RNA metabolism articles within Nature

Featured

  • Article |

    RNA polymerase (Pol) I transcribes ribosomal RNA that is critically required for ribosome assembly, and the enzyme is a major determinant of protein biosynthesis and cell growth; here the crystal structure of the complete 14-subunit Pol I from yeast is determined, providing insights into its unique architecture and the possible functional roles of its components.

    • Carlos Fernández-Tornero
    • , María Moreno-Morcillo
    •  & Christoph W. Müller

  • Article |

    RNAs undergo many types of post-transcriptional modification, including methylation of ribosomal RNAs; here the structure of the archaeal box C/D ribonucleoprotein complex bound to substrate RNA is determined, showing that the two methylation guide sequences exist in different contexts and revealing sequential regulation of methylation at the two sites.

    • Audrone Lapinaite
    • , Bernd Simon
    •  & Teresa Carlomagno

  • Letter |

    In the human pathogen Vibrio vulnificus, the riboswitch regulating gene expression of the adenosine deaminase is shown to exist in three distinct stable conformational states; this three-state mechanism allows control of gene expression over a broad temperature range, which is essential for Vibrio adaptation.

    • Anke Reining
    • , Senada Nozinovic
    •  & Harald Schwalbe

  • Article |

    This study reports a global analysis of binding sites for over 200 RNA-binding proteins (RBPs) from 24 species; conserved RNA-binding motifs are identified, and their analysis allows prediction of interaction sites based on the sequence of the RNA-binding domain alone.

    • Debashish Ray
    • , Hilal Kazan
    •  & Timothy R. Hughes

  • Letter |

    This study identifies MBNL proteins as negative regulators of alternative splicing events that are differentially regulated between ES cells and other cell types; several lines of evidence show that these proteins repress an ES cell alternative splicing program and the reprogramming of somatic cells to induced pluripotent stem cells.

    • Hong Han
    • , Manuel Irimia
    •  & Benjamin J. Blencowe

  • Letter |

    Members of the SAM-dependent methyltransferase superfamily are involved in the modification of wobble uridine to 5-oxacetyl uridine in Gram-negative bacteria; CmoA converts SAM to carboxy-SAM (Cx-SAM; a metabolite that was unknown previously), and CmoB uses Cx-SAM to convert 5-hydroxyuridine to 5-oxyacetyl uridine in tRNA.

    • Jungwook Kim
    • , Hui Xiao
    •  & Steven C. Almo

  • Letter |

    This study shows that Dis3l2 is the 3′–5′ exonuclease that mediates the degradation of uridylated precursor let-7 microRNA; this is the first physiological RNA substrate identified for this new exonuclease, which causes the Perlman syndrome of fetal overgrowth and Wilms’ tumour susceptibility when mutated.

    • Hao-Ming Chang
    • , Robinson Triboulet
    •  & Richard I. Gregory

  • Letter |

    CPEB1 is known to regulate cytoplasmic polyadenylation, and is now shown to have a second function in the nucleus; it associates with the cleavage and polyadenylation machinery, thereby promoting usage of an upstream poly(A) signal in many messenger RNAs, and affecting alternative splicing.

    • Felice-Alessio Bava
    • , Carolina Eliscovich
    •  & Raúl Méndez

  • Letter |

    To identify comprehensively factors involved in RNAi and microRNA-mediated gene expression regulation, this study performed a phylogenetic analysis of 86 eukaryotic species; the candidates this approach highlighted were subjected to Bayesian analysis with transcriptional and proteomic interaction data, identifying protein orthologues of already known RNAi silencing factors, as well as other hits involved in splicing, suggesting a connection between the two processes.

    • Yuval Tabach
    • , Allison C. Billi
    •  & Gary Ruvkun

  • Article |

    RNA-recognition elements are identified for the fragile-X-syndrome-associated RNA-binding protein FMRP, in addition to its target messenger RNAs; although many of FMRP gene targets discovered are involved in brain function and autism spectrum disorder, a proportion are also dysregulated in mouse ovaries, suggesting cross-regulation of signalling pathways in different tissues.

    • Manuel Ascano
    • , Neelanjan Mukherjee
    •  & Thomas Tuschl

  • Article |

    N6-methyladenosine (m6A) is the most prevalent internal modification in messenger RNA; here the human and mouse m6A modification landscape is presented in a transcriptome-wide manner, providing insights into this epigenetic modification.

    • Dan Dominissini
    • , Sharon Moshitch-Moshkovitz
    •  & Gideon Rechavi

  • Letter |

    Characterization of the human interactome of chromatin-associated messenger ribonucleoprotein particles identifies DBC1 and a new protein (ZIRD) as subunits of a protein complex (DBIRD) that binds directly to RNAPII, regulates alternative splicing of exons embedded in (A + T)-rich DNA, and whose depletion results in region-specific decreases in transcript elongation.

    • Pierre Close
    • , Philip East
    •  & Jesper Q. Svejstrup

  • News & Views |

    A previously unsuspected genetic mechanism underlies a type of muscular dystrophy common in Japan. A therapeutic approach based on this finding and tested in mice has come up with encouraging results. See Letter p.127

    • Masayuki Nakamori
    •  & Charles Thornton

  • Article |

    CRISPR is a microbial RNA-based immune system protecting against viral and plasmid invasions. The CRISPR system is thought to rely on cleavage of a precursor RNA transcript by Cas endonucleases, but not all species possessing CRISPR-type immunity encode Cas proteins. This study now describes an alternative pathway in Streptococcus pyogenes that employs trans-encoded small RNA that directs the processing of precursor RNA into crRNAs through endogenous RNase III and the CRISPR-associated Csn1 protein.

    • Elitza Deltcheva
    • , Krzysztof Chylinski
    •  & Emmanuelle Charpentier

  • 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

  • Letter |

    Various biological processes are entrained by the day–night cycle to occur at a specific time of day. One way the circadian system exerts these effects is through post-transcriptional regulation. These authors show that a protein that transfers methyl groups onto several spliceosome subunits, PRMT5, is regulated by the light–dark cycle. Methylation of these subunits affects alternative splicing of some genes, thus making them subject to circadian control.

    • Sabrina E. Sanchez
    • , Ezequiel Petrillo
    •  & Marcelo J. Yanovsky

  • Article |

    DEAD-box helicases use ATP hydrolysis to unwind duplex RNA and facilitate RNA or RNA–protein remodelling. One such helicase is Mss116, which targets a particular group II intron in RNA. Here, single-molecule fluorescence was used to monitor the effect of Mss16 on a minimal construct containing this intron. The data show that Mss16 stimulates the sampling of different folded states of the RNA. Moreover, the helicase promotes RNA folding through discrete ATP-independent and ATP-dependent steps.

    • Krishanthi S. Karunatilaka
    • , Amanda Solem
    •  & David Rueda

  • Article |

    Splicing is carried out by a collection of protein–RNA complexes known as snRNPs. The spliceosome contains equal quantities of the U1, U2, U4, U5 and U6 snRNPs, but the U1 snRNP is made in levels excess to the amounts needed to form spliceosomes, leading to the idea that excess U1s might have splicing independent functions. Here it is shown that the U1 snRNA interacts with some pre mRNAs whose introns have cryptic polyadenylation sites. This interaction prevents premature termination and polyadenylation of the pre mRNA.

    • Daisuke Kaida
    • , Michael G. Berg
    •  & Gideon Dreyfuss

  • Letter |

    Following their synthesis, eukaryotic messenger RNAs have a 7-methylguanosine cap added to their 5′ ends to protect the mRNAs from degradation. Here it is shown that, in vitro and in yeast, caps lacking a methyl group are recognized by the Rai1 protein, which clips off the incomplete cap. The data provide evidence that Rai1 is part of a quality-control mechanism that monitors, and promotes the digestion of, aberrant mRNAs that might arise during stress conditions.

    • Xinfu Jiao
    • , Song Xiang
    •  & Megerditch Kiledjian

  • Article |

    The coding capacity of the genome is greatly expanded by the process of alternative splicing, which enables a single gene to produce more than one distinct protein. Can the expression of these different proteins be predicted from sequence data? Here, modelling based on information theory has been used to develop a 'splicing code', which can predict, with good accuracy, tissue-dependent changes in alternative splicing.

    • Yoseph Barash
    • , John A. Calarco
    •  & Brendan J. Frey

  • Letter |

    The 'thermodynamic hypothesis' proposes that the sequence of a biological macromolecule defines its folded, active structure as a global energy minimum in the folding landscape; however, it is not clear whether there is only one global minimum or several local minima corresponding to active conformations. Here, using single-molecule experiments, an RNA enzyme is shown to fold into multiple distinct native states that interconvert.

    • Sergey V. Solomatin
    • , Max Greenfeld
    •  & Daniel Herschlag

Browse broader subjects

Browse narrower subjects

Browse RNA metabolism across other nature.com journals