Pathogenic Orphan Transduction Created by a Non-reference LINE-1 Retrotransposon.

Long INterspersed Element-1 (LINE-1) retrotransposons comprise 17% of the human genome, and move by a potentially mutagenic “copy and paste” mechanism via an RNA intermediate. Recently, the retrotransposition-mediated insertion of a new transcript was described as a novel cause of genetic disease, Duchenne muscular dystrophy, in a Japanese male. The inserted sequence was presumed to derive from a single-copy, non-coding RNA transcribed from chr. 11q22.3 that retrotransposed into the dystrophin gene on chr. X. Here, we demonstrate that a non-reference full-length LINE-1 (termed LRE4) is situated in the proband and maternal genome at chromosome 11q22.3, directly upstream of the sequence, whose copy was inserted into the dystrophin gene. LRE4 is highly active in a cell culture assay. LINE-1 insertions are often associated with 3′ transduction of adjacent genomic sequences. Thus, the likely explanation for the mutagenic insertion is a LINE-1-mediated 3′ transduction with severe 5′ truncation. This is the first example of LINE-1-induced human disease caused by an “orphan” 3′ transduction. This work was carried out with the help of the Genetic Resources Core Facility (GRCF) at the Johns Hopkins University. LRE4 was found to be present in one Japanese individual out of 15 unrelated individuals in a LINE-1 targeted resequencing dataset. This dataset was generated by Illumina sequencing of the human-specific subfamily of LINE-1s (Ewing and Kazazian, 2010), using the service offered by the GRCF High Throughput Sequencing Center. Sequencing of the PCR products from the patient, as well as the cloned LRE4 sequence was done by the GRCF DNA Analysis Facility.