Analysis of CDS-located miRNA target sites suggests that they can effectively inhibit translation

Hausser, Jean; Syed, Afzal Pasha; Bilen, Biter; Zavolan, Mihaela

doi:10.1101/gr.139758.112

Cited by 296 publications

(239 citation statements)

References 67 publications

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“…Another possibility is that multifunctional cis-acting elements, such as the FN1 EDA splicing enhancer, may directly couple splicing decisions to translational control (Lu and Cullen 2003;Nott et al 2004;Barberan-Soler et al 2009). There is also new evidence supporting the idea of functional microRNA targets sites within coding exons (Hausser et al 2013). This model, if true, provides an elegant mechanism(s) for coupling alternative splicing with isoform-specific mRNA translation.…”

Section: Discussionmentioning

confidence: 84%

Frac-seq reveals isoform-specific recruitment to polyribosomes

et al. 2013

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Pre-mRNA splicing is required for the accurate expression of virtually all human protein coding genes. However, splicing also plays important roles in coordinating subsequent steps of pre-mRNA processing such as polyadenylation and mRNA export. Here, we test the hypothesis that nuclear pre-mRNA processing influences the polyribosome association of alternative mRNA isoforms. By comparing isoform ratios in cytoplasmic and polyribosomal extracts, we determined that the alternative products of ∼30% (597/1954) of mRNA processing events are differentially partitioned between these subcellular fractions. Many of the events exhibiting isoform-specific polyribosome association are highly conserved across mammalian genomes, underscoring their possible biological importance. We find that differences in polyribosome association may be explained, at least in part by the observation that alternative splicing alters the cis-regulatory landscape of mRNAs isoforms. For example, inclusion or exclusion of upstream open reading frames (uORFs) in the 5′UTR as well as Alu-elements and microRNA target sites in the 3′UTR have a strong influence on polyribosome association of alternative mRNA isoforms. Taken together, our data demonstrate for the first time the potential link between alternative splicing and translational control of the resultant mRNA isoforms.

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Section: Discussionmentioning

confidence: 84%

Frac-seq reveals isoform-specific recruitment to polyribosomes

et al. 2013

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“…Although 3 ′ termini may be more accessible to FBF binding in vivo, major binding site peaks clearly occur across the whole transcript, implying that regions throughout the transcript can mediate PUF control. Recent studies of GLD-1, a conserved C. elegans RNA binding protein, demonstrated action via sites in both 5 ′ and 3 ′ UTRs (Jungkamp et al 2011), and regulatory elements in protein-coding regions have been found for miRNAs and the RNA binding proteins UPF1 and FMRP Hausser et al 2013;Zund et al 2013). Many FBF targets had primary and secondary peaks, with some containing over 15 peaks.…”

Section: Discussionmentioning

confidence: 99%

The PUF binding landscape in metazoan germ cells

Prasad

Porter

Kroll-Conner

et al. 2016

RNA

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PUF (Pumilio/FBF) proteins are RNA-binding proteins and conserved stem cell regulators. The Caenorhabditis elegans PUF proteins FBF-1 and FBF-2 (collectively FBF) regulate mRNAs in germ cells. Without FBF, adult germlines lose all stem cells. A major gap in our understanding of PUF proteins, including FBF, is a global view of their binding sites in their native context (i.e., their "binding landscape"). To understand the interactions underlying FBF function, we used iCLIP (individual-nucleotide resolution UV crosslinking and immunoprecipitation) to determine binding landscapes of C. elegans FBF-1 and FBF-2 in the germline tissue of intact animals. Multiple iCLIP peak-calling methods were compared to maximize identification of both established FBF binding sites and positive control target mRNAs in our iCLIP data. We discovered that FBF-1 and FBF-2 bind to RNAs through canonical as well as alternate motifs. We also analyzed crosslinking-induced mutations to map binding sites precisely and to identify key nucleotides that may be critical for FBF-RNA interactions. FBF-1 and FBF-2 can bind sites in the 5 ′ UTR, coding region, or 3 ′ UTR, but have a strong bias for the 3 ′ end of transcripts. FBF-1 and FBF-2 have strongly overlapping target profiles, including mRNAs and noncoding RNAs. From a statistically robust list of 1404 common FBF targets, 847 were previously unknown, 154 were related to cell cycle regulation, three were lincRNAs, and 335 were shared with the human PUF protein PUM2.

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“…To determine whether this is more generally the case, we performed the same computation to explain translational repression and transcript destabilization in human cells transfected with a microRNA. MicroRNA-guided Argonaute proteins are also known to bind both CDSs and 3 ′ UTRs (Hafner et al 2010;Hausser et al 2013) and to affect both the stability and translation rate of mRNAs (Bartel 2009). We used miR-155 binding sites predicted in CDS and 3 ′ UTR by the ElMMo algorithm (Gaidatzis et al 2007) and the mRNA-seq and polysome profile data provided by Guo et al (2010).…”

Section: A B C Dmentioning

confidence: 99%

Modeling the binding specificity of the RNA-binding protein GLD-1 suggests a function of coding region–located sites in translational repression

Brümmer

Kishore

Subasic

et al. 2013

RNA

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To understand the function of the hundreds of RNA-binding proteins (RBPs) that are encoded in animal genomes it is important to identify their target RNAs. Although it is generally accepted that the binding specificity of an RBP is well described in terms of the nucleotide sequence of its binding sites, other factors such as the structural accessibility of binding sites or their clustering, to enable binding of RBP multimers, are also believed to play a role. Here we focus on GLD-1, a translational regulator of Caenorhabditis elegans, whose binding specificity and targets have been studied with a variety of methods such as CLIP (crosslinking and immunoprecipitation), RIP-Chip (microarray measurement of RNAs associated with an immunoprecipitated protein), profiling of polysome-associated mRNAs and biophysical determination of binding affinities of GLD-1 for short nucleotide sequences. We show that a simple biophysical model explains the binding of GLD-1 to mRNA targets to a large extent, and that taking into account the accessibility of putative target sites significantly improves the prediction of GLD-1 binding, particularly due to a more accurate prediction of binding in transcript coding regions. Relating GLD-1 binding to translational repression and stabilization of its target transcripts we find that binding sites along the entire transcripts contribute to functional responses, and that CDS-located sites contribute most to translational repression. Finally, biophysical measurements of GLD-1 affinity for a small number of oligonucleotides appear to allow an accurate reconstruction of the sequence specificity of the protein. This approach can be applied to uncover the specificity and function of other RBPs.

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Analysis of CDS-located miRNA target sites suggests that they can effectively inhibit translation

Cited by 296 publications

References 67 publications

Frac-seq reveals isoform-specific recruitment to polyribosomes

Frac-seq reveals isoform-specific recruitment to polyribosomes

The PUF binding landscape in metazoan germ cells

Modeling the binding specificity of the RNA-binding protein GLD-1 suggests a function of coding region–located sites in translational repression

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