Long non-coding RNAs articles within Nature

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  • Article
    | Open Access

    Messenger RNAs transcribed from olfactory-receptor genes may have non-coding functions that include recruitment of transcriptional enhancers and inhibition of potentially thousands of competing alleles to ensure stable transcription of a single allele.

    • Ariel D. Pourmorady
    • , Elizaveta V. Bashkirova
    •  & Stavros Lomvardas

  • Article
    | Open Access

    The structures of single COOLAIR RNA isoforms change in abundance and shape in response to external conditions; structural mutation of these isoforms altered FLC expression and flowering time, consistent with a regulatory role of the COOLAIR structure in FLC transcription.

    • Minglei Yang
    • , Pan Zhu
    •  & Yiliang Ding

  • Article
    | Open Access

    In Arabidopsis thaliana, downregulation of the floral repressor FLC in response to cold occurs through a mechanism in which the FLC activator FRIGIDA is sequestered into biomolecular condensates away from the FLC promoter.

    • Pan Zhu
    • , Clare Lister
    •  & Caroline Dean

  • Article |

    The natural antisense transcript MAPT-AS1 interferes with translation of mRNA transcript into tau protein in the brain and may represent a general mechanism for controlling levels of intrinsically disordered proteins, with particular relevance for neurodegeneration.

    • Roberto Simone
    • , Faiza Javad
    •  & Rohan de Silva

  • Article |

    Telomeric-repeat-containing RNA is recruited to telomeres by a mechanism that involves the DNA recombinase RAD51 and the formation of DNA–RNA hybrids, or R-loops—a process similar to that involved in homology-directed DNA repair.

    • Marianna Feretzaki
    • , Michaela Pospisilova
    •  & Joachim Lingner

  • Article |

    A protein condensate formed by multivalent interactions between the long non-coding RNA Xist and specific RNA-binding proteins drives the compartmentalization required to perpetuate gene silencing on the inactive X chromosome.

    • Amy Pandya-Jones
    • , Yolanda Markaki
    •  & Kathrin Plath

  • Article |

    RNA polymerase II has an unexpected function in the nucleolus, helping to drive the expression of ribosomal RNA and to protect nucleolar structure through a mechanism involving triplex R-loop structures.

    • Karan J. Abraham
    • , Negin Khosraviani
    •  & Karim Mekhail

  • Article |

    Long noncoding RNAs and certain unstable transcripts tend to localize to chromatin, in a process that is shown here to depend on an RNA motif that recognizes the small nuclear ribonuclear protein U1, and to rely on transcription.

    • Yafei Yin
    • , J. Yuyang Lu
    •  & Xiaohua Shen

  • Article |

    A transcriptome dataset from seven organs and seven mammalian species throughout development is used to analyse the expression of long noncoding RNAs in tissues within and between species, and at different stages of organ development.

    • Ioannis Sarropoulos
    • , Ray Marin
    •  & Henrik Kaessmann

  • Letter |

    The activation of lipid X receptors (LXRs) in mouse liver not only promotes cholesterol efflux but also inhibits cholesterol synthesis simultaneously; this is mediated by the lipid-responsive long non-coding RNA LeXis, which is induced by a Western diet and orchestrates crosstalk between LXRs and the cholesterol biosynthetic pathway.

    • Tamer Sallam
    • , Marius C. Jones
    •  & Peter Tontonoz

  • Letter |

    A known oncogene, MITF, resides in a region of chromosome 3 that is amplified in melanomas and associated with poor prognosis; now, a long non-coding RNA gene, SAMMSON, is shown to also lie in this region, to also act as a melanoma-specific survival oncogene, and to be a promising therapeutic target for anti-melanoma therapy.

    • Eleonora Leucci
    • , Roberto Vendramin
    •  & Jean-Christophe Marine

  • Letter |

    This study demonstrates a role for the Integrator complex in the stimulus-dependent induction of eRNAs and their 3′ processing; together with previously known roles of Integrator in transcription elongation and RNA processing, these results indicate that Integrator has broad functions in the regulation of eukaryotic gene expression.

    • Fan Lai
    • , Alessandro Gardini
    •  & Ramin Shiekhattar

  • Letter |

    The mechanisms by which Xist, a long non-coding RNA, silences one X chromosome in female mammals are unknown; here a mass spectrometry-based approach is developed to identify several proteins that interact directly with Xist, including the transcriptional repressor SHARP that is required for transcriptional silencing through the histone deacetylase HDAC3.

    • Colleen A. McHugh
    • , Chun-Kan Chen
    •  & Mitchell Guttman

  • Letter |

    Here, a long noncoding RNA, termed Mhrt, is identified in the loci of myosin heavy chain (Myh) genes in mice and shown to be capable of suppressing cardiomyopathy in the animals, as well as being repressed in diseased human hearts.

    • Pei Han
    • , Wei Li
    •  & Ching-Pin Chang

  • Letter |

    During mammalian X-chromosome inactivation, the Xist long noncoding RNA coats the future inactive X chromosome and recruits polycomb repressive complex 2 to a nucleation site, but how Xist spreads silencing across the entire X chromosome is unclear; here high-resolution maps of Xist binding sites across the X chromosome are generated and show that Xist does not spread across the inactive X chromosome uniformly but in two steps, initially targeting gene-rich islands before later spreading to intervening gene-poor domains.

    • Matthew D. Simon
    • , Stefan F. Pinter
    •  & Jeannie T. Lee

  • Article |

    RNAs are shown to interact with DNA methyltransferase 1 and prevent DNA methylation of genes at their specific locus, providing evidence that active transcription directly regulates DNA methylation levels.

    • Annalisa Di Ruscio
    • , Alexander K. Ebralidze
    •  & Daniel G. Tenen

  • Letter |

    A study of prostate cancer cells reveals a transcriptional activation role for long non-coding RNAs (PRNCR1 and PCGEM1) that bind to the androgen receptor, and is also observed for the truncated androgen receptor characteristic of many aggressive prostate cancers.

    • Liuqing Yang
    • , Chunru Lin
    •  & Michael G. Rosenfeld

  • Letter |

    Variation among RNA transcript isoforms can be generated from alternative start and polyadenylation sites, and results in RNAs and proteins with different properties being generated from the same genomic sequence; here a new method termed transcript isoform sequencing is described in yeast, and the method allows a fuller exploration of transcriptome diversity across the compact yeast genome.

    • Vicent Pelechano
    • , Wu Wei
    •  & Lars M. Steinmetz

  • Letter |

    A natural circular RNA termed ciRS-7 is shown to function as a negative regulator of microRNA; ciRS-7 acts as an efficient sponge for the microRNA miR-7, and is resistant to the usual microRNA-mediated degradation pathway of exonucleolytic RNA decay.

    • Thomas B. Hansen
    • , Trine I. Jensen
    •  & Jørgen Kjems

  • Letter |

    A class of long non-coding RNA (lncRNA) with enhancer-like activity is found to associate with the co-activator complex Mediator and promote its genomic association and enzymatic activity; together with Mediator, the lncRNAs also help to maintain the chromosomal architecture of active regulatory elements.

    • Fan Lai
    • , Ulf A. Orom
    •  & Ramin Shiekhattar

  • Letter |

    Long intergenic non-coding RNAs (lincRNAs) have been implicated in both gene silencing and activation, and could be a means for long-range control of gene expression. Here a lincRNA termed HOTTIP is identified at the 5′ tip of the HOXA locus that coordinates the activation of multiple 5′ HOXA genes. Chromosomal looping brings HOTTIP into the proximity of its target genes, where it seems to be required to facilitate histone H3 lysine 4 trimethylation and gene transcription.

    • Kevin C. Wang
    • , Yul W. Yang
    •  & Howard Y. Chang

  • Letter |

    Staufen 1 (STAU1) protein binds regions of dsRNA in the 3′ UTR of mRNAs and promotes their degradation, a process known as SMD (Staufen-mediated mRNA decay). Although a specific stem-loop binding site had been defined for one SMD target, it was unclear how STAU1 was directed to other SMD targets that lack this structure. This paper reports that pairing of Alu element sequences in long non-coding RNAs (lncRNAs) and in the 3′ UTR of the SMD target generates a dsRNA structure that STAU1 recognizes. This result highlights a new function for lncRNAs.

    • Chenguang Gong
    •  & Lynne E. Maquat

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