RNA articles within Nature Communications

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  • Article
    | Open Access

    Excision of internal transcribed spacer 2 (ITS2) within eukaryotic pre-ribosomal RNA is essential for ribosome function. Here, the authors reconstitute the entire cycle of ITS2 processing in vitro using purified components, providing insights into the cleavage process and demonstrating that 26S pre-rRNA processing necessarily precedes 7S pre-rRNA processing.

    • Lisa Fromm
    • , Sebastian Falk
    •  & Ed Hurt

  • Article
    | Open Access

    Drosha and DGCR8 constitute the core Microprocessor complex, which processes primary microRNAs (pri-miRs) into mature microRNAs. Here the authors show that heme is essential for the proper processing of pri-miRs by Drosha-DGCR8, and the molecular mechanism by which heme enhances processing fidelity.

    • Alexander C. Partin
    • , Tri D. Ngo
    •  & Yunsun Nam

  • Article
    | Open Access

    The mitochondrial genome, being compressed to 16 kb, is an attractive model system to investigate how RNA-binding proteins chaperone mRNA lifecycles. Here the authors use RNase footprinting and PAR-CLIP to show that the LRPPRC–SLIRP complex stabilizes mRNA structures to expose sites required for translation and polyadenylation.

    • Stefan J. Siira
    • , Henrik Spåhr
    •  & Aleksandra Filipovska

  • Article
    | Open Access

    Small molecules correcting the splicing deficit of the survival of motor neuron 2 (SMN2) gene have been identified as having therapeutic potential. Here, the authors provide evidence that SMN2 mRNA forms a ribonucleoprotein complex that can be specifically targeted by these small molecules.

    • Manaswini Sivaramakrishnan
    • , Kathleen D. McCarthy
    •  & Friedrich Metzger

  • Article
    | Open Access

    RNA-binding proteins (RBPs) regulate RNA activity and are implicated in haematopoietic malignancies, but their role in myeloid cell specification is unclear. Here, the authors show a role for the RBP KSRP in promoting granulocyte fate over monocyte fate through the biogenesis of miR-129 and a decrease in RUNX1.

    • Hongmei Zhao
    • , Xiaoshuang Wang
    •  & Jia Yu

  • Article
    | Open Access

    RNA A-to-I editing introduces single nucleotide changes to RNA, but its role in cells remains unclear. Here, the authors analyse A-to-I editomes in human samples and find that A-to-I editing stabilizes RNA secondary structures and reduces the accessibility of AGO2-miRNA to target sites in mRNAs.

    • Anneke Brümmer
    • , Yun Yang
    •  & Xinshu Xiao

  • Article
    | Open Access

    Twister-sister is a self-cleaving ribozyme. Here, the authors report the 2.0 Å crystal structure of the four-way junctional twister-sister ribozyme in the pre-catalytic state and discuss mechanistic implications based on their mutagenesis experiments and comparisons with other ribozyme structures.

    • Luqian Zheng
    • , Elisabeth Mairhofer
    •  & Aiming Ren

  • Article
    | Open Access

    RNA G-quadruplexes (RG4) occur in vivo and have regulatory roles in mRNA metabolism. Here the authors show that the guanine residue stretches at the 5’ end of tRNA-derived stress-induced RNAs mediate the formation of tetramolecular RG4 structures, which play a role in the post-transcriptional regulation of gene expression.

    • Shawn M. Lyons
    • , Dorota Gudanis
    •  & Pavel Ivanov

  • Article
    | Open Access

    Ribosome biogenesis is a dynamic process that involves the ordered assembly of ribosomal proteins and numerous RNA structural rearrangements. Here the authors apply ChemModSeq, a high-throughput RNA structure probing method, to quantitatively measure changes in RNA flexibility during the nucleolar stages of 60S assembly in yeast.

    • Elena Burlacu
    • , Fredrik Lackmann
    •  & Sander Granneman

  • Article
    | Open Access

    When bacteria enter the stationary growth phase, protein translation is suppressed via the dimerization of 70S ribosomes into inactive complexes. Here the authors provide a structural basis for how the dual domain hibernation promotion factor promotes ribosome dimerization and hibernation in bacteria.

    • Linda E. Franken
    • , Gert T. Oostergetel
    •  & Albert Guskov

  • Article
    | Open Access

    Ribosomes assemble through the hierarchical addition of proteins to a ribosomal RNA scaffold. Here the authors use three-color single-molecule FRET to show how the dynamics of the rRNA dictate the order in which multiple proteins assemble on the 5′ domain of the E. coli 16S rRNA.

    • Sanjaya C. Abeysirigunawardena
    • , Hajin Kim
    •  & Sarah A. Woodson

  • Article
    | Open Access

    The mechanism of U6 small nuclear ribonucleoprotein (snRNP) biogenesis is not well understood. Here the authors characterize the enzymatic activities and structures of yeast and human U6 RNA processing enzyme Usb1, reconstitute post-transcriptional assembly of yeast U6 snRNP in vitro, and propose a model for U6 snRNP assembly.

    • Allison L. Didychuk
    • , Eric J. Montemayor
    •  & Samuel E. Butcher

  • Article
    | Open Access

    TDP-43 aggregation is observed in amyotrophic lateral sclerosis. Here the authors combine X-ray crystallography, nuclear magnetic resonance and electron microscopy studies and show that physiological oligomerization of TDP-43 is mediated through its N-terminal domain, which forms functional and dynamic oligomers antagonizing pathologic aggregation.

    • Tariq Afroz
    • , Eva-Maria Hock
    •  & Magdalini Polymenidou

  • Article
    | Open Access

    A single variant in mir-30c-1 found in breast and gastric cancer patients leads to increased levels of mature miRNA. Here the authors show that this variant alters the RNA structure of this pri-miRNA leading to enhanced binding of SRSF3 and increased Drosha-mediated processing.

    • Noemi Fernandez
    • , Ross A. Cordiner
    •  & Javier F. Cáceres

  • Article
    | Open Access

    Protein RNA interactions are dynamic and regulated in response to environmental changes. Here the authors describe ‘kinetic CRAC’, an approach that allows time resolved analyses of protein RNA interactions with minute time point resolution and apply it to gain insight into the function of the RNA-binding protein Nab3.

    • Rob van Nues
    • , Gabriele Schweikert
    •  & Sander Granneman

  • Article
    | Open Access

    In vivo, complex topologies have been identified in proteins and DNA, while their existence in RNA is still unclear. Here, the authors design synthetic topological structures containing single stranded RNA, offering tools for investigating biologically relevant questions about RNA topology.

    • Di Liu
    • , Yaming Shao
    •  & Yossi Weizmann

  • Article
    | Open Access

    The phosphorylation of serine/arginine-rich proteins by CDC-like kinase is a central regulatory mechanism for RNA splicing reactions. Here, the authors synthesize a novel small molecule CLK inhibitor and map CLK-responsive alternative splicing events and discover an effect on conjoined gene transcription.

    • Tyler Funnell
    • , Shinya Tasaki
    •  & Samuel Aparicio

  • Article
    | Open Access

    Translocation of the tRNA on the ribosome is associated with large-scale molecular movements of the ribosomal L1 stalk. Here the authors identify the key determinants that allow these dramatic movements, and suggest they represent general strategies used to enable large-scale motions in functional RNAs.

    • Srividya Mohan
    •  & Harry F Noller

  • Article
    | Open Access

    Riboswitches are non-coding RNA elements that detect metabolites and control expression by regulating mRNA levels or translation. Here, the authors provide evidence that theE. coli thiC riboswitch has a pause site in the translation initiation region that acts as a checkpoint for thiCexpression.

    • Adrien Chauvier
    • , Frédéric Picard-Jean
    •  & Daniel A. Lafontaine

  • Article
    | Open Access

    The RNA binding protein TRBP is a component of the Dicer complex but its role in microRNA biogenesis remains poorly understood. Here the authors use a crowded RNA environment and single-molecule imaging to show that TRBP acts as a gatekeeper to prevent Dicer engagement with pre miRNA-like substrates.

    • Mohamed Fareh
    • , Kyu-Hyeon Yeom
    •  & Chirlmin Joo

  • Article
    | Open Access

    Degradation of messenger RNA is a key regulatory step in controlling eukaryotic gene expression. Here the authors present xrFrag, a molecular tool to interrogate the extent and directionality of mRNA turnover by the detection of stabilized decay intermediates produced by several common decay pathways.

    • Volker Boehm
    • , Jennifer V. Gerbracht
    •  & Niels H. Gehring

  • Article
    | Open Access

    RBM7 and ZCCHC8 are two core subunits of the Nuclear Exosome Targeting complex, which regulates the degradation of selected non-coding RNAs in human cells. Here, the authors use structural and biochemical methods to show how ZCCHC8 recruits RBM7 in the complex, leaving the RNA binding site accessible and revealing possible implications for splicing.

    • Sebastian Falk
    • , Ksenia Finogenova
    •  & Elena Conti

  • Article
    | Open Access

    The chromatin-associated protein AKAP95 is known for its chromatin-related functions including enhancing transcription. Here the authors show that AKAP95 interacts with the splicing regulatory factors as well as RNAs to regulate the inclusion of exons and pre-mRNA splicing.

    • Jing Hu
    • , Alireza Khodadadi-Jamayran
    •  & Hao Jiang

  • Article
    | Open Access

    DNA methylation in the brain is a dynamic process, but gene-specific regulation of this process is poorly understood. Here, Day and colleagues show that extra-coding RNAs interact with DNA methyltransferases and regulate neuronal DNA methylation to control gene expression in locus-specific manner in neurons.

    • Katherine E. Savell
    • , Nancy V. N. Gallus
    •  & Jeremy J. Day

  • Article
    | Open Access

    The post-transcriptional 5-methylcytosine (m5C) modification occurs in a wide range of nuclear-encoded RNAs. Here the authors identify the mitochondrial tRNA-Met as a target for the m5C methyltransferase NSun3—found mutated in a mitochondrial disease patient—and link mitochondrial tRNA modifications with energy metabolism.

    • Lindsey Van Haute
    • , Sabine Dietmann
    •  & Michal Minczuk

  • Article
    | Open Access

    Current methods for mapping RNA-RNA interactions have to rely on an ‘anchor’ protein or RNA. Here, the authors report the MARIO (Mapping RNA interactome in vivo) technology that can massively reveal RNA-RNA interactions and RNA structure from unperturbed cells.

    • Tri C. Nguyen
    • , Xiaoyi Cao
    •  & Sheng Zhong

  • Article
    | Open Access

    What regulates mRNAs transcript localization in the germ granules in Drosophila is unclear. Here Trcek et al.identify that germ plasm proteins are homogeneously distributed in germ granules but once localized, individual mRNAs form homotypic clusters, contributing structure to the germ granules.

    • Tatjana Trcek
    • , Markus Grosch
    •  & Ruth Lehmann

  • Article
    | Open Access

    Translation of mRNA into proteins is the least accurate process during genetic information transfer. Here the authors suggest—based on 11 high-resolution ribosome crystal structures—that the origin of protein missense errors involves molecular mimicry via tautomerism or ionization.

    • Alexey Rozov
    • , Natalia Demeshkina
    •  & Gulnara Yusupova

  • Article
    | Open Access

    The k-turn is a widespread RNA element that adopts a kinked structure that mediates tertiary contacts and frequently binds specific proteins. Here, McPhee et al. show that the ability of a given k-turn to fold in the presence of metal ions alone—or to otherwise require protein binding—is attributable to a specific base pair.

    • Scott A. McPhee
    • , Lin Huang
    •  & David M. J. Lilley

  • Article |

    RNA is central to many cellular functions, but in vivo structures of most RNAs are unknown. Here Kwok et al. present a universally applicable method, DMS/SHAPE-LMPCR, to identify structures of low-abundance transcripts in living cells, which reveals important features that are uniquely present in vivo.

    • Chun Kit Kwok
    • , Yiliang Ding
    •  & Philip C Bevilacqua

  • Article |

    RNA detection is important in biomedical research and largely relies on the reverse transcription–PCR reaction. Zhao et al.report an isothermal reaction, which involves cleavage by a DNAzyme and signal amplification, to simultaneously amplify and detect RNA.

    • Yongyun Zhao
    • , Li Zhou
    •  & Zhuo Tang

  • Article |

    Sequence-specific DNA endonucleases have found numerous applications in biology, but similar manipulations of RNA have been limited by the lack of suitable enzymes. These authors combine a cleavage domain with a designable binding domain and demonstrate the resulting RNA endonuclease's utilityin vitroand in cells.

    • Rajarshi Choudhury
    • , Yihsuan S. Tsai
    •  & Zefeng Wang

  • Article |

    Nucleic acid superstructures are required to package genomes into the nucleus of cells. In this study, the superstructure of an RNA supercoil species is reported and is shown to be dependent on an RNA-binding protein that induces a higher level of organization compared with DNA superstructures.

    • Jason R. Stagno
    • , Buyong Ma
    •  & Xinhua Ji

  • Article |

    The 30S ribosomal subunit ofEscherichia coliinhibits the RNA-degrading enzyme Ribonuclease T2. Using mutational studies and hybrid ribosomes, Kitahara and Miyazaki show that helix 41 of the 30S ribosomal subunit blocks the enzyme activity, suggesting that helix 41 is required for preventing RNase T2 toxicity.

    • Kei Kitahara
    •  & Kentaro Miyazaki

  • Article
    | Open Access

    ADAR enzymes edit double-stranded RNA, converting adenosines to inosines, and are essential for neuronal function. Eggingtonet al. quantify edit sites in RNA using a Sanger sequencing protocol and use the resulting data to develop algorithms to predict RNA edit sites.

    • Julie M. Eggington
    • , Tom Greene
    •  & Brenda L. Bass

  • Article |

    The pre-mRNA splicing and TREX mRNA export machineries are found in nuclear speckle domains. Diaset al. microinject CMV-DNA constructs into cells and find that transcripts containing functional splice sites accumulate in nuclear speckles and that the TREX complex is required to release the mRNA once processed.

    • Anusha P. Dias
    • , Kobina Dufu
    •  & Robin Reed

  • Article |

    A crucial transition in the origin of life was the emergence of self-replicating RNA and its compartmentalization within protocellular structures. Here it is shown that the physicochemical properties of ice, a simple medium widespread on a temperate early earth, could have mediated this transition.

    • James Attwater
    • , Aniela Wochner
    •  & Philipp Holliger

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