Non-coding RNAs articles within Nature Communications

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  • Article
    | Open Access

    Bone remodeling involves a switch between bone formation and resorption, but the mechanisms is unclear. Here, the authors show that intercellular communication via extracellular vesicles secreted by mature osteoblasts is a key factor for the switching, via a microRNA-mediated mechanism.

    • Maki Uenaka
    • , Erika Yamashita
    •  & Masaru Ishii

  • 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

    Mutations in the non-coding RNA RMRP cause primary immunodeficiency. Robertson et al show that a disease-associated mutation in RMRP impairs pre-ribosomal RNA processing and reduces ribosome abundance, establishing this disorder as a ribosomopathy.

    • Nic Robertson
    • , Vadim Shchepachev
    •  & David Tollervey

  • Article
    | Open Access

    An abnormal cardiac action potential underlies different types of cardiac arrhythmias. Here the authors show that microRNA-365 regulates the cardiac action potential by modulating key cardiac repolarizing channels.

    • Dena Esfandyari
    • , Bio Maria Ghéo Idrissou
    •  & Stefan Engelhardt

  • Article
    | Open Access

    CLASSY (CLSY) proteins regulate DNA methylation at specific loci in the Arabidopsis genome. Here the authors show that the CLSYs also control tissue-specific DNA methylation, including at siren loci in ovules, and that the lack of an individual CLSYs can shift the epigenetic landscape between tissues.

    • Ming Zhou
    • , Ceyda Coruh
    •  & Julie A. Law

  • 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

    Long non-coding RNAs (lncRNAs) play roles in key cellular processes, but remain largely unexplored in fungal pathogens such as Candida. Here, Hovhannisyan and Gabaldón analyze thousands of sequencing datasets to infer and characterize the lncRNA repertoires of five Candida species, paving the way for their future functional characterization.

    • Hrant Hovhannisyan
    •  & Toni Gabaldón

  • Article
    | Open Access

    Facioscapulohumeral muscular dystrophy is a myopathy caused by aberrant de-repression of the DUX4 gene. Here, the authors show that miR-675 inhibits DUX4 expression and protects muscles from DUX4-mediated cell death when administered to mice using AAV, and that upregulation of miR-675 via small molecules inhibits DUX4 and DUX4-associated biomarkers in myotubes derived from patients.

    • Nizar Y. Saad
    • , Mustafa Al-Kharsan
    •  & Scott Q. Harper

  • Article
    | Open Access

    The RNA genome of the Hepatitis C Virus binds to the liver-specific miR122. Here the authors report the crystal structure of the Ago2:miR122:HCV complex showing that the viral RNA’s structural element traps the Ago2:miR-122 complex on the 5’ end of the viral genome to protect it from degradation.

    • Luca F. R. Gebert
    • , Mansun Law
    •  & Ian J. MacRae

  • Article
    | Open Access

    Understanding which patients will respond to FOLFIRINOX therapy is important for clinical outcome. Here, the authors show that the MIR1307 is increased pancreatic cancer cell lines and inhibition of the microRNA sensitises cells to treatment.’ stratifying patients to achieve the best clinical outcome. Here, the authors show that the MIR1307 is increased in a subgroup of human pancreatic cancers and inhibition of the microRNA in in vitro and in vivo models of pancreatic cancer sensitises cells to treatment.

    • Pietro Carotenuto
    • , Francesco Amato
    •  & Chiara Braconi

  • Article
    | Open Access

    The cereal endosperm is a major determinant of seed size and shape. Here the authors show that a lncRNA, MISSEN, is expressed from the maternally derived allele in rice seeds and regulates a helicase family protein to support efficient nuclear division, distribution and cellularization in the endosperm.

    • Yan-Fei Zhou
    • , Yu-Chan Zhang
    •  & Yue-Qin Chen

  • 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

    Exercise induces structural and functional adaptations in skeletal muscle that involve transcriptomic remodeling, including of miRNA expression. Here the authors examine the expression of miRNAs in human muscle following exercise training and investigate the functions of miR-19b-3p on glucose metabolism in cells and mouse muscle.

    • Julie Massart
    • , Rasmus J. O. Sjögren
    •  & Anna Krook

  • Article
    | Open Access

    Here, cryo-EM reconstructions of human cytomegalovirus (HCMV) virions reveal host tRNAs associated with the virion’s capsid-bound tegument protein, pp150. tRNA recruitment is mediated by the interactions specific for HCMV only, suggesting the explanation for the absence of such tRNA densities in related herpesviruses.

    • Yun-Tao Liu
    • , David Strugatsky
    •  & Z. Hong Zhou

  • 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

    Myocardial regeneration and proliferation of heart muscle cells is limited to a short period after birth early postnatal life, after which heart muscle cells can only grow in size and not in number. Here, the authors identified that the expression level of an endogenous microRNA cluster in heart muscle promotes the passage of the proliferative state to adult heart growth, and modulating the expression of this cluster can stimulate heart regeneration after myocardial infarction.

    • Andrea Raso
    • , Ellen Dirkx
    •  & Leon J. De Windt

  • Article
    | Open Access

    Ribosome biogenesis is crucially dependent on proper rRNA folding, a process assisted by chaperones. Here the authors reveal how Puf6 promotes correct rRNA folding at low temperature, a condition where mis-paired RNA folding intermediates frequently accumulate.

    • Stefan Gerhardy
    • , Michaela Oborská-Oplová
    •  & Vikram Govind Panse

  • 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

    The Argonaute protein CSR-1 is essential for fertility and viability in C. elegans. Here the authors show that CSR-1A isoform associates preferentially with small RNAs mapping to spermatogenesis-specific genes while CSR-1B isoform binds small RNAs mapping to oogenesis-specific genes. Arginine methylation of CSR-1A promotes small RNA-binding specificity.

    • Dieu An H. Nguyen
    •  & Carolyn M. Phillips

  • Article
    | Open Access

    Osteoarthritis is caused by an imbalance between extracellular matrix synthesis and degradation. Here, the authors show that both strands of microRNA-455, -5p and -3p, target HIF2α and regulate cartilage homeostasis, and show that overexpression of these miRNAs is protective against osteoarthritis in mice.

    • Yoshiaki Ito
    • , Tokio Matsuzaki
    •  & Hiroshi Asahara

  • Article
    | Open Access

    PIWI protein contains arginine rich motifs that are post-translationally modified to symmetrically methylated arginine (sDMA) residues. Here the authors show that piRNA loading into Aub triggers sDMA modification which is recognized by Krimper to promote formation of Krimper-Aub-Ago3 complex for piRNA amplification in Drosophila.

    • Xiawei Huang
    • , Hongmiao Hu
    •  & Sisi Li

  • Article
    | Open Access

    Long noncoding RNAs (lncRNAs) are known to regulate the DNA damage response (DDR), however their role in the brain is less well studied. Here, the authors demonstrate a neuron-specific role for Brain Specific DNA-damage Related lncRNA1 (BS-DRL1) and show BS-DRL1 modulates DDR by interacting with HMGB1 in a cell-type specific manner.

    • Min-Min Lou
    • , Xiao-Qiang Tang
    •  & Wen-Yuan Wang

  • Article
    | Open Access

    The therapeutic application of small interfering RNA (siRNA) is challenging due to its non-specific targeting and delivery issues. Here, the authors report an endogenous micro-RNA guided and hybridisation chain reaction-promoted siRNA delivery system encapsulated in tumour-derived extracellular vesicles, with cancer-specific activation, and achieve silencing of hypoxia-related genes.

    • Xue Gong
    • , Haizhou Wang
    •  & Fuan Wang

  • Article
    | Open Access

    TERRA RNA has previously been linked to Alternative lengthening of telomeres (ALT). Here the authors developed a tool to rapidly inhibit TERRA transcription from different chromosome ends in an ALT cell line to show that TERRA transcription actively promotes break induced replication (BIR) and destabilizes telomere integrity in ALT cells.

    • Bruno Silva
    • , Rajika Arora
    •  & Claus M. Azzalin

  • Article
    | Open Access

    A comprehensive transcriptomic survey of the pig could enable mechanistic understanding of tissue specialization and accelerate its use as a biomedical model. Here the authors characterize four distinct transcript types in 31 adult pig tissues to dissect their distinct structural and transcriptional features and uncover transcriptomic variability related to tissue physiology.

    • Long Jin
    • , Qianzi Tang
    •  & Mingzhou Li

  • Article
    | Open Access

    miRNA profiling from patient blood can be used for cancer diagnosis. Here the authors present an electro-optical nanopore sensing platform which allows sensitive and specific miRNA detection directly in human serum and apply to monitoring of miR-141-3p and miR-375-3p in different stage of prostate cancer.

    • Shenglin Cai
    • , Thomas Pataillot-Meakin
    •  & Joshua B. Edel

  • Article
    | Open Access

    BRCA1-mediated resolution of R-loops has previously been described. Here the authors reveal a functional association of BRCA1 with TERRA RNA at telomeres, which develops in an R-loop-, and a cell cycle-dependent manner.

    • Jekaterina Vohhodina
    • , Liana J. Goehring
    •  & David M. Livingston

  • 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

    Cells infected with pathogens can release signals that instruct neighbouring cells to mount an immune response or that reduce these cells’ susceptibility to infection. Here, Aguilar et al. show the opposite effect: cells infected with Salmonella Typhimurium secrete host factors that facilitate the infection of bystander cells by activating their ER-stress response.

    • Carmen Aguilar
    • , Susana Costa
    •  & Ana Eulalio

  • Article
    | Open Access

    Homeostasis of the intestinal epithelium is crucial for the maintenance of the epithelial barrier. Here, the authors show that mir-802 ablation in the mouse intestine impairs enterocyte differentiation and glucose absorption, enhances Paneth cell function by increasing Tmed9-mediated defensin secretion, and increases epithelial cell turnover.

    • Algera Goga
    • , Büsra Yagabasan
    •  & Markus Stoffel

  • Article
    | Open Access

    Hyperphosphorylated Tau accumulation promotes neurodegeneration in Alzheimer’s disease. Here, the authors screen a miRNA library in Drosophila and identify a conserved ubiquitin ligase that directs Tau for autophagic degradation, uncovering a potential target to treat Tau-mediated neurodegeneration.

    • Manivannan Subramanian
    • , Seung Jae Hyeon
    •  & Kweon Yu

  • Article
    | Open Access

    Long noncoding RNAs (lncRNAs) have been shown to play a role in cardiac physiology and disease. Here the authors identify the lncRNA Caren as a cytoplasmic RNA that decreases the translation of a distant gene encoding Hint1, thereby maintaining cardiomyocyte function due to inactivation of the DNA damage response and activation of mitochondrial bioenergetics.

    • Michio Sato
    • , Tsuyoshi Kadomatsu
    •  & Yuichi Oike

  • Article
    | Open Access

    Osteoporosis and bone disease are common in patients with systemic mastocytosis. Here, the authors show that extracellular vesicles released by neoplastic mast cells of the patients block osteoblast differentiation and bone mineralization when injected into mice, via a mechanism involving suppression of osteogenic factors via miRNA-30a and miRNA-23a.

    • Do-Kyun Kim
    • , Geethani Bandara
    •  & Ana Olivera

  • Article
    | Open Access

    Senescence-associated secretory phenotype (SASP) involves secretion of factors such as pro-inflammatory cytokines. Here the authors show that MIR31HG regulates the expression and secretion of a subset of SASP components that induce paracrine invasion, through interaction with YBX1 and induction of IL1A translation.

    • Marta Montes
    • , Michal Lubas
    •  & Anders H. Lund

  • Article
    | Open Access

    C. elegans miRNAs associate with AGO proteins ALG-1 and ALG-2. Here the authors provide a map of miRNAs loaded into ALG-1 and ALG-2 from intestine, body wall muscles and nervous system in C. elegans providing insights into spatial and temporal AGO loading flexibility.

    • Christopher A. Brosnan
    • , Alexander J. Palmer
    •  & Steven Zuryn

  • Article
    | Open Access

    Wild-type KRAS amplification is known to induce KRAS activation in cancer leading to poor prognostic outcomes. Here the authors identify a KRAS-responsive lncRNA, KIMAT1 that maintains KRAS signalling in lung cancer, suggesting that its targeting may prevent KRAS-driven tumourigenesis.

    • Lei Shi
    • , Peter Magee
    •  & Michela Garofalo

  • 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

    Nascent non-coding RNA can mediate chromatin silencing, however mechanistically this process is poorly understood. Here the authors show that resolution of an R-loop during 3'-end processing of a plant antisense transcript recruits chromatin modifiers to promote chromatin silencing.

    • Congyao Xu
    • , Zhe Wu
    •  & Caroline Dean

  • Article
    | Open Access

    Piwi deficiency results in sterility and is associated with transposon expression and genomic instability. Here the authors show that sterility of C. elegans Piwi prg-1 mutant is not associated with transposon-induced DNA damage but is associated with and is phenocopied by dysfunction of germ granules.

    • Maya Spichal
    • , Bree Heestand
    •  & Shawn Ahmed

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