L1 retrotransposition in human neural progenitor cells

Laboratory of Genetics, The Salk Institute for Biological Studies, 10010 North Torrey Pines Road, La Jolla, California 92037, USA.
Nature (Impact Factor: 41.46). 09/2009; 460(7259):1127-31. DOI: 10.1038/nature08248
Source: PubMed


Long interspersed element 1 (LINE-1 or L1) retrotransposons have markedly affected the human genome. L1s must retrotranspose in the germ line or during early development to ensure their evolutionary success, yet the extent to which this process affects somatic cells is poorly understood. We previously demonstrated that engineered human L1s can retrotranspose in adult rat hippocampus progenitor cells in vitro and in the mouse brain in vivo. Here we demonstrate that neural progenitor cells isolated from human fetal brain and derived from human embryonic stem cells support the retrotransposition of engineered human L1s in vitro. Furthermore, we developed a quantitative multiplex polymerase chain reaction that detected an increase in the copy number of endogenous L1s in the hippocampus, and in several regions of adult human brains, when compared to the copy number of endogenous L1s in heart or liver genomic DNAs from the same donor. These data suggest that de novo L1 retrotransposition events may occur in the human brain and, in principle, have the potential to contribute to individual somatic mosaicism.

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Available from: Nicole G Coufal,
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    • "Previously, evidence for L1 insertions in normal somatic cells has come from two sources. A number of studies have shown that somatic L1 insertions occur in neuronal development and are present in various sites in the human and mouse brain (Muotri et al. 2005; Coufal et al. 2009; Baillie et al. 2011; Evrony et al. 2012; Upton et al. 2015). Moreover, a small number of examples of L1, SVA, and processed pseudogene insertions have been reported to occur in early human development (van den Hurk et al. 2007; de Boer et al. 2014; Vogt et al. 2014). "
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    ABSTRACT: Somatic L1 retrotransposition events have been shown to occur in epithelial cancers. Here, we attempted to determine how early somatic L1 insertions occurred during the development of gastrointestinal (GI) cancers. Using L1-targeted resequencing (L1-seq), we studied different stages of four colorectal cancers arising from colonic polyps, seven pancreatic carcinomas, as well as seven gastric cancers. Surprisingly, we found somatic L1 insertions not only in all cancer types and metastases, but also in colonic adenomas, well-known cancer precursors. Some insertions were also present in low quantities in normal GI tissues, occasionally caught in the act of being clonally fixed in the adjacent tumors. Insertions in adenomas and cancers numbered in the hundreds and many were present in multiple tumor sections implying clonal distribution. Our results demonstrate that extensive somatic insertional mutagenesis occurs very early during the development of GI tumors, probably before dysplastic growth. Published by Cold Spring Harbor Laboratory Press.
    Genome Research 08/2015; 25(10). DOI:10.1101/gr.196238.115 · 14.63 Impact Factor
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    • "The genomic load of endogenous L1-ORF2 and IAPΔ1 elements was within normal values in 4N (meiotic ), 2N (non-meiotic), and even apoptotic Dnmt3L −/− cells. This is in striking contrast to formerly described situations of TE reactivation in which de novo integration events were readily detectable using similar methods (Coufal et al. 2009; Ciaudo et al. 2013). Although we cannot exclude that a few TEs may mobilize, these data collectively argue that the genome of Dnmt3L −/− spermatocytes does not undergo massive retrotransposition. "
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    ABSTRACT: DNA methylation is essential for protecting the mammalian germline against transposons. When DNA methylation-based transposon control is defective, meiotic chromosome pairing is consistently impaired during spermatogenesis: How and why meiosis is vulnerable to transposon activity is unknown. Using two DNA methylation-deficient backgrounds, the Dnmt3L and Miwi2 mutant mice, we reveal that DNA methylation is largely dispensable for silencing transposons before meiosis onset. After this, it becomes crucial to back up to a developmentally programmed H3K9me2 loss. Massive retrotransposition does not occur following transposon derepression, but the meiotic chromatin landscape is profoundly affected. Indeed, H3K4me3 marks gained over transcriptionally active transposons correlate with formation of SPO11-dependent double-strand breaks and recruitment of the DMC1 repair enzyme in Dnmt3L(-/-) meiotic cells, whereas these features are normally exclusive to meiotic recombination hot spots. Here, we demonstrate that DNA methylation restrains transposons from adopting chromatin characteristics amenable to meiotic recombination, which we propose prevents the occurrence of erratic chromosomal events. © 2015 Zamudio et al.; Published by Cold Spring Harbor Laboratory Press.
    Genes & development 06/2015; 29(12). DOI:10.1101/gad.257840.114 · 10.80 Impact Factor
    • "But an additional potential mechanism of canalization involves retrotransposons, originally called " jumping genes " when first discovered by Barbara McClintock but now referred to as mobile DNA elements. These ubiquitous and prevalent stretches of non-gene coding DNA are remnants of viral DNA insertions into the genome and while the overwhelming majority are silenced, a surprising number remain active and capable of transpositioning to new sites after production of RNA and key enzymes (see (Coufal et al, 2009)). LINE-1 is the most prevalent of the mobile DNA elements and is most active in neural progenitor and germ cell tissue (Belancio et al, 2010; Singer et al, 2010). "
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    ABSTRACT: Discerning the biologic origins of neuroanatomical sex differences has been of interest since they were first reported in the late 60's and early 70's. The centrality of gonadal hormone exposure during a developmental critical window cannot be denied but hormones are indirect agents of change, acting to induce gene transcription or modulate membrane bound signaling cascades. Sex differences in the brain include regional volume differences due to differential cell death, neuronal and glial genesis, dendritic branching and synaptic patterning. Early emphasis on mechanism therefore focused on neurotransmitters and neural growth factors, but by and large these endpoints failed to explain the origins of neural sex differences. More recently evidence has accumulated in favor of inflammatory mediators and immune cells as principle regulators of brain sexual differentiation and reveal that the establishment of dimorphic circuits is not cell autonomous but instead requires extensive cell-to-cell communication including cells of non-neuronal origin. Despite the multiplicity of cells involved the nature of the sex differences in the neuroanatomical endpoints suggests canalization, a process that explains the robustness of individuals in the face of intrinsic and extrinsic variability. We propose that some neuroanatomical endpoints are canalized to enhance sex differences in the brain by reducing variability within one sex while also preventing the sexes from diverging too greatly. We further propose mechanisms by which such canalization could occur and discuss what relevance this may have to sex differences in behavior. Copyright © 2015. Published by Elsevier Inc.
    Hormones and Behavior 04/2015; DOI:10.1016/j.yhbeh.2015.04.013 · 4.63 Impact Factor
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