Mobile interspersed repeats are major structural variants in the human genome.

Institute of Genetic Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA.
Cell (Impact Factor: 33.12). 06/2010; 141(7):1171-82. DOI: 10.1016/j.cell.2010.05.026
Source: PubMed

ABSTRACT Characterizing structural variants in the human genome is of great importance, but a genome wide analysis to detect interspersed repeats has not been done. Thus, the degree to which mobile DNAs contribute to genetic diversity, heritable disease, and oncogenesis remains speculative. We perform transposon insertion profiling by microarray (TIP-chip) to map human L1(Ta) retrotransposons (LINE-1 s) genome-wide. This identified numerous novel human L1(Ta) insertional polymorphisms with highly variant allelic frequencies. We also explored TIP-chip's usefulness to identify candidate alleles associated with different phenotypes in clinical cohorts. Our data suggest that the occurrence of new insertions is twice as high as previously estimated, and that these repeats are under-recognized as sources of human genomic and phenotypic diversity. We have just begun to probe the universe of human L1(Ta) polymorphisms, and as TIP-chip is applied to other insertions such as Alu SINEs, it will expand the catalog of genomic variants even further.

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    ABSTRACT: Transposable elements comprise more than 45% of the human genome and LINE-1 (L1) is the only autonomous mobile element remaining active. Since its identification, it has been proposed that L1 contributes to the mobilization and amplification of other cellular RNAs and more recently, experimental demonstrations of this function has been described for many transcripts such as Alu, a non-autonomous mobile element, cellular mRNAs or small non-coding RNAs. Detailed examination of the mobilization of various cellular RNAs revealed distinct pathways by which they could be recruited during retrotransposition; template choice or template switching. Here, by analysing genomic structures and retrotransposition signatures associated to small nuclear RNA (snRNA) sequences, we identified distinct recruiting steps during the L1 retrotransposition cycle for the formation of snRNA-processed pseudogenes. Interestingly, some of the identified recruiting steps take place in the nucleus. Moreover, after comparison to other vertebrate genomes, we established that snRNA amplification by template switching is common to many LINE families from several LINE clades. Finally, we suggest that U6 snRNA copies can serve as markers of L1 retrotransposition dynamics in mammalian genomes. © The Author(s) 2015. Published by Oxford University Press on behalf of the Society for Molecular Biology and Evolution.
    Molecular Biology and Evolution 03/2015; DOI:10.1093/molbev/msv062 · 14.31 Impact Factor
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    ABSTRACT: The Cancer Genome Atlas project was initiated by the National Cancer Institute in order to characterize the genomes of hundreds of tumors of various cancer types. While much effort has been put into detecting somatic genomic variation in these data, somatic structural variation induced by the activity of transposable element insertions has not been reported. Transposable elements (TEs) are particularly relevant in cancer in part because of several known cases in which a TE insertion is directly linked to cancer formation and studies linking the epigenetic status of retrotransposons to carcinogenesis and patient outcome. Additionally, evidence for somatic retrotransposition in eukaryotic genomes suggests that some tissues and therefore some cancer types may be disposed to increased retrotransposition. We built upon previous work to develop a highly efficient computational pipeline for the detection of non-reference mobile ele- ment insertions from high-throughput paired-end whole genome sequencing data that is capable of detecting breakpoints through a local assembly strategy. Using this, we analyzed 33 whole genome tumor datasets with paired normal samples from TCGA across 3 different cancer types: glioblastoma multiforme (GBM), ovarian serous cystoadenocarcinoma (OV) and colorectal ade- nocarcinoma (COAD). We detected 72 insertions in colon samples, almost all of them LINE-1 elements, and none in GBM or OV. The amount of somatic retrotransposition varies widely between samples with 61 insertions present in one case. The lack of somatic retrotransposon insertions in GBM and OV samples suggests that TE activity in cancer is restricted to certain cancer types.
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    ABSTRACT: Background: LINE-1 (L1) retrotransposons are common occupants of mammalian genomes representing about a fifth of the genetic content. Ongoing L1 retrotransposition in the germ line and somatic tissues has contributed to structural genomic variations and disease-causing mutations in the human genome. L1 mobilization relies on the function of two, self-encoded proteins, ORF1 and ORF2. The ORF2 protein contains two characterized domains: endonuclease and reverse transcriptase. Results: Using a bacterially purified endonuclease domain of the human L1 ORF2 protein, we have generated a monoclonal antibody specific to the human ORF2 protein. We determined that the epitope recognized by this monoclonal antibody includes amino acid 205, which is required for the function of the L1 ORF2 protein endonuclease. Using an in vitro L1 cleavage assay, we demonstrate that the monoclonal anti-ORF2 protein antibody partially inhibits L1 endonuclease activity without having any effect on the in vitro activity of the human AP endonuclease. Conclusions: Overall, our data demonstrate that this anti-ORF2 protein monoclonal antibody is a useful tool for human L1-related studies and that it provides a rationale for the development of antibody-based inhibitors of L1-induced damage.
    Mobile DNA 12/2014; 5(29):1-13. DOI:10.1186/s13100-014-0029-x · 2.43 Impact Factor

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