RNA G-quadruplexes and their potential regulatory roles in translation

Abstract: DNA guanine (G)-rich 4-stranded helical nucleic acid structures called G-quadruplexes (G4), have been extensively studied during the last decades. However, emerging evidence reveals that 50- and 30-untranslated regions (50- and 30-UTRs) as well as open reading frames (ORFs) contain putative RNA G-quadruplexes. These stable secondary structures play key roles in telomere homeostasis and RNA metabolism including pre-mRNA splicing, polyadenylation, mRNA targeting and translation. Interestingly, multiple RNA binding proteins such as nucleolin, FMRP, DHX36, and Aven were identified to bind RNA G-quadruplexes. Moreover, accumulating reports suggest that RNA G-quadruplexes regulate translation in cap-dependent and -independent manner. Herein, we discuss potential roles of RNA G-quadruplexes and associated trans-acting factors in the regulation of mRNA translation

Road User Detection in Videos

Successive frames of a video are highly redundant, and the most popular object detection methods do not take advantage of this fact. Using multiple consecutive frames can improve detection of small objects or difficult examples and can improve speed and detection consistency in a video sequence, for instance by interpolating features between frames. In this work, a novel approach is introduced to perform online video object detection using two consecutive frames of video sequences involving road users. Two new models, RetinaNet-Double and RetinaNet-Flow, are proposed, based respectively on the concatenation of a target frame with a preceding frame, and the concatenation of the optical flow with the target frame. The models are trained and evaluated on three public datasets. Experiments show that using a preceding frame improves performance over single frame detectors, but using explicit optical flow usually does not

Road User Detection in Videos

Successive frames of a video are highly redundant, and the most popular object detection methods do not take advantage of this fact. Using multiple consecutive frames can improve detection of small objects or difficult examples and can improve speed and detection consistency in a video sequence, for instance by interpolating features between frames. In this work, a novel approach is introduced to perform online video object detection using two consecutive frames of video sequences involving road users. Two new models, RetinaNet-Double and RetinaNet-Flow, are proposed, based respectively on the concatenation of a target frame with a preceding frame, and the concatenation of the optical flow with the target frame. The models are trained and evaluated on three public datasets. Experiments show that using a preceding frame improves performance over single frame detectors, but using explicit optical flow usually does not

A conserved target site in HIV-1 Gag RNA is accessible to inhibition by both an HDV ribozyme and a short hairpin RNA

Abstract: Antisense-based molecules targeting HIV-1 RNA have the potential to be used as part of gene or drug therapy to treat HIV-1 infection. In this study, HIV-1 RNA was screened to identify more conserved and accessible target sites for ribozymes based on the hepatitis delta virus motif. Using a quantitative screen for effects on HIV-1 production, we identified a ribozyme targeting a highly conserved site in the Gag coding sequence with improved inhibitory potential compared to our previously described candidates targeting the overlapping Tat/Rev coding sequence. We also demonstrate that this target site is highly accessible to short hairpin directed RNA interference, suggesting that it may be available for the binding of antisense RNAs with different modes of action. We provide evidence that this target site is structurally conserved in diverse viral strains and that it is sufficiently different from the human transcriptome to limit off-target effects from antisense therapies. We also show that the modified hepatitis delta virus ribozyme is more sensitive to a mismatch in its target site compared to the short hairpin RNA. Overall, our results validate the potential of a new target site in HIV-1 RNA to be used for the development of antisense therapies

Exploring mRNA 3'-UTR G-quadruplexes: evidence of roles in both alternative polyadenylation and mRNA shortening

Abstract: Guanine-rich RNA sequences can fold into noncanonical, four stranded helical structures called G-quadruplexes that have been shown to be widely distributed within the mammalian transcriptome, as well as being key regulatory elements in various biological mechanisms. That said, their role within the 30-untranslated region (UTR) of mRNA remains to be elucidated and appreciated. A bioinformatic analysis of the 30-UTRs of mRNAs revealed enrichment in G-quadruplexes. To shed light on the role(s) of these structures, those found in the LRP5 and FXR1 genes were characterized both in vitro and in cellulo. The 30- UTR G-quadruplexes were found to increase the efficiencies of alternative polyadenylation sites, leading to the expression of shorter transcripts and to possess the ability to interfere with the miRNA regulatory network of a specific mRNA. Clearly, G-quadruplexes located in the 30-UTRs of mRNAs are cis-regulatory elements that have a significant impact on gene expression

Target-dependent on/off switch increases ribozyme fidelity

Ribozymes, RNA molecules that catalyze the cleavage of RNA substrates, provide an interesting alternative to the RNA interference (RNAi) approach to gene inactivation, especially given the fact that RNAi seems to trigger an immunological response. Unfortunately, the limited substrate specificity of ribozymes is considered to be a significant hurdle in their development as molecular tools. Here, we report the molecular engineering of a ribozyme possessing a new biosensor module that switches the cleavage activity from ‘off’ (a ‘safety lock’) to ‘on’ solely in the presence of the appropriate RNA target substrate. Both proof-of-concept and the mechanism of action of this man-made riboswitch are demonstrated using hepatitis delta virus ribozymes that cleave RNA transcripts derived from the hepatitis B and C viruses. To our knowledge, this is the first report of a ribozyme bearing a target-dependent module that is activated by its RNA substrate, an arrangement which greatly diminishes non-specific effects. This new approach provides a highly specific and improved tool with significant potential for application in the fields of both functional genomics and gene therapy

Structurexplor : a platform for the exploration of structural features of RNA secondary structures

Abstract : Summary: Discovering function-related structural features, such as the cloverleaf shape of transfer RNA secondary structures, is essential to understand RNA function. With this aim, we have developed a platform, named Structurexplor, to facilitate the exploration of structural features in populations of RNA secondary structures. It has been designed and developed to help biologists interactively search for, evaluate and select interesting structural features that can potentially explain RNA functions