LINE- and Alu-containing genomic instability hotspot at 16q24.1 associated with recurrent and nonrecurrent CNV deletions causative for ACDMPV

Przemyslaw Szafranski, Ewelina Kośmider, Qian Liu, Justyna A. Karolak, Lauren Currie, Sandhya Parkash, Stephen G. Kahler, Elizabeth Roeder, Rebecca O. Littlejohn, Thomas S. DeNapoli, Felix R. Shardonofsky, Cody Henderson, George Powers, Virginie Poisson, Denis Bérubé, Luc Oligny, Jacques L. Michaud, Sandra Janssens, Kris De Coen, Jo Van DorpeAnnelies Dheedene, Matthew T. Harting, Matthew D. Weaver, Amir M. Khan, Nina Tatevian, Jennifer Wambach, Kathleen A. Gibbs, Edwina Popek, Anna Gambin, Paweł Stankiewicz

Research output: Contribution to journalArticle

4 Scopus citations

Abstract

Transposable elements modify human genome by inserting into new loci or by mediating homology-, microhomology-, or homeology-driven DNA recombination or repair, resulting in genomic structural variation. Alveolar capillary dysplasia with misalignment of pulmonary veins (ACDMPV) is a rare lethal neonatal developmental lung disorder caused by point mutations or copy-number variant (CNV) deletions of FOXF1 or its distant tissue-specific enhancer. Eighty-five percent of 45 ACDMPV-causative CNV deletions, of which junctions have been sequenced, had at least one of their two breakpoints located in a retrotransposon, with more than half of them being Alu elements. We describe a novel ∼35 kb-large genomic instability hotspot at 16q24.1, involving two evolutionarily young LINE-1 (L1) elements, L1PA2 and L1PA3, flanking AluY, two AluSx, AluSx1, and AluJr elements. The occurrence of L1s at this location coincided with the branching out of the Homo-Pan-Gorilla clade, and was preceded by the insertion of AluSx, AluSx1, and AluJr. Our data show that, in addition to mediating recurrent CNVs, L1 and Alu retrotransposons can predispose the human genome to formation of variably sized CNVs, both of clinical and evolutionary relevance. Nonetheless, epigenetic or other genomic features of this locus might also contribute to its increased instability.

Original languageEnglish
Pages (from-to)1916-1925
Number of pages10
JournalHuman mutation
Volume39
Issue number12
DOIs
StatePublished - Dec 2018

Keywords

  • DNA repair
  • genome instability
  • nonrecurrent structural variants

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