Mixture models and wavelet transforms reveal high confidence RNA-protein interaction sites in MOV10 PAR-CLIP data

Abstract

The Photo-Activatable Ribonucleoside-enhanced CrossLinking and ImmunoPrecipitation (PAR-CLIP) method was recently developed for global identification of RNAs interacting with proteins. The strength of this versatile method results from induction of specific T to C transitions at sites of interaction. However, current analytical tools do not distinguish between non-experimentally and experimentally induced transitions. Furthermore, geometric properties at potential binding sites are not taken into account. To surmount these shortcomings, we developed a two-step algorithm consisting of a non-parametric two-component mixture model and a wavelet-based peak calling procedure. Our algorithm can reduce the number of false positives up to 24% thereby identifying high confidence interaction sites. We successfully employed this approach in conjunction with a modified PAR-CLIP protocol to study the functional role of nuclear Moloney leukemia virus 10, a putative RNA helicase interacting with Argonaute2 and Polycomb. Our method, available as the package , is generally applicable to any substitution-based inference problem in genomics.

Host Protein Moloney Leukemia Virus 10 (MOV10) Acts as a Restriction Factor of Influenza A Virus by Inhibiting the Nuclear Import of the Viral Nucleoprotein

“…In our study, we elucidated a novel NP-interacting cellular protein, MOV10, which could inhibit NP binding to importin-␣ and block the nuclear import of NP. Both MOV10 and NP are RNA-binding proteins, and they bind to different kinds of RNAs (31,47,55,67). Our observations indicate that the interaction between MOV10 and NP is dependent on RNAs.…”

MOV10 and FMRP Regulate AGO2 Association with MicroRNA Recognition Elements

“…In addition, there are two studies of RNAs associated with ectopically-expressed MOV10 (Gregersen et al 2014; Sievers et al 2012), which can result in altered intracellular localization (Messaoudi-Aubert et al, 2010). Because FMRP and MOV10 associate in a partially RNA-dependent manner (Fig.1C,D), we used two independent approaches to identify mRNAs associated with endogenous MOV10 (Fig.S1).…”

“…MOV10 has a physical and functional association with AGO (Meister et al, 2005; Sievers et al, 2012). The high abundance of MOV10 mapped sites in the 3’ UTRs of target mRNAs is consistent with a role for MOV10 in post-translational regulation through the miRNA pathway.…”

“…Like FMRP, MOV10 has been implicated in miRNA-mediated translational suppression (Banerjee et al, 2009; Meister et al, 2005; Sievers et al, 2012). We show here that MOV10 has an effect on the fate of its bound RNAs: usually facilitating translation suppression, reflecting its role in the miRNA pathway; however, for a subset of its RNAs, MOV10 increases their expression by blocking AGO2 binding.…”

Global analyses of UPF1 binding and function reveal expanded scope of nonsense-mediated mRNA decay

“…The CLIP assay likely captures multiple distinct states, including UPF1 that is stably loaded onto the RNA before interaction with UPF2 or ATP (Chakrabarti et al 2011), helicase-active UPF1 (post-UPF2 interaction) (Melero et al 2012), and UPF1 that is actively involved in disassembly of mRNPs as degradation progresses (Franks et al 2010). RNA helicases often transit through or rearrange mRNP complexes associated with a wide variety of RNA sequences or bind at specific mRNA locations without recognizable primary sequence motifs (Bohnsack et al 2009;Sievers et al 2012). UPF1 bound locations lacked a detectable sequence motif but displayed increased G content (Fig.…”