetics, Department of Medical Genetics, CHU Montpellier, Montpellier, Hérault, France

    Franck Pellestor

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Hancks, D.C. (2018). A Role for Retrotransposons in Chromothripsis. In: Pellestor, F. (eds) Chromothripsis. Methods in Molecular Biology, vol 1769. Humana Press, New York, NY. https://doi.org/10.1007/978-1-4939-7780-2_11

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  • DOI: https://doi.org/10.1007/978-1-4939-7780-2_11

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  • Publisher Name: Humana Press, New York, NY

  • Print ISBN: 978-1-4939-7779-6

  • Online ISBN: 978-1-4939-7780-2

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