Chromothripsis pp 169-181 | Cite as

A Role for Retrotransposons in Chromothripsis

Protocol
Part of the Methods in Molecular Biology book series (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.

Key words

Chromothripsis Retrotransposon Alu L1 LINE-1 SVA Nonallelic homologous recombination Deletion Inversion 

Notes

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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Copyright information

© Springer Science+Business Media, LLC, part of Springer Nature 2018

Authors and Affiliations

  1. 1.Eccles Institute of Human Genetics, School of Medicine, University of UtahSalt Lake CityUSA
  2. 2.Department of ImmunologyUT Southwestern Medical CenterDallasUSA

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