Epigenetic silencing of engineered L1 retrotransposition events in human embryonic carcinoma cells. Nature

Department of Human Genetics, 1241 East Catherine Street, University of Michigan Medical School, Ann Arbor, Michigan 48109-5618, USA.
Nature (Impact Factor: 41.46). 08/2010; 466(7307):769-73. DOI: 10.1038/nature09209
Source: PubMed


Long interspersed element-1 (LINE-1 or L1) retrotransposition continues to affect human genome evolution. L1s can retrotranspose in the germline, during early development and in select somatic cells; however, the host response to L1 retrotransposition remains largely unexplored. Here we show that reporter genes introduced into the genome of various human embryonic carcinoma-derived cell lines (ECs) by L1 retrotransposition are rapidly and efficiently silenced either during or immediately after their integration. Treating ECs with histone deacetylase inhibitors rapidly reverses this silencing, and chromatin immunoprecipitation experiments revealed that reactivation of the reporter gene was correlated with changes in chromatin status at the L1 integration site. Under our assay conditions, rapid silencing was also observed when reporter genes were delivered into ECs by mouse L1s and a zebrafish LINE-2 element, but not when similar reporter genes were delivered into ECs by Moloney murine leukaemia virus or human immunodeficiency virus, suggesting that these integration events are silenced by distinct mechanisms. Finally, we demonstrate that subjecting ECs to culture conditions that promote differentiation attenuates the silencing of reporter genes delivered by L1 retrotransposition, but that differentiation, in itself, is not sufficient to reactivate previously silenced reporter genes. Thus, our data indicate that ECs differ from many differentiated cells in their ability to silence reporter genes delivered by L1 retrotransposition.

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    • "Important open questions are which mechanisms have animals evolved to limit TEs from mobilizing and disrupting essential genes, how TEs can evade this control to fulfill their own needs to replicate, and what is the impact on global gene expression from these competing events. While genetics can explore these questions in gonads of intact animals (for review, see Lau 2010; Siomi et al. 2011), biochemical approaches with somatic and stem cells have also yielded much insight in TE biology, such as in Han and Boeke (2004), Coufal et al. (2009), Garcia-Perez et al. (2010), and Quinlan et al. (2011). The Drosophila ovarian somatic sheet (OSS) cell line serves as a niche for examining TE control in a gonad-like context because these cells are derived from follicle cells of the Drosophila ovary and express the Piwi pathway—an important gonad-specific mechanism of TE repression (Lau et al. 2009; Robine et al. 2009; Saito et al. 2009; Haase et al. 2010). "
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    ABSTRACT: Piwi proteins and Piwi-interacting RNAs (piRNAs) repress transposable elements (TEs) from mobilizing in gonadal cells. To determine the spectrum of piRNA-regulated targets that may extend beyond TEs, we conducted a genome-wide survey for transcripts associated with PIWI and for transcripts affected by PIWI knockdown in Drosophila Ovarian Somatic Sheet (OSS) cells, a follicle cell line expressing the Piwi pathway. Despite the immense sequence diversity amongst OSS cell piRNAs, our analysis indicates TE transcripts were the major transcripts associated with and directly regulated by PIWI. However, several coding genes were indirectly regulated by PIWI via an adjacent de novo TE insertion that generated a nascent TE transcript. Interestingly, we noticed that PIWI-regulated genes in OSS cells greatly differed from genes affected in a related follicle cell culture, Ovarian Somatic Cells (OSCs). Therefore, we characterized the distinct genomic TE insertions across four OSS and OSC lines, and discovered dynamic TE landscapes in gonadal cultures that were defined by a subset of active TEs. Particular de novo TEs appeared to stimulate the expression of novel candidate long non-coding RNAs (lncRNAs) in a cell-lineage specific manner, and some of these TE-associated lncRNAs were associated with PIWI and overlapped PIWI-regulated genes. Our analyses of OSCs and OSS cells demonstrate that despite having a Piwi pathway to suppress endogenous mobile elements, gonadal cell TE landscapes can still dramatically change and create transcriptome diversity.
    Genome Research 09/2014; 24(12). DOI:10.1101/gr.178129.114 · 14.63 Impact Factor
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    • "Notably, additional studies have demonstrated that TE methylation differs between cell types, these epigenetic modifications being related to global gene regulation patterns [83] [84] [85]. On the other hand, an active epigenetic response to new L1 insertions in pluripotent cells seem to be related to controlling the load of germline mobilization throughout evolution ([86], reviewed in [57] [78]). Additionally, in adult somatic stem cells such as neural stem cells (NSCs), Methyl-CpG-binding protein 2 (MeCP2), a protein involved in global DNA methylation and human neurodevelopmental diseases, along with transcriptional factors such as Sox2 and the histone deacetylase 1 protein (HDAC1), form a repressor complex on the L1 promoter region controlling L1 neuronal transcription and thus retrotransposition [87] [88] [89]. "
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    ABSTRACT: Transposable Elements are pieces of DNA able to mobilize from one location to another within genomes. Although they constitute more than 50% of the human genome, they have been classified as selfish DNA, with the only mission to spread within genomes and generate more copies of themselves that will ensure their presence over generations. Despite their remarkable prevalence, only a minor group of transposable elements remain active in the human genome and can sporadically be associated with the generation of a genetic disorder due to their ongoing mobility. Most of the transposable elements identified in the human genome corresponded to fixed insertions that no longer move in genomes. As selfish DNA, transposable element insertions accumulate in cell types where genetic information can be passed to the next generation. Indeed, work from different laboratories has demonstrated that the main heritable load of TE accumulation in humans occurs during early embryogenesis. Thus, active transposable elements have a clear impact on our pluripotent genome. However, recent findings suggest that the main proportion of fixed non-mobile transposable elements might also have emerging roles in cellular plasticity. In this concise review, we provide an overview of the impact of currently active transposable elements in our pluripotent genome and further discuss new roles of transposable elements (active or not) in regulating pluripotency. This article is part of a Special Issue entitled: Stress as a fundamental theme in cell plasticity.
    Biochimica et Biophysica Acta (BBA) - Gene Regulatory Mechanisms 07/2014; 1849(4). DOI:10.1016/j.bbagrm.2014.07.007 · 6.33 Impact Factor
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    • "CpG sites [Cordaux et al., 2006]. The many host silencing mechanisms , although largely unexplored, appear to be particularly complex [Bogerd et al., 2006; Tanay et al., 2007; Aravin and Bourc'his, 2008; Edwards et al., 2010; Garcia-Perez et al., 2010; McCue and Slotkin, 2012; Schmidt et al., 2012; Ahn et al., 2013; Horn et al., 2013; Ward et al., 2013]. Despite the sophisticated machinery used by the cell to regulate TE activity, some TEs escape repression and generate new insertions in germ cells during early embryonic development, as well as, in somatic tissues later in life [Baillie et al., 2011; Kazazian, 2011; Lee et al., 2012]. "
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    ABSTRACT: Transposable Elements (TEs) or transposons are low-complexity elements (e.g., LINEs, SINEs, SVAs, and HERVs) that make up to two-thirds of the human genome. There is mounting evidence that TEs play an essential role in genomic architecture and regulation related to both normal function and disease states. Recently, the identification of active TEs in several different human brain regions suggests that TEs play a role in normal brain development and adult physiology and quite possibly in psychiatric disorders. TEs have been implicated in hemophilia, neurofibromatosis, and cancer. With the advent of next-generation whole-genome sequencing approaches, our understanding of the relationship between TEs and psychiatric disorders will greatly improve. We will review the biology of TEs and early evidence for TE involvement in psychiatric disorders. © 2014 Wiley Periodicals, Inc.
    American Journal of Medical Genetics Part B Neuropsychiatric Genetics 04/2014; 165(3). DOI:10.1002/ajmg.b.32225 · 3.42 Impact Factor
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