A large genomic deletion in thePDHX gene caused by the retrotranspositional insertion of a full-length LINE-1 element

Abstract

The long interspersed element-1 (LINE-1 or L1) retrotransposition has altered the human genome in many ways. In particular, recent in vitro studies have demonstrated that the retrotranspositional insertion of L1 elements has resulted in significant genomic deletions. Here we provide evidence for its operation in the human genome by identifying a approximately 46-kb pathological genomic deletion in the PDHX gene directly linked to the insertion of a full-length L1 element, in a patient with pyruvate dehydrogenase complex (PDHc) deficiency. Both the deduced bottom and top strand cleavage sites in the PDHX gene coincide with the consensus L1 endonuclease (EN) target sequence 5'-TTTT/A-3', while the full-length L1 element is followed by a 67-bp poly(A) tail. Interestingly, two hairpin structures, potentially formed by the inverted repeats present immediately 5' to the top strand nick site and 3' to the bottom strand nick site, may have facilitated the accessibility of L1 EN to the target sequences and also brought the two otherwise distantly located sequences into close proximity. Since the L1 element inserted in the PDHX gene is full-length, we favor the model of the template jumping as opposed to that of the microhomology-mediated end-joining for linking the 5' end of the nascent L1 copy to its genomic target. Our finding not only serves as an important complement to the in vitro approaches to studying L1 retrotransposition, but also reveals a novel mechanism causing human genetic disease.

Progress in understanding the biology of the human mutagen LINE-1

“…While the majority of L1 and other L1-mediated insertions (e.g., Alu and SVA insertions) land in intergenic and intronic sequences with little or no consequence to their host, occasional insertions have disrupted gene expression and caused human disease [Kazazian et al, 1988;Deininger and Batzer, 1999;Batzer and Deininger, 2002;Chen et al, 2005bChen et al, , 2006bOstertag and Kazazian, 2005;Hulme et al, 2006;Mine et al, 2006;Musova et al, 2006]. Because these insertions are typically identified in patients presenting with overt disease, the majority of characterized cases are X-linked or dominant single-gene genetic disorders, such as hemophilia A (MIM] 306700) or Apert syndrome (MIM] 101200).…”

“…The predominance of exonic insertions reflects the fact that they are most likely to disrupt a gene by causing frameshifts and subsequent premature stop codons or exon-skipping. Rarely, an integration event may be accompanied by a large genomic deletion at the insertion site that may eliminate coding sequence [Gilbert et al, , 2005Symer et al, 2002;Chen et al, 2005bChen et al, , 2006bMine et al, 2006]; in one recent case, an intronic L1 insertion in the PDHX gene was accompanied by a $46-kb deletion eliminating exons 3 to 9 of the PDHX gene and causing pyruvate dehydrogenase complex deficiency (MIM] 608769) [Mine et al, 2006]. The remainder of disease-causing insertions disrupt introns, or the 5 0 or 3 0 UTRs of genes; in these cases gene disruption has been attributed to missplicing, exon skipping, or a general decrease in mRNA levels, but in the majority of cases the molecular mechanism leading to decrease in expression has not been characterized [Ostertag and Kazazian, 2005;Chen et al, 2006b].…”

“…Because these insertions are typically identified in patients presenting with overt disease, the majority of characterized cases are X-linked or dominant single-gene genetic disorders, such as hemophilia A (MIM] 306700) or Apert syndrome (MIM] 101200). Occasional cases of recessive inactivating mutations have been found on the background of incidental inherited mutation in the other allele (e.g., pyruvate dehydrogenase complex deficiency; MIM] 608769) [Mine et al, 2006], in consanguineous populations (e.g. gyrate atrophy of the choroid and retina; MIM] 258870) [Mitchell et al, 1991], as well as in cases where secondhit mutations are more frequent and likely to produce disease (e.g., insertions into tumor suppressor genes, such as the APC gene; MIM] 175100) [Miki et al, 1992] (reviewed in Ostertag and Kazazian [2005]).…”

Retroelements: molecular features and implications for disease

“…In other cases, LINE insertion into APC and MYC gene can cause colon and breast cancer, respectively (Miki et al, 1992). LINE element-mediated elimination of target-site DNA by retrotransposition can cause critical diseases (Kondo-Iida et al, 1999;Narita et al, 1993;Miné et al, 2007). Very few of these events have been reported.…”

“…A deletion of 1 base pair in DMD causes Duchenne Muscular Dystrophy (Narita et al, 1993), and a 6-bp deletion in FCMD causes Fukuyama-type congeni- (Meischl et al, 2000) RP2 Xp L1 X-linked retinitis pigmentosa (Schwahn et al, 1998;Ostertag and Kazazian, 2001a) (Miki et al, 1996) FGFR2 10q Alu Apert syndrome (Oldridge et al, 1999) GK Xp Alu Glycerol kinase defiency (Zhang et al, 2000) OPA1 3q Alu Autosomal dominant optic atrophy (Gallus et al, 2010) α-galactosidase A Xq Alu Fabry disease (Kornreich et al, 1990) HEXB 5q Alu Sandhoff disease (Neote et al, 1990) tal muscular dystrophy (Kondo-Iida et al, 1999). Further deletion of PDHX located on chromosome 11 results in pyruvate dehydrogenase-complex deficiency (Miné et al, 2007). HR of copies of LINE elements also results in disease; however, this rarely occurs, because they are very critical and rare .…”