Germ line insertion of mtDNA at the breakpoint junction of a reciprocal constitutional translocation

Abstract

Constitutional chromosomal translocations are relatively common causes of human morbidity, yet the DNA double-strand break (DSB) repair mechanisms that generate them are incompletely understood. We cloned, sequenced and analyzed the breakpoint junctions of a familial constitutional reciprocal translocation t(9;11)(p24;q23). Within the 10-kb region flanking the breakpoints, chromosome 11 had 25% repeat elements, whereas chromosome 9 had 98% repeats, 95% of which were L1-type LINE elements. The breakpoints occurred within an L1-type repeat element at 9p24 and at the 3'-end of an Alu sequence at 11q23. At the breakpoint junction of derivative chromosome 9, we discovered an unusually large 41-bp insertion, which showed 100% identity to 12S mitochondrial DNA (mtDNA) between nucleotides 896 and 936 of the mtDNA sequence. Analysis of the human genome failed to show the preexistence of the inserted sequence at normal chromosomes 9 and 11 breakpoint junctions or elsewhere in the genome, strongly suggesting that the insertion was derived from human mtDNA and captured into the junction during the DSB repair process. To our knowledge, these findings represent the first observation of spontaneous germ line insertion of modern human mtDNA sequences and suggest that DSB repair may play a role in inter-organellar gene transfer in vivo. Our findings also provide evidence for a previously unrecognized insertional mechanism in human, by which non-mobile extra-chromosomal fragments can be inserted into the genome at DSB repair junctions.

Capture of Extranuclear DNA at Fission Yeast Double-Strand Breaks

“…Consistent with this view, the de novo chromosomal integration of mtDNA associated with Pallister-Hall syndrome in a patient exposed to Chernobyl radiations may be the consequence of NHEJmediated repair of radiation-induced DSBs (Turner et al 2003). Human mtDNA insertion has also been detected at the breakpoint junction of a reciprocal constitutive translocation (Willett-Brozick et al 2001). Genome sequence analysis of budding yeast (Ricchetti et al 1999), human (Mourier et al 2001;Tourmen et al 2002;Woischnik and Moraes 2002;Ricchetti et al 2004), and various plant species (Richly and Leister 2004) provided more evidence in favor of nuclear genome colonization by mtDNA.…”

“…Interestingly, recent studies reported the association of human genetic diseases with de novo insertions of mtDNA in the nuclear genome (Willett-Brozick et al 2001;Borensztajn et al 2002;Turner et al 2003;Goldin et al 2004). Reported cases included a patient exposed to Chernobyl radiation, suggesting that DSB repairdriven chromosomal integration of mtDNA may not occur exclusively under experimental conditions.…”

Illegitimate DNA integration in mammalian cells

“…4 Alternatively, in approximately one cell per thousand, the introduced foreign DNA will integrate into chromosomal DNA (although this figure may vary somewhat depending on cell type). 5,6 This phenomenon is not limited to laboratory transfections as many natural cellular processes, such as integration of DNA from apoptotic bodies, 7 repair of chromosomal lesions by insertion of mitochondrial DNA, 8 or retrotransposition events, give rise to de novo integration of DNA. 9, 10 Thus DNA integration may be seen as an ongoing natural process, which can be harnessed to artificially introduce modifications to a cell's genetic content.…”

The SET domain protein Metnase mediates foreign DNA integration and links integration to nonhomologous end-joining repair

“…In addition, extrachromosomal DNA can contribute to repair of chromosomal breaks. For example, damaged chromosomes have been found to repair by insertion of mitochondrial DNA (8). Finally, in lower organisms, internal retrotransposition is a common natural occurrence to produce genomic alteration and is widely used in the laboratory study of such organisms (9).…”