Small RNAs articles within Nature Communications

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  • Article
    | Open Access

    Small RNAs (sRNAs) turn bacterial genes on or off by base pairing with mRNAs. Here the authors employ single molecule fluorescence to show how sRNAs and their chaperone Hfq quickly locate the proper target by repeatedly scanning an mRNA until a stable match is found.

    • Ewelina M. Małecka
    •  & Sarah A. Woodson

  • Article
    | Open Access

    Short prokaryotic Argonaute and Sir2 proteins function as an antivirus system. Here the authors describe structures of SPARSA (a heterodimer of Sir2-APAZ and prokaryotic Argonaute) with and without template DNA and guide RNA, providing structural basis of its assembly and activation by the recognition of the invading virus.

    • Xiangkai Zhen
    • , Xiaolong Xu
    •  & Songying Ouyang

  • Article
    | Open Access

    Germ granules are membraneless organelles that act as organizing centers for small RNA biogenesis during germline development. Here they show the LOTUS domain protein eggd-1 organizes germ granules, and reveal a germ line-to-soma communication pathway activated upon perturbation of germ granules.

    • Ian F. Price
    • , Jillian A. Wagner
    •  & Wen Tang

  • Article
    | Open Access

    The presence and/or biological functionality of circular RNAs in bacteria are unclear. Here, the authors identify a dual-conformation (linear and circular) noncoding RNA that promotes tolerance to oxidative stress in Bacillus altitutidinis, and provide evidence for the existence of other circular RNAs in diverse bacterial species.

    • Ting-Ting He
    • , Yun-Fan Xu
    •  & Hai-Yan Wang

  • Article
    | Open Access

    U6 snRNA plays a catalytic role in pre-mRNA splicing. Here the authors report the structure of human terminal uridyltransferase, TUT1, complexed with U6 snRNA revealing the mechanism of specific uridylation of U6 snRNA by TUT1.

    • Seisuke Yamashita
    •  & Kozo Tomita

  • Article
    | Open Access

    Small regulatory RNAs (sRNAs) often act in concert with the RNA-chaperone Hfq to regulate the expression of multiple target transcripts in bacteria. Here, the authors identify Hfq-interacting sRNAs and their targets in the pathogen Vibrio cholerae, including an RNA sponge that binds and inactivates four sRNAs that modulate the quorum sensing pathway.

    • Michaela Huber
    • , Anne Lippegaus
    •  & Kai Papenfort

  • Article
    | Open Access

    RNA modifications are important regulators of RNA biology. Here we report N1-methyladenosine (m1A) enrichment on 22-nucleotide tRNA fragments and its effect on gene-silencing. Higher level of m1A in bladder cancer is accompanied by gene dysregulation in unfolded protein response.

    • Zhangli Su
    • , Ida Monshaugen
    •  & Anindya Dutta

  • Article
    | Open Access

    MicroRNA precursors are cleaved by DICER to generate mature microRNAs in the cytoplasm. Here the authors employ high-throughput analysis of DICER cleavage activity and identify RNA secondary elements in precursor miRNAs and shRNAs, including a single nucleotide bulge, which govern its cleavage efficiency and accuracy.

    • Trung Duc Nguyen
    • , Tam Anh Trinh
    •  & Tuan Anh Nguyen

  • Article
    | Open Access

    Protein Hfq regulates bacterial mRNA translation and stability by interacting with mRNAs and small noncoding RNAs. Here, the authors identify Hfq-interacting RNAs in three strains representing major phylogenetic lineages of Pseudomonas aeruginosa, highlighting intra-species diversity in post-transcriptional regulatory networks.

    • Julian Trouillon
    • , Kook Han
    •  & Stephen Lory

  • Article
    | Open Access

    The parasitic nematode Ascaris lacks piRNAs. Here the authors compare Argonaute proteins and small RNAs from C. elegans and Ascaris, expanding our understanding of the conservation, divergence, and flexibility of Argonautes and small RNA pathways in nematodes.

    • Maxim V. Zagoskin
    • , Jianbin Wang
    •  & Richard E. Davis

  • Article
    | Open Access

    A single molecule fluorescence study revealed three dynamically interconverting conformations of the fluoride riboswitch from Bacillus cereus, where an anionic ligand snap-locks a docked conformation through a long-range interaction necessary for downstream gene regulation.

    • Rajeev Yadav
    • , Julia R. Widom
    •  & Nils G. Walter

  • Article
    | Open Access

    The molecular events underlying the assembly and maturation of the early pre-60S particles during eukaryotic ribosome synthesis are not well understood. Here, the authors combine yeast genetics and biochemical experiments to characterise the functions of two important players of eukaryotic ribosome biogenesis, the box C/D snoRNP snR190 and the helicase Dbp7, which both interact. They show that the snR190 snoRNA acts as a RNA chaperone that assists the structuring of the 25S rRNA during the maturation of early pre-60S particles and that Dbp7 is important for facilitating remodeling events in the peptidyl transferase center region of the 25S rRNAs during the maturation of early pre-60S particles.

    • Mariam Jaafar
    • , Julia Contreras
    •  & Anthony K. Henras

  • Article
    | Open Access

    Lipid induced stress contributes to metabolic diseases. Here the authors identify small nucleolar RNA 73 (SNORA73) in a screen for genes that protect against lipotoxicity and show that deficiency of SNORA73 reprograms oxidative metabolism and protects against steatohepatitis in mice.

    • Arthur C. Sletten
    • , Jessica W. Davidson
    •  & Jean E. Schaffer

  • Article
    | Open Access

    The small RNA RepG modulates expression of chemotaxis receptor TlpB in Helicobacter pylori by targeting a length-variable G-repeat in the tlpB mRNA. Here, Pernitzsch et al. show that RepG also gradually controls lipopolysaccharide biosynthesis, antibiotic susceptibility, and in-vivo colonization of the stomach, by regulating a gene that is co-transcribed with tlpB.

    • Sandy R. Pernitzsch
    • , Mona Alzheimer
    •  & Cynthia M. Sharma

  • Article
    | Open Access

    22G-RNAs are single-stranded antisense small RNAs that are expressed in C. elegans germline. Here the authors show that CSR-1 dependent 22G-RNAs are produced in the cytosol on mRNAs actively engaged in translation and that codon usage of an mRNA regulates the biogenesis of CSR-1 dependent 22G-RNAs.

    • Meetali Singh
    • , Eric Cornes
    •  & Germano Cecere

  • Article
    | Open Access

    Biogenesis of small nucleolar RNAs ribonucleoproteins (snoRNPs) requires dedicated assembly machinery. Here, the authors show that a subset of snoRNP assembly factors interacts, genetically or directly, with factors modulating chromatin architecture, suggesting a link between ribosome formation and chromatin functions.

    • Benoît Bragantini
    • , Christophe Charron
    •  & Bruno Charpentier

  • Article
    | Open Access

    Transcription factor TFIIIC plays roles in Pol III transcription and in chromatin organization. CryoEM structure of the yeast TFIIIC subcomplex τA, a negative stain reconstruction of τA bound to the TFIIIB subunits Brf1 and TBP and accompanying biochemistry suggest how τA achieves positioning of TFIIIB upstream of the TSS and remodeling of the TFIIIC complex during assembly of TFIIIB.

    • Matthias K. Vorländer
    • , Anna Jungblut
    •  & Christoph W. Müller

  • Article
    | Open Access

    Small non-coding RNAs contribute to the regulation of aging. Here the authors identify a small nucleolar RNA, the snoRNA jouvence, which extends the lifespan of fruit flies through its function in the gut, and is conserved in humans.

    • Stéphanie Soulé
    • , Lucille Mellottée
    •  & Jean-René Martin

  • Article
    | Open Access

    Argonaute protein is loaded with small RNA and scans long stretch of sequences to find complementary target sites. Here, using single-molecule FRET and kinetic modelling, the authors showed that prokaryotic Argonaute protein binds target DNA loosely and slides along the DNA during target search.

    • Tao Ju Cui
    • , Misha Klein
    •  & Chirlmin Joo

  • Article
    | Open Access

    PIWI-interacting RNAs (piRNAs) are ~25–33 nt small RNAs expressed in animal germ cells. Here, the authors develop a single-cell small RNA sequencing method and report that a class of ~20-nt piRNAs lacking 3′ end 2′-O-methylation are associated with PIWIL3 protein and predominantly expressed in human and monkey oocytes.

    • Qiyuan Yang
    • , Ronghong Li
    •  & Ligang Wu

  • Article
    | Open Access

    AGO2 is a core component of the RNAi machinery and contributes to plant immunity during bacterial infection. Here the authors show that AGO2 activity is suppressed by arginine methylation which not only promotes AGO2 degradation but also recruits TSN proteins to degrade AGO2-associated small RNAs.

    • Po Hu
    • , Hongwei Zhao
    •  & Hailing Jin

  • Article
    | Open Access

    Transient aneuploidy enables cells to survive sudden environmental changes before longterm cellular adaptations are established. Here, the authors show that yeast cells respond to the acute loss of Ulp2 SUMO protease by rapid induction of aneuploidy, and reveal predictable long-term adaptation mechanisms that restore euploidy.

    • Hong-Yeoul Ryu
    • , Francesc López-Giráldez
    •  & Mark Hochstrasser

  • Article
    | Open Access

    Small RNA degrading nucleases (SDNs) can degrade short RNAs. Here the authors report the crystal structure of Arabidopsis SDN1 in complex with a single-stranded RNA, and provide new insight into 3′ end trimming mechanism of 3′ to 5′ riboexonucleases in the metabolism of various species of small RNAs.

    • Jiayi Chen
    • , Li Liu
    •  & Jinbiao Ma

  • Article
    | Open Access

    While circulating DNA has been extensively explored as a potential cancer biomarker, RNA potential has been overlooked so far. Here the authors present a comprehensive analysis of extracellular RNA secreted by glioblastoma cells that could prove a valuable resource for biomarker discovery and a means of intercellular communication.

    • Zhiyun Wei
    • , Arsen O. Batagov
    •  & Anna M. Krichevsky

  • 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

    The DNA damage response (DDR) involves site-specific small non-coding RNAs. Here the authors show that telomere dysfunction induces transcription of telomeric DNA damage response RNAs that are necessary for DDR activation, which can be specifically muted by antisense inhibitory oligonucleotides.

    • Francesca Rossiello
    • , Julio Aguado
    •  & Fabrizio d’Adda di Fagagna

  • Article
    | Open Access

    Extracellular miRNAs are present in a variety of bodily fluids. Here, Freedman et al. analysed plasma-derived RNA by RNA-seq from 40 people followed by targeted RT-qPCR in an additional 2,763 people, and report over 1,000 extracellular RNAs including microRNAs, piwi-interacting RNA and small nucleolar RNAs.

    • Jane E. Freedman
    • , Mark Gerstein
    •  & Kahraman Tanriverdi

  • Article |

    The elongation factors DSIF and NELF have established roles in polymerase pausing, elongation and 3'-end processing of replication-dependent histone mRNAs. Here the authors demonstrate that DSIF and NELF form a complex with Integrator and allow proper 3'-processing of snRNA transcripts by preventing the recruitment of CstF.

    • Junichi Yamamoto
    • , Yuri Hagiwara
    •  & Yuki Yamaguchi

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