Although TPRT-mediated L1 mobilisation occurs in many cancers and neural cells, several recent studies employing high-throughput sequencing have reported a surprising absence of somatic L1 insertions in brain tumours. L1 and Alu elements can also participate in DNA rearrangements driven by recombination. Notably, L1 can mobilise other polyadenylated RNAs, such as Alu retrotransposons, in trans. Endonuclease-independent (ENi) L1 mobilisation can also occur into pre-existing DNA double strand breaks, producing insertions that lack TPRT hallmarks. Hallmarks of L1 integration by TPRT include use of an L1 EN recognition motif (5′-TT/AAAA), target site duplications (TSDs), and an L1 poly-A tail. Once the RNP enters the nucleus, the L1-encoded EN can cleave genomic DNA and, typically, generate a new L1 insertion via target-primed reverse transcription (TPRT). Canonical L1 mobilisation depends on the transcription and translation of L1 and the formation of a ribonucleoprotein particle (RNP) consisting of ORF1p and ORF2p, and their encoding mRNA. The L1 5′UTR bears an internal promoter with sense and antisense activity and a recently described antisense open reading frame (ORF0). A full-length human L1 is ~6 kb long and contains a 5′ untranslated region (UTR), two non-overlapping open reading frames that encode respectively for a 40KDa RNA binding protein (ORF1p) and a 150KDa protein with both endonuclease (EN) and reverse transcriptase (RT) activities (ORF2p), and a 3′UTR. L1 retrotransposons are endogenous mutagens known to cause sporadic disease, including cancer. Despite the extensive genomic analyses performed thus far, the GBM genome may yet harbour additional etiological clues that could improve treatment and patient outcomes. Defects in several DNA repair mechanisms, especially in the repair of DNA double strand breaks (DSBs), are known to enable genomic aberrations, such as deletions and amplifications, in GBM. To date, genomic analyses have elucidated somatic mutations and intra-tumoural heterogeneity governing GBM progression and resistance to therapy. Primary and secondary GBM tumours are histologically indistinguishable. Ninety-five percent of diagnosed GBM tumours originate de novo (primary GBM), while the remainder progress from a lower grade glioma (secondary GBM). Glioblastoma multiforme (GBM) is the most common and aggressive brain tumour in adults. These experiments altogether highlight the consistent absence of canonical L1 retrotransposition in GBM tumours and cultured cell lines, as well as atypical L1-associated sequence rearrangements following DNA damage in vivo. In a complementary in vitro assay, wild-type and endonuclease mutant L1 reporter constructs each mobilised very inefficiently in four cultured GBM cell lines. Whole genome sequencing analysis of the tumours carrying the MeCP2 and EGFR L1 mutations also revealed no endonuclease-dependent L1 insertions. Despite sequencing L1 integration sites at up to 250× depth by RC-seq, we found no tumour-specific, endonuclease-dependent L1 insertions. These mutations included PCR validated intronic events in MeCP2 and EGFR. In four GBM tumours, we characterised one probable endonuclease-independent L1 insertion, two L1-associated rearrangements and one likely Alu- Alu recombination event adjacent to an L1. Here, using retrotransposon capture sequencing (RC-seq), we surveyed L1 mutations in 14 tumours classified as glioblastoma multiforme (GBM) or as a lower grade glioma. Recent reports suggest that L1 is mobile in epithelial tumours and neural cells but, paradoxically, not in brain cancers. Notably, cancer cells can support unusual L1 retrotransposition and L1-associated sequence rearrangement mechanisms following DNA damage. NOT FOR USE IN DIAGNOSTIC PROCEDURES (EXCEPT AS SPECIFICALLY NOTED).LINE-1 (L1) retrotransposons are a notable endogenous source of mutagenesis in mammals. Our mission is to develop high-quality innovative tools and services to accelerate discovery.įOR RESEARCH USE ONLY. As a member of the Takara Bio Group, Takara Bio USA is part of a company that holds a leadership position in the global market and is committed to improving the human condition through biotechnology. provides kits, reagents, instruments, and services that help researchers explore questions about gene discovery, regulation, and function.
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