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

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

Optimization and automatic differentiation in Ada : some practical experience

This paper describes an investigation into the performance of three Ada packages for automatic differentiation. Two of these implement the forward accumulation approach while the third employs reverse accumulation. Each package is used to provide gradient information required by a number of optimization calculations, including examples of unconstrained, constrained and least-squares problems. The results show how automatic differentiation methods can be influenced in practice by the size, complexity and sparsity of a problem. They also demonstrate ways in which the methods should interface with different types of optimization procedure. Finally, and perhaps most significantly, the results show how the performance of automatic differentiation codes can depend on hardware and system software considerations that are sometimes ignored by numerical mathematicians. A subsidiary aim of this paper is to provide a “shop window” for user friendly forms of automatic differentiation. The underlying mathematical ideas have been quite widely discussed in the literature: but their implementation and use seems to have been perceived as too difficult for the non-specialist. The examples in this paper are intended to demonstrate that this need not be the casePeer reviewe

L1 siRNA specifically inhibits the expression of a hybrid luciferase transcript driven by the L1 5′-UTR internal promoter

<p><b>Copyright information:</b></p><p>Taken from "A potential role for RNA interference in controlling the activity of the human LINE-1 retrotransposon"</p><p>Nucleic Acids Research 2005;33(3):846-856.</p><p>Published online 8 Feb 2005</p><p>PMCID:PMC549394.</p><p>© The Author 2005. Published by Oxford University Press. All rights reserved</p> HCT116 cells were co-transfected with the indicated firefly (FF) luciferase expression vector and increasing amounts of L1 siRNA or control siRNA. Relative FF luciferase activity in the absence of siRNA was set at 1.0. The amount of each specific siRNA is indicated below the graphs. () Luciferase assays performed with ‘diced’ siRNA. Diced LacZ siRNA and synthetic FF luciferase siRNA served as negative and positive controls, respectively. () Luciferase assays performed with synthetic siRNA targeting nucleotides 749–769 of the L1 5′-UTR. Irrelevant synthetic siRNA targeting the HIV Rev transcript was included as the negative control