RNA articles within Nature Communications

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  • Article
    | Open Access

    Many RNA viruses employ programmed –1 ribosomal frameshifting (PRF) to expand their coding capacity and optimize production of viral proteins. Here, the authors report structural and biophysical analysis of protein 2A from a cardiovirus, with insights into the mechanism of its PRF-stimulatory function.

    • Chris H. Hill
    • , Lukas Pekarek
    •  & Ian Brierley

  • Article
    | Open Access

    Mannosyl-queuosine (manQ) is a non-canonical RNA nucleoside present in the anticodon loop of certain tRNAs. Here, the authors use a combination of total synthesis and mass spectrometry to contradict the literature-reported structure and show that manQ features an alpha-allyl connectivity of its mannose moiety.

    • Markus Hillmeier
    • , Mirko Wagner
    •  & Thomas Carell

  • Article
    | Open Access

    RNA of some viruses is protected from degradation by a 5′ triphosphate group. Here the authors identify nudix hydrolase 2 (NUDT2) as novel antiviral defense protein that dephosphorylates viral RNA and thereby enables its degradation.

    • Beatrice T. Laudenbach
    • , Karsten Krey
    •  & Andreas Pichlmair

  • Article
    | Open Access

    Start codon selection is commonly thought to occur through the unidirectional scanning of the mRNA by the 40 S ribosome. Here the authors provide evidence that the pre-initiation complex can backslide on the mRNA to initiate translation at upstream AUG codons.

    • Yifei Gu
    • , Yuanhui Mao
    •  & Shu-Bing Qian

  • 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

    RNA-protein interactions play critical roles in post-transcriptional gene regulation. Here the authors demonstrate pRBS-ID, an updated MS/MS-based method that combines the benefits of photoactivatable ribonucleosides and the chemical cleavage of RNA.

    • Jong Woo Bae
    • , Sangtae Kim
    •  & Jong-Seo Kim

  • Article
    | Open Access

    Ribosome can mediate piRNA biogenesis from long non-coding RNAs following translation of the short open reading frames. Here the authors show that 80S ribosome also guides piRNA production from 3’ UTR of protein-coding genes after translation of long open reading frames, indicating a general piRNA biogenesis mechanism regardless of their precursor ORF length.

    • Yu H. Sun
    • , Ruoqiao Huiyi Wang
    •  & Xin Zhiguo Li

  • Article
    | Open Access

    Mutations within subunits of the tRNA splicing endonuclease complex (TSEN) are associated with pontocerebellar hypoplasia (PCH). Here the authors show that tRNA intron excision is catalyzed by tetrameric TSEN assembled from inactive heterodimers, and provide evidence that modulation of TSEN stability may contribute to PCH phenotypes.

    • Samoil Sekulovski
    • , Pascal Devant
    •  & Simon Trowitzsch

  • Article
    | Open Access

    RNA secondary structure is important for viral replication, transcription and translation. Here the authors employ SPLASH method and map in vivo RNA interactions and dynamics of SARS-CoV-2 RNA genome in different viral life cycles.

    • Yan Zhang
    • , Kun Huang
    •  & Zhihu Zhao

  • Article
    | Open Access

    Current high-throughput single-cell transcriptomic methods are incompatible with paraformaldehyde, a common cell fixation technique. Here the authors present FD-seq, a method for droplet-based RNA sequencing of paraformaldehyde-fixed, stained and sorted single cells.

    • Hoang Van Phan
    • , Michiel van Gent
    •  & Savaş Tay

  • Article
    | Open Access

    C. elegans piRNA biogenesis and chromosome segregation (PICS) complex is composed of TOFU-6, PICS-1, ERH-2, and two mutually exclusive factors PID-1 and TOST-1. By employing biochemical, structural, and cellular biology methods, the authors show that the PICS complex is an octamer consisting of two copies of each subunit, and functions in piRNA biogenesis and mitosis.

    • Xiaoyang Wang
    • , Chenming Zeng
    •  & Chao Xu

  • Article
    | Open Access

    Met1-linked linear ubiquitination (M1-Ubi) is catalyzed by linear ubiquitin chain assembly complex (LUBAC). Here the authors show that Ago2 protein is M1-Ubi modified by LUBAC complex under hypoxia condition leading to less association of miRNA target mRNAs to Ago2 protein and de-repression of miRNA targets.

    • Hailong Zhang
    • , Xian Zhao
    •  & Jianxiu Yu

  • Article
    | Open Access

    m6A RNA post-transcriptional modification changes RNA hybridization kinetics. Here the authors show that the methylamino group can adopt syn-conformation pairing with uridine with a mismatch-like conformation in RNA duplex. They also develop a quantitative model that predicts how m6A affects the kinetics of hybridization.

    • Bei Liu
    • , Honglue Shi
    •  & Hashim M. Al-Hashimi

  • Article
    | Open Access

    Ribosome profiling has become the gold standard to analyze mRNA translation dynamics, and the translation inhibitor cycloheximide (CHX) is often used in its application. Here the authors systematically demonstrate that CHX does not bias the outcome of ribosome profiling experiments in most organisms.

    • Puneet Sharma
    • , Jie Wu
    •  & Sebastian A. Leidel

  • Article
    | Open Access

    Proximity labeling is used to map and discover proteins in specific subcellular compartments. Here the authors combine APEX-mediated proximity labeling with organic-aqueous phase separation to identify nuclear, nucleolar, and outer mitochondrial membrane RNA binding proteins.

    • Wei Qin
    • , Samuel A. Myers
    •  & Alice Y. Ting

  • Article
    | Open Access

    RNA polyadenosine tails are important for the export, translation and stability of mRNAs and play a role in non-coding RNA biogenesis. Here the authors measure yeast poly(A) tail lengths by direct RNA sequencing, revealing its dynamics in yeast exonuclease, deadenylase and poly(A) polymerase mutants.

    • Agnieszka Tudek
    • , Paweł S. Krawczyk
    •  & Andrzej Dziembowski

  • Article
    | Open Access

    Trans-translation, mediated by small protein B (SmpB) and transfer-messenger RNA (tmRNA), enables recycling of the ribosomes stalled on defective mRNAs in bacteria. Here, the authors report structures of the ribosome during trans-translation that reveal a translocation intermediate and elucidate the movements of the tmRNA-SmpB complex in the ribosome.

    • Charlotte Guyomar
    • , Gaetano D’Urso
    •  & Reynald Gillet

  • Article
    | Open Access

    Translational regulation by riboswitches is an important mechanism for the modulation of gene expression in bacteria. Here the authors show that the ligand-induced allosteric switch in the adenine-sensing riboswitch from V. vulnificus is insufficient and leads only to a partial opening of the ribosome binding site and requires interaction with 30S-bound ribosomal protein S1, which acts as an RNA chaperone.

    • Vanessa de Jesus
    • , Nusrat S. Qureshi
    •  & Boris Fürtig

  • 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

    Assembly of the mitoribosome requires assistance from numerous specialized factors. Here, structures of the human 39S late assembly intermediates identify several assembly factors which keep the 16S rRNA in immature conformations, and reveal deacylated tRNA in the ribosomal E-site, suggesting a role in 39S assembly.

    • Jingdong Cheng
    • , Otto Berninghausen
    •  & Roland Beckmann

  • Article
    | Open Access

    Fly Dicer-2 is thought to use two distinct – processive or distributive – modes of cleavage by distinguishing the terminal structures of double-stranded RNA (dsRNA) substrates with the help of its cofactor LoquaciousPD (Loqs-PD). Here the authors show by single-molecule imaging that dsRNA terminal structures and Loqs-PD change the probability for Dicer to initiate processive cleavage but not the mode of cleavage action per se.

    • Masahiro Naganuma
    • , Hisashi Tadakuma
    •  & Yukihide Tomari

  • Article
    | Open Access

    RNA modifications appear to play a role in determining RNA structure and function. Here, the authors develop a deep learning model that predicts the location of 12 RNA modifications using primary sequence, and show that several modifications are associated, which suggests dependencies between them.

    • Zitao Song
    • , Daiyun Huang
    •  & Jia Meng

  • Article
    | Open Access

    In humans, protein methyltransferase is responsible for RNA methylation using S-adenosylmethionine as a methyl group donor. Here the authors report a self-methylation activity of a bacterial riboswitch.

    • Laurin Flemmich
    • , Sarah Heel
    •  & Ronald Micura

  • Article
    | Open Access

    Mitochondrial ribosomes (mitoribosomes) are characterized by a distinct architecture and thus biogenesis pathway. Here, cryo-EM structures of mitoribosome large subunit assembly intermediates elucidate final steps of 16 S rRNA folding, methylation and peptidyl transferase centre (PTC) completion, as well as functions of several mitoribosome assembly factors.

    • Miriam Cipullo
    • , Genís Valentín Gesé
    •  & Joanna Rorbach

  • Article
    | Open Access

    Mitochondrial ribosomes (mitoribosomes) are characterized by a distinct architecture and thus biogenesis pathway. Here, cryo-EM structures of mitoribosome large subunit assembly intermediates elucidate final steps of 16 S rRNA folding, methylation and peptidyl transferase centre (PTC) completion, as well as functions of several mitoribosome assembly factors.

    • Caillan Crowe-McAuliffe
    • , Victoriia Murina
    •  & Daniel N. Wilson

  • Article
    | Open Access

    Fluorogenic RNA aptamers such as Chili display strong fluorescence enhancement upon aptamer–ligand complex formation. Here, the authors provide insights into the mechanism of fluorescence activation of Chili by solving the crystal structures of Chili with its bound positively charged ligands DMHBO+ and DMHBI+, and they reveal that Chili uses an excited state proton transfer mechanism based on time-resolved optical spectroscopy measurements.

    • Mateusz Mieczkowski
    • , Christian Steinmetzger
    •  & Claudia Höbartner

  • Article
    | Open Access

    Sequencing methods such as icSHAPE were developed to probe RNA structures transcriptome-wide in cells. To probe intact RNA structures, the authors develop icSHAPE-MaP and apply to Dicer-bound substrates showing that distance measuring is important for Dicer cleavage of pre-miRNAs.

    • Qing-Jun Luo
    • , Jinsong Zhang
    •  & Qiangfeng Cliff Zhang

  • Article
    | Open Access

    Long non coding RNA TERRA transcripts can form R-loops at chromosome ends. Here, the authors reveal a role for the helicase RTEL in affecting TERRA levels and localization.

    • Fiorella Ghisays
    • , Aitor Garzia
    •  & John H. J. Petrini

  • Article
    | Open Access

    Macrolide antibiotics inhibit bacterial translation in a context-specific manner, arresting ribosomes at defined sites within mRNAs and selectively inhibiting synthesis of only a subset of cellular proteins. Here the authors provide a structural basis for the context-specific activity of macrolides on the eukaryotic ribosome.

    • Maxim S. Svetlov
    • , Timm O. Koller
    •  & Alexander S. Mankin

  • Article
    | Open Access

    In some systems, a single protein comprising reverse transcriptase (RT), integrase and maturase enables concerted sequence integration and crRNA production. Here, analyses including the structure of a Cas6-RT-Cas1—Cas2 complex suggest coordination between all three active sites and capacity to acquire CRISPR sequences from RNA and DNA substrates.

    • Joy Y. Wang
    • , Christopher M. Hoel
    •  & Jennifer A. Doudna

  • Article
    | Open Access

    Flaviviruses use a ~70 nucleotide stem-loop structure called stem-loop A (SLA) at the 5’ end of the RNA genome as a promoter for RNA synthesis by the viral polymerase NS5. Here the authors describe the structures of dengue and Zika virus SLAs, identify the SLA-binding site on NS5, and propose models for how NS5 recognizes the RNA promoter.

    • Eunhye Lee
    • , Paul J. Bujalowski
    •  & Kyung H. Choi

  • Article
    | Open Access

    Initiation of HIV-1 reverse transcription occurs at the host tRNALys3, which forms a complex with the 5’ end of the HIV-1 viral RNA and reverse transcriptase (RT). Here, the authors present the 2.8 Å cryo-EM structure of a minimal HIV-1 RT–vRNA–tRNALys3 initiation complex (miniRTIC), and miniRTIC structures with the bound non-nucleoside reverse transcriptase inhibitors nevirapine and efavirenz at 3.1 and 2.9 Å resolution, respectively.

    • Betty Ha
    • , Kevin P. Larsen
    •  & Elisabetta Viani Puglisi

  • Article
    | Open Access

    RNA crosslinking and proximity ligation methods are used to identify transcriptome-wide base pairing interactions. Here, the authors report PARIS2 (psoralen analysis of RNA interactions and structures 2), a method for RNA duplex determination in vivo with higher efficiency than the previous PARIS method.

    • Minjie Zhang
    • , Kongpan Li
    •  & Zhipeng Lu

  • Article
    | Open Access

    Time-resolved crystallography (TRX) is used for monitoring only small conformational changes of biomacromolecules within the same lattice. Here, the authors report the interplay between synchronous molecular rearrangements and lattice phase transitions in RNA crystals, providing the basis for the investigation of large conformational changes using TRX.

    • Saminathan Ramakrishnan
    • , Jason R. Stagno
    •  & Yun-Xing Wang

  • Article
    | Open Access

    The demethylase FTO was shown to remove on N6-methyladenosine (m6A) and N6, 2’-O-dimethyladenosine (m6Am) modifications on RNAs. Here the authors show that FTO impedes cancer stem cell-like abilities in colorectal cancer cells through its m6Am demethylase activity, not through internal m6A demethylase activity.

    • Sébastien Relier
    • , Julie Ripoll
    •  & Alexandre David

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