Long intervening noncoding RNAs (lincRNAs) are transcribed from thousands of loci in mammalian genomes and might play widespread roles in gene regulation and other cellular processes. This Review ...outlines the emerging understanding of lincRNAs in vertebrate animals, with emphases on how they are being identified and current conclusions and questions regarding their genomics, evolution and mechanisms of action.
Metazoan MicroRNAs Bartel, David P.
Cell,
03/2018, Letnik:
173, Številka:
1
Journal Article
Recenzirano
Odprti dostop
MicroRNAs (miRNAs) are ∼22 nt RNAs that direct posttranscriptional repression of mRNA targets in diverse eukaryotic lineages. In humans and other mammals, these small RNAs help sculpt the expression ...of most mRNAs. This article reviews advances in our understanding of the defining features of metazoan miRNAs and their biogenesis, genomics, and evolution. It then reviews how metazoan miRNAs are regulated, how they recognize and cause repression of their targets, and the biological functions of this repression, with a compilation of knockout phenotypes that shows that important biological functions have been identified for most of the broadly conserved miRNAs of mammals.
MicroRNAs are pervasive sculptors of gene expression in animals. This review describes these small regulatory RNAs and their biogenesis, regulation, target recognition, mechanism of action, evolution, and biological functions.
MicroRNAs (miRNAs) are endogenous ∼23 nt RNAs that play important gene-regulatory roles in animals and plants by pairing to the mRNAs of protein-coding genes to direct their posttranscriptional ...repression. This review outlines the current understanding of miRNA target recognition in animals and discusses the widespread impact of miRNAs on both the expression and evolution of protein-coding genes.
Thousands of long intervening noncoding RNAs (lincRNAs) have been identified in mammals. To better understand the evolution and functions of these enigmatic RNAs, we used chromatin marks, ...poly(A)-site mapping and RNA-Seq data to identify more than 550 distinct lincRNAs in zebrafish. Although these shared many characteristics with mammalian lincRNAs, only 29 had detectable sequence similarity with putative mammalian orthologs, typically restricted to a single short region of high conservation. Other lincRNAs had conserved genomic locations without detectable sequence conservation. Antisense reagents targeting conserved regions of two zebrafish lincRNAs caused developmental defects. Reagents targeting splice sites caused the same defects and were rescued by adding either the mature lincRNA or its human or mouse ortholog. Our study provides a roadmap for identification and analysis of lincRNAs in model organisms and shows that lincRNAs play crucial biological roles during embryonic development with functionality conserved despite limited sequence conservation.
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► The zebrafish genome encodes hundreds of long intervening noncoding RNAs (lincRNAs) ► Only 29 of 567 lincRNAs have detectable sequence homology with mammalian lincRNAs ► Two lincRNAs,
cyrano and
megamind, are required for proper embryonic development ► The functionality of these two lincRNAs is retained in their human/mouse orthologs
Some long RNA molecules have unknown functions because they lack ability to code for proteins. Ulitsky et al. show that zebrafish have hundreds of genes that produce these long intervening noncoding RNAs (lincRNAs), only few of which share detectable sequence homology with the thousands of different lincRNAs previously identified in mammals. Functional tests of two zebrafish lincRNAs show that each is required for proper embryonic development and that this functionality is retained by their respective human or mouse orthologs.
In vitro, some RNAs can form stable four-stranded structures known as G-quadruplexes. Although RNA G-quadruplexes have been implicated in posttranscriptional gene regulation and diseases, direct ...evidence for their formation in cells has been lacking. Here, we identified thousands of mammalian RNA regions that can fold into G-quadruplexes in vitro, but in contrast to previous assumptions, these regions were overwhelmingly unfolded in cells. Model RNA G-quadruplexes that were unfolded in eukaryotic cells were folded when ectopically expressed in Escherichia coli; however, they impaired translation and growth, which helps explain why we detected few G-quadruplex-forming regions in bacterial transcriptomes. Our results suggest that eukaryotes have a robust machinery that globally unfolds RNA G-quadruplexes, whereas some bacteria have instead undergone evolutionary depletion of G-quadruplex-forming sequences.
The inability to predict long noncoding RNAs from genomic sequence has impeded the use of comparative genomics for studying their biology. Here, we develop methods that use RNA sequencing (RNA-seq) ...data to annotate the transcriptomes of 16 vertebrates and the echinoid sea urchin, uncovering thousands of previously unannotated genes, most of which produce long intervening noncoding RNAs (lincRNAs). Although in each species, >70% of lincRNAs cannot be traced to homologs in species that diverged >50 million years ago, thousands of human lincRNAs have homologs with similar expression patterns in other species. These homologs share short, 5′-biased patches of sequence conservation nested in exonic architectures that have been extensively rewired, in part by transposable element exonization. Thus, over a thousand human lincRNAs are likely to have conserved functions in mammals, and hundreds beyond mammals, but those functions require only short patches of specific sequences and can tolerate major changes in gene architecture.
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•Hundreds of lncRNAs have homologs with similar expression throughout amniotes•Gene structure evolves rapidly, and conserved patches are short and have 5′ bias•Transposable elements often contribute new sequence elements to conserved lncRNAs•Syntenic counterparts of hundreds of mammalian lncRNAs were found in fish and urchin
Hezroni et al. identified long noncoding RNAs (lncRNAs) in 17 species, including 16 vertebrates and sea urchin. Their comparative analysis showed that broadly conserved lncRNAs share only short and 5′-biased patches of conserved sequence and that lncRNA gene architecture is extensively rewired during evolution, in part by exonization of transposable elements.
Noncoding RNAs (ncRNAs) play increasingly appreciated gene-regulatory roles. Here, we describe a regulatory network centered on four ncRNAs—a long ncRNA, a circular RNA, and two microRNAs—using gene ...editing in mice to probe the molecular consequences of disrupting key components of this network. The long ncRNA Cyrano uses an extensively paired site to miR-7 to trigger destruction of this microRNA. Cyrano-directed miR-7 degradation is much more effective than previously described examples of target-directed microRNA degradation, which come primarily from studies of artificial and viral RNAs. By reducing miR-7 levels, Cyrano prevents repression of miR-7–targeted mRNAs and enables accumulation of Cdr1as, a circular RNA known to regulate neuronal activity. Without Cyrano, excess miR-7 causes cytoplasmic destruction of Cdr1as in neurons, in part through enhanced slicing of Cdr1as by a second miRNA, miR-671. Thus, several types of ncRNAs can collaborate to establish a sophisticated regulatory network.
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•A long noncoding RNA, a circular RNA, and two microRNAs form a regulatory network•The Cyrano long noncoding RNA directs potent, multiple-turnover destruction of miR-7•Unchecked miR-7 prevents accumulation of Cdr1as circular RNA in cytoplasm of neurons•miR-7 prevents this accumulation by enhancing the miR-671–directed slicing of Cdr1as
Three different classes of noncoding RNA converge in a regulatory network whereby a long noncoding RNA represses a microRNA via target-directed microRNA degradation, which in turn enables the accumulation of a circular RNA in the mouse brain.
To use microRNAs to downregulate mRNA targets, cells must first process these ∼22 nt RNAs from primary transcripts (pri-miRNAs). These transcripts form RNA hairpins important for processing, but ...additional determinants must distinguish pri-miRNAs from the many other hairpin-containing transcripts expressed in each cell. Illustrating the complexity of this recognition, we show that most Caenorhabditis elegans pri-miRNAs lack determinants required for processing in human cells. To find these determinants, we generated many variants of four human pri-miRNAs, sequenced millions that retained function, and compared them with the starting variants. Our results confirmed the importance of pairing in the stem and revealed three primary-sequence determinants, including an SRp20-binding motif (CNNC) found downstream of most pri-miRNA hairpins in bilaterian animals, but not in nematodes. Adding this and other determinants to C. elegans pri-miRNAs imparted efficient processing in human cells, thereby confirming the importance of primary-sequence determinants for distinguishing pri-miRNAs from other hairpin-containing transcripts.
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► C. elegans pri-miRNAs are not processed in human cells, despite similar structure ► In vitro selection reveals sequence motifs that help define human pri-miRNAs ► The motifs are conserved in pri-miRNAs of other animals but not those of nematodes ► Adding the motifs to C. elegans pri-miRNAs rescues their processing in human cells
Primary-sequence determinants important for processing human pri-miRNAs were uncovered by comparative analysis of functional pri-miRNA sequences selected from a pool of variants.
Recent studies have reported that competitive endogenous RNAs (ceRNAs) can act as sponges for a microRNA (miRNA) through their binding sites and that changes in ceRNA abundances from individual genes ...can modulate the activity of miRNAs. Consideration of this hypothesis would benefit from knowing the quantitative relationship between a miRNA and its endogenous target sites. Here, we altered intracellular target site abundance through expression of an miR-122 target in hepatocytes and livers and analyzed the effects on miR-122 target genes. Target repression was released in a threshold-like manner at high target site abundance (≥1.5 × 105 added target sites per cell), and this threshold was insensitive to the effective levels of the miRNA. Furthermore, in response to extreme metabolic liver disease models, global target site abundance of hepatocytes did not change sufficiently to affect miRNA-mediated repression. Thus, modulation of miRNA target abundance is unlikely to cause significant effects on gene expression and metabolism through a ceRNA effect.
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•Target repression is released only after adding many competing target sites•The number of added sites required for derepression is independent of miRNA levels•The apparent abundance of intracellular target sites exceeds that of the miRNAs•Changes in ceRNAs are typically too small to influence miRNA-mediated repression
Denzler et al. investigate the stoichiometric relationship of a microRNA and its target sites in primary cells. They find that microRNA target sites exceed microRNA copy numbers and that changes in the number of target sites that occur across physiological and disease conditions are typically too small to detectibly influence microRNA activity.
The recent reports of two circular RNAs (circRNAs) with strong potential to act as microRNA (miRNA) sponges suggest that circRNAs might play important roles in regulating gene expression. However, ...the global properties of circRNAs are not well understood.
We developed a computational pipeline to identify circRNAs and quantify their relative abundance from RNA-seq data. Applying this pipeline to a large set of non-poly(A)-selected RNA-seq data from the ENCODE project, we annotated 7,112 human circRNAs that were estimated to comprise at least 10% of the transcripts accumulating from their loci. Most circRNAs are expressed in only a few cell types and at low abundance, but they are no more cell-type-specific than are mRNAs with similar overall expression levels. Although most circRNAs overlap protein-coding sequences, ribosome profiling provides no evidence for their translation. We also annotated 635 mouse circRNAs, and although 20% of them are orthologous to human circRNAs, the sequence conservation of these circRNA orthologs is no higher than that of their neighboring linear exons. The previously proposed miR-7 sponge, CDR1as, is one of only two circRNAs with more miRNA sites than expected by chance, with the next best miRNA-sponge candidate deriving from a gene encoding a primate-specific zinc-finger protein, ZNF91.
Our results provide a new framework for future investigation of this intriguing topological isoform while raising doubts regarding a biological function of most circRNAs.
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