Natural RNA circles function as efficient microRNA sponges
TL;DR: This study serves as the first functional analysis of a naturally expressed circular RNA, ciRS-7, which contains more than 70 selectively conserved miRNA target sites, and is highly and widely associated with Argonaute proteins in a miR-7-dependent manner.
Abstract: MicroRNAs (miRNAs) are important post-transcriptional regulators of gene expression that act by direct base pairing to target sites within untranslated regions of messenger RNAs. Recently, miRNA activity has been shown to be affected by the presence of miRNA sponge transcripts, the so-called competing endogenous RNA in humans and target mimicry in plants. We previously identified a highly expressed circular RNA (circRNA) in human and mouse brain. Here we show that this circRNA acts as a miR-7 sponge; we term this circular transcript ciRS-7 (circular RNA sponge for miR-7). ciRS-7 contains more than 70 selectively conserved miRNA target sites, and it is highly and widely associated with Argonaute (AGO) proteins in a miR-7-dependent manner. Although the circRNA is completely resistant to miRNA-mediated target destabilization, it strongly suppresses miR-7 activity, resulting in increased levels of miR-7 targets. In the mouse brain, we observe overlapping co-expression of ciRS-7 and miR-7, particularly in neocortical and hippocampal neurons, suggesting a high degree of endogenous interaction. We further show that the testis-specific circRNA, sex-determining region Y (Sry), serves as a miR-138 sponge, suggesting that miRNA sponge effects achieved by circRNA formation are a general phenomenon. This study serves as the first, to our knowledge, functional analysis of a naturally expressed circRNA.
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TL;DR: This study developed starBase v2.0, which has been updated to provide the most comprehensive CLIP-Seq experimentally supported miRNA-mRNA and mi RNA-lncRNA interaction networks to date, and developed miRFunction and ceRNAFunction web servers to predict the function of miRNAs and other ncRNAs from themiRNA-mediated regulatory networks.
Abstract: Although microRNAs (miRNAs), other non-coding RNAs (ncRNAs) (e.g. lncRNAs, pseudogenes and circRNAs) and competing endogenous RNAs (ceRNAs) have been implicated in cell-fate determination and in various human diseases, surprisingly little is known about the regulatory interaction networks among the multiple classes of RNAs. In this study, we developed starBase v2.0 (http://starbase.sysu.edu.cn/) to systematically identify the RNA-RNA and protein-RNA interaction networks from 108 CLIP-Seq (PAR-CLIP, HITS-CLIP, iCLIP, CLASH) data sets generated by 37 independent studies. By analyzing millions of RNA-binding protein binding sites, we identified ∼9000 miRNA-circRNA, 16 000 miRNA-pseudogene and 285,000 protein-RNA regulatory relationships. Moreover, starBase v2.0 has been updated to provide the most comprehensive CLIP-Seq experimentally supported miRNA-mRNA and miRNA-lncRNA interaction networks to date. We identified ∼10,000 ceRNA pairs from CLIP-supported miRNA target sites. By combining 13 functional genomic annotations, we developed miRFunction and ceRNAFunction web servers to predict the function of miRNAs and other ncRNAs from the miRNA-mediated regulatory networks. Finally, we developed interactive web implementations to provide visualization, analysis and downloading of the aforementioned large-scale data sets. This study will greatly expand our understanding of ncRNA functions and their coordinated regulatory networks.
3,597 citations
Cites background from "Natural RNA circles function as eff..."
...Inspired by the observation that CDR1as circRNA (6,7) acts as a miR-7 super-sponge that contains multiple target sites from the same miRNA at the same transcript or 30-UTR, we tested whether the other class of ncRNAs and protein-coding genes hosted in our database also can act as miRNA super-sponges....
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...(8)All Canonical Pathways (6)Biocarta Pathways (7)Reactome Pathways...
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TL;DR: Understanding this novel RNA crosstalk will lead to significant insight into gene regulatory networks and have implications in human development and disease.
Abstract: Recent reports have described an intricate interplay among diverse RNA species, including protein-coding messenger RNAs and non-coding RNAs such as long non-coding RNAs, pseudogenes and circular RNAs. These RNA transcripts act as competing endogenous RNAs (ceRNAs) or natural microRNA sponges — they communicate with and co-regulate each other by competing for binding to shared microRNAs, a family of small non-coding RNAs that are important post-transcriptional regulators of gene expression. Understanding this novel RNA crosstalk will lead to significant insight into gene regulatory networks and have implications in human development and disease.
2,869 citations
TL;DR: The function of lncRNAs in developmental processes, such as in dosage compensation, genomic imprinting, cell differentiation and organogenesis, with a particular emphasis on mammalian development are described.
Abstract: Genomes of multicellular organisms are characterized by the pervasive expression of different types of non-coding RNAs (ncRNAs). Long ncRNAs (lncRNAs) belong to a novel heterogeneous class of ncRNAs that includes thousands of different species. lncRNAs have crucial roles in gene expression control during both developmental and differentiation processes, and the number of lncRNA species increases in genomes of developmentally complex organisms, which highlights the importance of RNA-based levels of control in the evolution of multicellular organisms. In this Review, we describe the function of lncRNAs in developmental processes, such as in dosage compensation, genomic imprinting, cell differentiation and organogenesis, with a particular emphasis on mammalian development.
2,464 citations
TL;DR: Advances in high-throughput RNA sequencing and circRNA-specific computational tools have driven the development of state-of-the-art approaches for their identification, and novel approaches to functional characterization are emerging.
Abstract: Circular RNAs (circRNAs) are covalently closed, endogenous biomolecules in eukaryotes with tissue-specific and cell-specific expression patterns, whose biogenesis is regulated by specific cis-acting elements and trans-acting factors. Some circRNAs are abundant and evolutionarily conserved, and many circRNAs exert important biological functions by acting as microRNA or protein inhibitors ('sponges'), by regulating protein function or by being translated themselves. Furthermore, circRNAs have been implicated in diseases such as diabetes mellitus, neurological disorders, cardiovascular diseases and cancer. Although the circular nature of these transcripts makes their detection, quantification and functional characterization challenging, recent advances in high-throughput RNA sequencing and circRNA-specific computational tools have driven the development of state-of-the-art approaches for their identification, and novel approaches to functional characterization are emerging.
2,372 citations
TL;DR: This review categorizes lncRNA loci into those that regulate gene expression in cis versus those that perform functions in trans and proposes an experimental approach to dissect lncRNAs activity based on these classifications.
2,241 citations
Cites background from "Natural RNA circles function as eff..."
...A major clue for understanding the function of CDR1as came from its highly unique sequence, containing over 70 conserved seed matches for miR-7 and one nearly perfectly complementary binding site for miR-671 (Figure 2C) (Hansen et al., 2013; Hansen et al., 2011; Memczak et al., 2013)....
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...Due to its circular structure, CDR1as lacks a 50 cap and polyA tail, rendering it resistant to miRNA-induced deadenylation and decay....
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...CDR1as, an abundant cytoplasmic circRNA, is broadly conserved in mammals and highly expressed in the brain....
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...Thus, CDR1as has the capacity to bind and sequester free miR-7, resulting in de-repression of miR-7 targets when the circRNA is heterologously expressed in human cell lines in vitro and in zebrafish embryos in vivo (Hansen et al., 2013; Memczak et al., 2013)....
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...Despite the ability of CDR1as to inhibit miR-7 in experimental models, however, recent results obtained from the study of Cdr1as knockout mice revealed a more complex relationship between this circRNA and miR-7 activity in vivo (Piwecka et al., 2017)....
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References
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TL;DR: The current understanding of miRNA target recognition in animals is outlined and the widespread impact of miRNAs on both the expression and evolution of protein-coding genes is discussed.
18,036 citations
Proceedings Article•
01 Jan 1994TL;DR: The algorithm described in this paper discovers one or more motifs in a collection of DNA or protein sequences by using the technique of expectation maximization to fit a two-component finite mixture model to the set of sequences.
Abstract: The algorithm described in this paper discovers one or more motifs in a collection of DNA or protein sequences by using the technique of expectation maximization to fit a two-component finite mixture model to the set of sequences Multiple motifs are found by fitting a mixture model to the data, probabilistically erasing the occurrences of the motif thus found, and repeating the process to find successive motifs The algorithm requires only a set of unaligned sequences and a number specifying the width of the motifs as input It returns a model of each motif and a threshold which together can be used as a Bayes-optimal classifier for searching for occurrences of the motif in other databases The algorithm estimates how many times each motif occurs in each sequence in the dataset and outputs an alignment of the occurrences of the motif The algorithm is capable of discovering several different motifs with differing numbers of occurrences in a single dataset
4,978 citations
TL;DR: It is demonstrated that linc-MD1 exerts the same control over differentiation timing in human myoblasts, and that its levels are strongly reduced in Duchenne muscle cells, indicating that the ceRNA network plays an important role in muscle differentiation.
2,231 citations
"Natural RNA circles function as eff..." refers methods in this paper
...The specificity of the signal was tested by hybridizing parallel sections with: (1) 100-fold excess of unlabelled probe, (2) pre-treatment with RNase A (Pharmacia Biotech), (3) buffer alone, or (4) Cy5-labelled miR-449 probe....
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TL;DR: It is shown that, in human cell extracts, the miRNA let-7 naturally enters the RNAi pathway, which suggests that only the degree of complementarity between a miRNA and its RNA target determines its function.
Abstract: In animals, the double-stranded RNA-specific endonuclease Dicer produces two classes of functionally distinct, tiny RNAs: microRNAs (miRNAs) and small interfering RNAs (siRNAs). miRNAs regulate mRNA translation, whereas siRNAs direct RNA destruction via the RNA interference (RNAi) pathway. Here we show that, in human cell extracts, the miRNA let-7 naturally enters the RNAi pathway, which suggests that only the degree of complementarity between a miRNA and its RNA target determines its function. Human let-7 is a component of a previously identified, miRNA-containing ribonucleoprotein particle, which we show is an RNAi enzyme complex. Each let-7-containing complex directs multiple rounds of RNA cleavage, which explains the remarkable efficiency of the RNAi pathway in human cells.
2,229 citations
TL;DR: It is found that PTENP1 is biologically active as it can regulate cellular levels of PTEN and exert a growth-suppressive role, and this analysis extended to other cancer-related genes that possess pseudogenes, and revealed a non-coding function for mRNAs.
Abstract: The canonical role of messenger RNA (mRNA) is to deliver protein-coding information to sites of protein synthesis. However, given that microRNAs bind to RNAs, we hypothesized that RNAs could possess a regulatory role that relies on their ability to compete for microRNA binding, independently of their protein-coding function. As a model for the protein-coding-independent role of RNAs, we describe the functional relationship between the mRNAs produced by the PTEN tumour suppressor gene and its pseudogene PTENP1 and the critical consequences of this interaction. We find that PTENP1 is biologically active as it can regulate cellular levels of PTEN and exert a growth-suppressive role. We also show that the PTENP1 locus is selectively lost in human cancer. We extended our analysis to other cancer-related genes that possess pseudogenes, such as oncogenic KRAS. We also demonstrate that the transcripts of protein-coding genes such as PTEN are biologically active. These findings attribute a novel biological role to expressed pseudogenes, as they can regulate coding gene expression, and reveal a non-coding function for mRNAs.
2,107 citations
"Natural RNA circles function as eff..." refers methods in this paper
...The specificity of the signal was tested by hybridizing parallel sections with: (1) 100-fold excess of unlabelled probe, (2) pre-treatment with RNase A (Pharmacia Biotech), (3) buffer alone, or (4) Cy5-labelled miR-449 probe....
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