Article

Molecular Mechanisms of Long Noncoding RNAs

Howard Hughes Medical Institute and Program in Epithelial Biology, Stanford University School of Medicine, Stanford, CA 94305, USA.
Molecular cell (Impact Factor: 14.02). 09/2011; 43(6):904-14. DOI: 10.1016/j.molcel.2011.08.018
Source: PubMed

ABSTRACT

Long noncoding RNAs (lncRNAs) are an important class of pervasive genes involved in a variety of biological functions. Here we discuss the emerging archetypes of molecular functions that lncRNAs execute-as signals, decoys, guides, and scaffolds. For each archetype, examples from several disparate biological contexts illustrate the commonality of the molecular mechanisms, and these mechanistic views provide useful explanations and predictions of biological outcomes. These archetypes of lncRNA function may be a useful framework to consider how lncRNAs acquire properties as biological signal transducers and hint at their possible origins in evolution. As new lncRNAs are being discovered at a rapid pace, the molecular mechanisms of lncRNAs are likely to be enriched and diversified.

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    • "The principal role of RNAs, including message RNAs, ribosomal RNAs (rRNAs) and transfer RNAs (tRNAs), is known as the essential components of gene expression. But it is now widely accepted that RNA can perform diverse roles, the novel functions of non-coding RNAs (ncRNAs) lead the revolution of concept in life science (Bali and Kuner, 2014; Hu and Gatti, 2011; Landau and Slack, 2011; Wang and Chang, 2011). After biologists realized that ncRNA should be an ignored key player in life science, identification of enormous ncRNA genes was the main purpose in decade years ago. "
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    ABSTRACT: The poor reproducibility of the reverse transcription combined with quantitative polymerase chain reaction (RT-qPCR) results in an unacceptable reliability of publications based on these data. We established a novel method, in which two short complementary DNA oligos were hybridized with target ncRNA molecules and linked by DNA ligase to obtain a long DNA strand (HL-DNA) replacing cDNA for qPCR detection (HL-qPCR). A series of diluted samples prepared from the same total RNA resource were measured by HL-qPCR and RT-qPCR respectively to acquire their relative concentration of RNU4-1, AK026510 and SNORA73B. For every tested sample, the relative concentration of RNU4-1, AK026510 and SNORA73B obtained by HL-qPCR instead of RT-qPCR is closer to its corresponding true value without significant difference, demonstrating that HL-qPCR exhibits higher accuracy compared with RT-qPCR. With three independent repeats, no significant difference was observed among AK026510/RNU4-1 values of four samples diluted from the same RNA resource, by employing HL-qPCR but not RT-qPCR. It strongly suggests that the good reproducibility of HL-qPCR results from the stable efficiency of HL-DNA production regardless of the concentration and individual features of ncRNA. The novel HL-qPCR could be applied for the regular relative ncRNA concentration detection in the future.
    Full-text · Article · Jan 2016 · Journal of Biotechnology
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    • "NF-YA induces transcription of some apoptotic genes. Accordingly, this interaction titrates NF- YA away from proapoptotic target genes and results in cell immortality (Wang and Chang 2011; Shahandeh 2013). Some lncRNAs mediate posttranscriptional gene regulation . "

    Full-text · Dataset · Dec 2015
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    • "Long noncoding RNAs (lncRNAs), a class of important non-protein coding transcripts with lengths more than 200 nucleotides [1], have gained wide attention recently, and a large number of lncRNAs have been discovered by analysis of chromatin-state maps [2] and full-length complementary DNA (cDNA) [3] based on RNA-seq data [4]. Recent researches show that lncRNAs play critical roles in complex cellular processes, such as epigenetic regulation of gene expression [5] [6] [7] [8] [9], chromatin modification [10], and cell differentiation . "
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    ABSTRACT: Recent study shows that long noncoding RNAs (lncRNAs) are participating in diverse biological processes and complex diseases. However, at present the functions of lncRNAs are still rarely known. In this study, we propose a network-based computational method, which is called lncRNA-protein interaction prediction based on Heterogeneous Network Model (LPIHN), to predict the potential lncRNA-protein interactions. First, we construct a heterogeneous network by integrating the lncRNA-lncRNA similarity network, lncRNA-protein interaction network, and protein-protein interaction (PPI) network. Then, a random walk with restart is implemented on the heterogeneous network to infer novel lncRNA-protein interactions. The leave-one-out cross validation test shows that our approach can achieve an AUC value of 96.0%. Some lncRNA-protein interactions predicted by our method have been confirmed in recent research or database, indicating the efficiency of LPIHN to predict novel lncRNA-protein interactions.
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