A potential role for RNA interference in controlling the activity of the human LINE-1 retrotransposon

Division of Molecular Biology, Beckman Research Institute of the City of Hope 1450 East Duarte Road, Duarte, CA 91010-3011, USA.
Nucleic Acids Research (Impact Factor: 9.11). 02/2005; 33(3):846-56. DOI: 10.1093/nar/gki223
Source: PubMed


Long interspersed nuclear elements (LINE-1 or L1) comprise 17% of the human genome, although only 80–100 L1s are considered
retrotransposition-competent (RC-L1). Despite their small number, RC-L1s are still potential hazards to genome integrity through
insertional mutagenesis, unequal recombination and chromosome rearrangements. In this study, we provide several lines of evidence
that the LINE-1 retrotransposon is susceptible to RNA interference (RNAi). First, double-stranded RNA (dsRNA) generated in vitro from an L1 template is converted into functional short interfering RNA (siRNA) by DICER, the RNase III enzyme that initiates
RNAi in human cells. Second, pooled siRNA from in vitro cleavage of L1 dsRNA, as well as synthetic L1 siRNA, targeting the 5′-UTR leads to sequence-specific mRNA degradation of
an L1 fusion transcript. Finally, both synthetic and pooled siRNA suppressed retrotransposition from a highly active RC-L1
clone in cell culture assay. Our report is the first to demonstrate that a human transposable element is subjected to RNAi.

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Available from: John J Rossi, Jun 22, 2015
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    • "L1 element may integrate into several hundred thousand genomic locations, at a loosely defined consensus site (5′-TTTT/AA-3′), which is nicked by L1-EN [8]. The host limits the spread of such elements by transcriptional and post-transcriptional silencing mechanisms that reduce activity to tolerable levels [9]. "
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    ABSTRACT: Background Long interspersed nuclear element-1 (LINE-1 or L1), the most abundant and only autonomously active family of non-LTR retrotransposons in the human genome, expressed not only in the germ lines but also in somatic tissues. It contributes to genetic instability, aging, and age-related diseases, such as cancer. Our previous study identified in human gastric adenocarcinoma an upregulated transcript GCRG213, which shared 88% homology with human L1 sequence and contained a putative conserved apurinic/apyrimidinic endonucleas1 domain. Methods Immunohistochemistry was carried out by using a monoclonal mouse anti-human GCRG213 protein (GCRG213p) antibody produced in our laboratory, on tissue microarray constructed with specimens from 175 gastric adenocarcinoma patients. The correlation between GCRG213p expression and patient clinicopathological parameters was evaluated. GCRG213p expression in gastric cancer cell lines were studied using Western blotting analysis. L1 promoter methylation status of gastric cancer cells was tested using methylation-specific PCR. BLASTP was used at the NCBI Blast server to identify GCRG213p sequence to any alignments in the Protein Data Bank databases. Results Most primary gastric cancer, lymph node metastases and gastric intestinal metaplasia glands showed positive GCRG213p immunoreactivity. High GCRG213p immunostaining score in the primary gastric cancer was positively correlated with tumor differentiation (well differentiated, p = 0.001), Lauren’s classification (intestinal type, p < 0.05) and a late age onset of gastric adenocarcinoma (≥65 yrs; p < 0.05). GCRG213p expression has no association with other clinicopathological parameters, including survival. Western blotting analysis of GCRG213p expression in gastric cancer cells indicated that GCRG213p level was higher in gastric cancer cell lines than in human normal gastric epithelium immortalized cell line GES-1. Partial methylation of L1 in gastric cancer cells was confirmed by methylation-specific PCR. BLASTP program analysis revealed that GCRG213p peptide shared 83.0% alignment with the C-terminal region of L1 endonuclease (L1-EN). GCRG213p sequence possesses the important residues that compose the conserved features of L1-EN. Conclusions GCRG213p could be a variant of L1-EN, a functional member of L1-EN family. Overexpression of GCRG213p is common in both primary gastric cancer and lymph node metastasis. These findings provide evidence of somatic L1 expression in gastric cancer, and its potential consequences in the form of tumor.
    Full-text · Article · May 2013 · BMC Cancer
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    • "However, in animals the apparent absence of RdRPs in their genomes prevented the search for endogenous siRNAs until the accidental discovery of LINE-1, a retro-transposon detected in human cell cultures able to produce a bidirectional RNA transcript using a double promoter system in the sense and antisense orientations [65,66]. In flies, next generation sequencing data of RNA pools obtained from AGO2 immunoprecipitation allowed also to identify a siRNA population clearly distinguisible from the miRNAs and piRNAs. "
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    ABSTRACT: Non-coding RNAs are dominant in the genomic output of the higher organisms being not simply occasional transcripts with idiosyncratic functions, but constituting an extensive regulatory network. Among all the species of non-coding RNAs, small non-coding RNAs (miRNAs, siRNAs and piRNAs) have been shown to be in the core of the regulatory machinery of all the genomic output in eukaryotic cells. Small non-coding RNAs are produced by several pathways containing specialized enzymes that process RNA transcripts. The mechanism of action of these molecules is also ensured by a group of effector proteins that are commonly engaged within high molecular weight protein-RNA complexes. In the last decade, the contribution of structural biology has been essential to the dissection of the molecular mechanisms involved in the biosynthesis and function of small non-coding RNAs.
    Full-text · Article · Dec 2012 · International Journal of Molecular Sciences
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    • "Secondly, retrotransposable elements are also susceptible to post-transcriptional regulation. For instance, endogenously encoded small interfering RNAs have been shown to reduce L1 retrotransposition in vitro (Soifer et al., 2005; Yang and Kazazian, 2006). Additionally, L1 transcripts that contain multiple polyadenylation signals lead to premature polyadenylation , resulting in the attenuation of L1 activity via truncation of its full-length transcripts (Perepelitsa-Belancio and Deininger, 2003). "
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    ABSTRACT: Retroelements comprise a large and successful family of transposable genetic elements that, through intensive infiltration, have shaped the genomes of humans and other mammals over millions of years. In fact, retrotransposons now account for approximately 45% of the human genome. Because of their genomic mobility called retrotransposition, some retroelements can cause genetic diseases; such retrotransposition events occur not only in germ cells but also in somatic cells, posing a threat to genomic stability throughout all cellular populations. In response, mammals have developed intrinsic immunity mechanisms that provide resistance against the deleterious effects of retrotransposition. Among these, seven members of the APOBEC3 (A3) family of cytidine deaminases serve as highly active, intrinsic, antiretroviral host factors. Certain A3 proteins effectively counteract infections of retroviruses such as HIV-1, as well as those of other virus families, while also blocking the transposition of retroelements. Based on their preferential expression in the germ cells, in which retrotransposons may be active, it is likely that A3 proteins were acquired through mammalian evolution primarily to inhibit retrotransposition and thereby maintain genomic stability in these cells. This review summarizes the recent advances in our understanding of the interplay between the retroelements currently active in the human genome and the anti-retroelement A3 proteins.
    Preview · Article · Aug 2012 · Frontiers in Microbiology
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