RNA articles within Nature Communications

Featured

• Article
  09 June 2023 | Open Access

  Systematic detection of tertiary structural modules in large RNAs and RNP interfaces by Tb-seq

  Compact RNA structural motifs control many aspects of gene expression, but methods for their identification are lacking. Here the authors present a sequencing-based terbium probing approach to detect complex 3D structural elements, which can be used to pinpoint potential riboregulatory elements.

  • Shivali Patel
  • , Alec N. Sexton
  •  & Anna Marie Pyle

• Article
  09 June 2023 | Open Access

  In vivo PAR-CLIP (viP-CLIP) of liver TIAL1 unveils targets regulating cholesterol synthesis and secretion

  Here the authors develop viP-CLIP, a technique allowing the identification of RNA binding proteins (RBP) targets in mouse tissues, and identify the RBP Tial1 as a regulator of cholesterol metabolism in the liver.

  • Hasan Vatandaslar
  • , Aitor Garzia
  •  & Markus Stoffel

• Article
  07 June 2023 | Open Access

  The preference signature of the SARS-CoV-2 Nucleocapsid NTD for its 5’-genomic RNA elements

  SARS-CoV-2 genome turnover is mediated by its N protein, but precise parameters driving the necessary RNA specificity have remained enigmatic. Here, Korn et al. reveal N’s N-terminal domain to distinguish regulatory viral RNA motifs with a preference for transiently folded elements of functional impact.

  • Sophie Marianne Korn
  • , Karthikeyan Dhamotharan
  •  & Andreas Schlundt

• Article
  24 May 2023 | Open Access

  Intracellular RNA and DNA tracking by uridine-rich internal loop tagging with fluorogenic bPNA

  Commonly used protein-based tools to monitor intracellular RNA and DNA can impact steric accessibility and native nucleic acid biology. Here, the authors show that fluorogenic uridine-rich internal loop tagging bPNA probes can be used to label nucleic acids in fixed and live cells.

  • Yufeng Liang
  • , Sydney Willey
  •  & Dennis Bong

• Article
  23 May 2023 | Open Access

  Co-crystal structures of the fluorogenic aptamer Beetroot show that close homology may not predict similar RNA architecture

  The recently discovered aptamer Beetroot is a homodimeric RNA that binds and activates DFAME, a conditional, red-shifted fluorophore derived from GFP. Here the authors determine the Beetroot-DFAME co-crystal structure, which is distinctively different from that of similar RNA aptamer Corn.

  • Luiz F. M. Passalacqua
  • , Mary R. Starich
  •  & Adrian R. Ferré-D’Amaré

• Article
  11 May 2023 | Open Access

  Cap analogs with a hydrophobic photocleavable tag enable facile purification of fully capped mRNA with various cap structures

  Removing immunogenic uncapped mRNA from transcribed mRNA can be challenging, but is critical in mRNA research and clinical applications such as vaccines. Here, authors develop hydrophobic photocaged tag-modified cap analogs, which can be used to separate capped mRNA from uncapped mRNA, with subsequent tag removal using photo-irradiation.

  • Masahito Inagaki
  • , Naoko Abe
  •  & Hiroshi Abe

• Article
  22 April 2023 | Open Access

  Observation of structural switch in nascent SAM-VI riboswitch during transcription at single-nucleotide and single-molecule resolution

  Observation of single nascent RNA at single-nucleotide resolution enables building a conformation landscape of how RNAs change during transcription. Here the authors develop a method to monitor the conformational change of individual SAM-VI riboswitch RNA (riboSAM) during transcription at single-nucleotide resolution as it is synthesized by transcription.

  • Yanyan Xue
  • , Jun Li
  •  & Yu Liu

• Article
  21 April 2023 | Open Access

  RNA binding protein SYNCRIP maintains proteostasis and self-renewal of hematopoietic stem and progenitor cells

  Hematopoietic stem cells (HSCs) are essential for long-term repopulation after secondary transplantation. Here they show that SYNCRIP safeguards HSC self-renewal during regenerative stress by maintaining both proteostasis and CDC42-regulated cell polarity.

  • Florisela Herrejon Chavez
  • , Hanzhi Luo
  •  & Michael G. Kharas

• Article
  18 April 2023 | Open Access

  Copy number variation in tRNA isodecoder genes impairs mammalian development and balanced translation

  Enigmatically tRNA genes exist in several hundred copies in mammalian genomes. Here the authors find a precipitous failure of development and increased amino acid misincorporation upon systematic elimination of tRNA-Phe genes in mice using CRISPR.

  • Laetitia A. Hughes
  • , Danielle L. Rudler
  •  & Aleksandra Filipovska

• Article
  13 April 2023 | Open Access

  Screening of Drosophila microRNA-degradation sequences reveals Argonaute1 mRNA’s role in regulating miR-999

  miRNAs typically bind to target mRNAs to induce their degradation but when base-pairing between miRNAs and the target RNAs are extended, miRNAs themselves can be degraded. Here, by employing AGO1-CLASH in Drosophila cells, the authors show that RNA sequence in AGO1 mRNA 3′UTR induces decay of miR-999.

  • Peike Sheng
  • , Lu Li
  •  & Mingyi Xie

• Article
  07 April 2023 | Open Access

  Crystal structure of a highly conserved enteroviral 5′ cloverleaf RNA replication element

  A cloverleaf-like RNA domain within the enterovirus genome is essential for replication. Here, the authors determine the 1.9 Å resolution crystal structure of such RNA from coxsackievirus B3 – a model enterovirus to study many other human viruses.

  • Naba K. Das
  • , Nele M. Hollmann
  •  & Deepak Koirala

• Article
  07 April 2023 | Open Access

  Bombyx Vasa sequesters transposon mRNAs in nuage via phase separation requiring RNA binding and self-association

  Bombyx Vasa assembles Vasa bodies, the site of transposon silencing by Siwi and Ago3-piRISC formation. Here, the authors show Vasa sequesters transposon mRNAs in Vasa bodies via phase separation requiring RNA binding and self-association of Vasa.

  • Hiroya Yamazaki
  • , Yurika Namba
  •  & Mikiko C. Siomi

• Article
  25 March 2023 | Open Access

  Multi-modal quantification of pathway activity with MAYA

  Pathways can be activated through various signaling cascades depending on cell type. Here, the authors introduce MAYA, a computational method that can detect and score multiple modes of activation for each pathway, improving the granularity of pathway analysis for single-cell datasets.

  • Yuna Landais
  •  & Céline Vallot

• Article
  16 March 2023 | Open Access

  Snapshots of the second-step self-splicing of Tetrahymena ribozyme revealed by cryo-EM

  The Tetrahymena ribozyme changes conformations to perform its self-splicing function. Here, the authors capture six structural snapshots of ribozyme during the second step of self-splicing from a single specimen, revealing the structural basis of how it promotes and coordinates self-splicing reactions.

  • Shanshan Li
  • , Michael Z. Palo
  •  & Kaiming Zhang

• Article
  07 March 2023 | Open Access

  Well-TEMP-seq as a microwell-based strategy for massively parallel profiling of single-cell temporal RNA dynamics

  Gene expression of cells is a heterogeneous and dynamic program involved in various biological processes. Here, authors develop Well-TEMPseq, a high-throughput, cost-effective, and accurate method for massively parallel profiling of the temporal dynamics of single-cell gene expression.

  • Shichao Lin
  • , Kun Yin
  •  & Chaoyong Yang

• Article
  03 March 2023 | Open Access

  Periodic temperature changes drive the proliferation of self-replicating RNAs in vesicle populations

  How primordial cells could achieve inheritance of encapsulated components is still an open question. Here, the authors show that ribozymes can assemble in active forms and replicate in populations of membrane vesicles thanks to freeze-thaw cycles.

  • Elia Salibi
  • , Benedikt Peter
  •  & Hannes Mutschler

• Article
  24 February 2023 | Open Access

  Evaluating native-like structures of RNA-protein complexes through the deep learning method

  RNA-protein docking is a very challenging area. Here, the authors develop a deep-learning based method, DRPScore, to evaluate RNA-protein complexes. DRPScore is robust and consistently performs better than existing methods on representative testing sets.

  • Chengwei Zeng
  • , Yiren Jian
  •  & Yunjie Zhao

• Article
  17 February 2023 | Open Access

  Mechanisms of the RNA helicases DDX42 and DDX46 in human U2 snRNP assembly

  The U2 snRNP recognizes the intron during spliceosome assembly. Here the authors report the high-resolution structures of two assembly precursors of human U2 snRNP and reveal that the RNA helicases DDX42 and DDX46 are mutually exclusive in terms of SF3B1-binding.

  • Fenghua Yang
  • , Tong Bian
  •  & Yigong Shi

• Article
  17 February 2023 | Open Access

  Cryo-EM captures early ribosome assembly in action

  The production of ribosomes is a precisely orchestrated energy consuming cellular process of highest priority. Here, the authors use cryo-EM to show that bacterial ribosomal subunits, self-assembled from their purified RNA and protein components, mature along parallel pathways.

  • Bo Qin
  • , Simon M. Lauer
  •  & Rainer Nikolay

• Article
  16 February 2023 | Open Access

  Visualizing orthogonal RNAs simultaneously in live mammalian cells by fluorescence lifetime imaging microscopy (FLIM)

  No multi-color RNA fluorescent tags are currently available for use in live cells. Here, the authors show that fluorescence lifetime imaging microscopy is advantageous for multiplexed RNA visualization while achieving robust cellular contrast.

  • Nadia Sarfraz
  • , Emilia Moscoso
  •  & Esther Braselmann

• Article
  15 February 2023 | Open Access

  Chemoproteomic discovery of a human RNA ligase

  RNA ligases are present across all forms of life. Here, the hitherto uncharacterised human protein C12orf29 was identified as a human enzyme promoting RNA ligation between 5′-PO₄ and 3′-OH termini. This data provides the groundwork for establishing a human RNA repair pathway.

  • Yizhi Yuan
  • , Florian M. Stumpf
  •  & Andreas Marx

• Article
  09 February 2023 | Open Access

  Visualizing RNA conformational and architectural heterogeneity in solution

  RNA conformational heterogeneity is important to diverse functions. Here, the authors use AFM to directly visualize individual RNA molecules that are in various conformational states under near physiological solution conditions for the first time.

  • Jienyu Ding
  • , Yun-Tzai Lee
  •  & Yun-Xing Wang

• Article
  09 February 2023 | Open Access

  Two distinct binding modes provide the RNA-binding protein RbFox with extraordinary sequence specificity

  Here the authors show that the RRM of RbFox accomplishes extraordinary sequence specificity by employing functionally and structurally distinct binding modes - one for its cognate RNA and one for all non-cognate RNAs.

  • Xuan Ye
  • , Wen Yang
  •  & Fan Yang

• Article
  02 February 2023 | Open Access

  Reanalysis of ribosome profiling datasets reveals a function of rocaglamide A in perturbing the dynamics of translation elongation via eIF4A

  The compound Rocaglamide A (RocA) is known for repressing translation initiation. Here the authors identify a dual mode of action for RocA in blocking translation initiation and elongation via eIF4A using previous datasets and new analyses.

  • Fajin Li
  • , Jianhuo Fang
  •  & Xuerui Yang

• Article
  01 February 2023 | Open Access

  A paralog of Pcc1 is the fifth core subunit of the KEOPS tRNA-modifying complex in Archaea

  Many eukaryotic and archaeal tRNAs carry a modified adenosine (t⁶A) that is synthesized by the KEOPS complex, which is composed of four subunits. A fifth subunit (Gon7) is found only in fungi and metazoa. Here the authors show that archaea also possess a fifth subunit, which is structurally and functionally similar to eukaryotic Gon7.

  • Marie-Claire Daugeron
  • , Sophia Missoury
  •  & Tamara Basta

• Article
  13 January 2023 | Open Access

  Preclinical development of kinetin as a safe error-prone SARS-CoV-2 antiviral able to attenuate virus-induced inflammation

  The search for antivirals against SARS-CoV-2 continue due to the emergence of variants of concerns, able to escape the vaccinal humoral response. In this work, authors pre-clinically explore the potential of kinetin against SARS-CoV-2, which could be used alone or in combination with other antivirals.

  • Thiago Moreno L. Souza
  • , Vagner D. Pinho
  •  & Jaime A. Rabi

• Article
  10 January 2023 | Open Access

  Decoding of the ubiquitin code for clearance of colliding ribosomes by the RQT complex

  The colliding ribosomes are ubiquitinated by the sensor protein Hel2, leading to noncanonical subunit dissociation by the ribosome associated quality control trigger (RQT) complex. Here the authors reveal the decoding mechanism of the ribosome ubiquitin code by the RQT complex.

  • Yoshitaka Matsuo
  • , Takayuki Uchihashi
  •  & Toshifumi Inada

• Article
  06 January 2023 | Open Access

  Targeted systematic evolution of an RNA platform neutralizing DNMT1 function and controlling DNA methylation

  Here the authors generate an RNA-based platform to neutralize the major epigenetic player DNMT1. Using this targeted approach, aberrant DNA methylation in cancer can be corrected.

  • Carla L. Esposito
  • , Ida Autiero
  •  & Annalisa Di Ruscio

• Article
  17 December 2022 | Open Access

  Translation factor eIF5a is essential for IFNγ production and cell cycle regulation in primary CD8⁺ T lymphocytes

  The translational elongation factor eIF5a may have a function in T cell protein translation. Here the authors show that hypusination of eIF5a or deletion of eIF5a alters the profile of mRNA translation in T cells and that eIF5 regulates the proliferation and effector function of these T cells.

  • Thomas C. J. Tan
  • , Van Kelly
  •  & Rose Zamoyska

• Article
  12 December 2022 | Open Access

  Broad misappropriation of developmental splicing profile by cancer in multiple organs

  The molecular mechanisms underlying the overlap between oncogenic and embryonic development remain to be explored. Here, the authors use temporal transcriptomic data during development in multiple human organs and suggest the involvement of alternative splicing events, splicing factors, and transcription factors.

  • Arashdeep Singh
  • , Arati Rajeevan
  •  & Sridhar Hannenhalli

• Article
  06 December 2022 | Open Access

  DAP5 enables main ORF translation on mRNAs with structured and uORF-containing 5′ leaders

  RNA structure and upstream ORFs can modulate the translation of human transcripts. Here, the authors show that structured mRNAs with pervasive uORF translation require DAP5, an eIF4G-like protein, for translation of the main ORF.

  • Ramona Weber
  • , Leon Kleemann
  •  & Cátia Igreja

• Article
  28 November 2022 | Open Access

  Altered tRNA processing is linked to a distinct and unusual La protein in Tetrahymena thermophila

  La proteins are conserved factors critical for the maturation of RNA polymerase III transcripts. In the ciliate T. thermophila and related alveolates, La proteins have a novel domain arrangement and are linked to a distinct pre-tRNA processing pathway.

  • Kyra Kerkhofs
  • , Jyoti Garg
  •  & Mark A. Bayfield

• Article
  18 November 2022 | Open Access

  Structural basis for recognition of transcriptional terminator structures by ProQ/FinO domain RNA chaperones

  In this work, the authors determine the crystal structure of a ProQ/FinO RNA chaperone bound to its RNA target. This provides insight into how this family of bacterial proteins recognize transcriptional terminator structures.

  • Hyeong Jin Kim
  • , Mazzen Black
  •  & J. N. Mark Glover

• Article
  07 November 2022 | Open Access

  Structure of the IscB–ωRNA ribonucleoprotein complex, the likely ancestor of CRISPR-Cas9

  The cryo-EM structure of the IscB–ωRNA–target DNA complex provide insights into the ωRNA-guided DNA cleavage mechanism by IscB and the evolution of the type II CRISPR-Cas9 effector complexes

  • Kazuki Kato
  • , Sae Okazaki
  •  & Hiroshi Nishimasu

• Article
  05 November 2022 | Open Access

  RNA-binding proteins of KHDRBS and IGF2BP families control the oncogenic activity of MLL-AF4

  The establishment of a mouse model of MLL-AF4-induced leukaemia is a challenge as the introduction of fusion gene of human MLL-AF4 does not cause leukaemia in mice. Here the authors reveal that MLL-AF4 is post-transcriptionally regulated by RNA-binding proteins that inhibits MLL-AF4 translation, thus, hampering MLL-AF4-mediated leukemic transformation.

  • Hiroshi Okuda
  • , Ryo Miyamoto
  •  & Akihiko Yokoyama

• Article
  25 October 2022 | Open Access

  Termination of the unfolded protein response is guided by ER stress-induced HAC1 mRNA nuclear retention

  Chromatin remodeler Isw1 prevents export of maturing ribonucleoprotein particles. Here, the authors show that Isw1 inhibits the Unfolded Protein Response (UPR) from the nucleus by binding and restricting export of the mRNA encoding the main effector of UPR, thereby tuning adaptation to ER stress.

  • Laura Matabishi-Bibi
  • , Drice Challal
  •  & Anna Babour

• Article
  21 October 2022 | Open Access

  Splicing factor BUD31 promotes ovarian cancer progression through sustaining the expression of anti-apoptotic BCL2L12

  Altered expression of splicing factors can contribute to tumour progression. Here the authors show that splicing factor BUD31 enhances ovarian cancer progression by promoting exon inclusion in the anti-apoptotic BCL2 family member, BCL2L12.

  • Zixiang Wang
  • , Shourong Wang
  •  & Zhaojian Liu

• Article
  11 October 2022 | Open Access

  Sequential action of a tRNA base editor in conversion of cytidine to pseudouridine

  C-to-Ψ conversion is a previously uncharacterized form of base editing. Here, the authors describe how the TrcP enzyme catalyzes this process in a stepwise fashion and how this editing process is controlled by a network of modifications and nutrient availability to optimize translation efficiency.

  • Satoshi Kimura
  • , Veerasak Srisuknimit
  •  & Matthew K. Waldor

• Article
  06 October 2022 | Open Access

  The solution structure of Dead End bound to AU-rich RNA reveals an unusual mode of tandem RRM-RNA recognition required for mRNA regulation

  The authors report an unusual mode of AU-rich RNA recognition by the RNA recognition motifs of DND1, a protein essential for germline development, in a 27.5 kDa NMR structure and provide additional insight on DND1 function from cell-based experiments.

  • Malgorzata M. Duszczyk
  • , Harry Wischnewski
  •  & Frédéric H.-T. Allain

• Article
  02 September 2022 | Open Access

  Structural basis for Gemin5 decamer-mediated mRNA binding

  Structural biology, complemented by biochemistry experiments and RNA-binding assays show that the Gemin5 C-terminal region adopts a decamer architecture. Gemin5 decamerization is essential for its role in regulating mRNA translation.

  • Qiong Guo
  • , Shidong Zhao
  •  & Chao Xu

• Article
  23 August 2022 | Open Access

  Duplicated ribosomal protein paralogs promote alternative translation and drug resistance

  Most yeast ribosomal protein genes are duplicated but the functional significance of this duplication remains unclear. This study identifies a natural program where changing the ratio of proteins produced from duplicated genes modifies translation in response to drugs regardless of ribosome number.

  • Mustafa Malik Ghulam
  • , Mathieu Catala
  •  & Sherif Abou Elela

• Article
  17 August 2022 | Open Access

  Experimental exploration of a ribozyme neutral network using evolutionary algorithm and deep learning

  Neutral networks, which are sets of genotypes connected via single mutations that share the same phenotype, are important for evolvability. Here, the authors provide experimental evidence of a neutral network in an RNA enzyme using a high-throughput assay and deep learning.

  • Rachapun Rotrattanadumrong
  •  & Yohei Yokobayashi

• Article
  09 August 2022 | Open Access

  Structural and biochemical basis for DNA and RNA catalysis by human Topoisomerase 3β

  The authors revealed novel roles of catalytic residues and divalent metal ions for hsTOP3B, the human RNA topoisomerase, and demonstrated the structural elements that kinetically modulate the DNA and RNA topoisomerase activities of TOP3B.

  • Xi Yang
  • , Sourav Saha
  •  & Yves Pommier

• Article
  04 August 2022 | Open Access

  A comprehensive thermodynamic model for RNA binding by the Saccharomyces cerevisiae Pumilio protein PUF4

  Traditional genomic methods identify RNA-binding proteins (RBPs) and the genes they regulate, but do not provide predictive models. The authors used an emerging technology to obtain a complete thermodynamic model for RNA binding to the PUF4 RBP.

  • Christoph Sadée
  • , Lauren D. Hagler
  •  & Daniel Herschlag

• Article
  19 July 2022 | Open Access

  Reactivity-dependent profiling of RNA 5-methylcytidine dioxygenases

  Kleiner and co-workers profile RNA 5-methylcytidine (m⁵C) dioxygenase enzymes using an activity-based metabolic probing strategy. They reveal ALKBH1 as the major 5-formylcytidine (f⁵C) writer and characterize modification sites across mRNA and tRNA.

  • A. Emilia Arguello
  • , Ang Li
  •  & Ralph E. Kleiner

• Article
  18 July 2022 | Open Access

  N⁶-methyladenosine modification-mediated mRNA metabolism is essential for human pancreatic lineage specification and islet organogenesis

  Ma et al. profile the dynamic landscape of m⁶A during pancreatic differentiation, and identify ALKBH5 as an essential m⁶A regulator supporting pancreatic differentiation, indicating a role for m⁶A-mediated mRNA metabolism in cell-fate specification.

  • Xiaojie Ma
  • , Jie Cao
  •  & Saiyong Zhu

• Article
  02 July 2022 | Open Access

  Single-molecule FRET uncovers hidden conformations and dynamics of human Argonaute 2

  Single-molecule FRET measurements provide detailed insights into the conformational states and dynamics of human Argonaute 2 that are required for its function at the core of the eukaryotic RNA silencing pathway.

  • Sarah Willkomm
  • , Leonhard Jakob
  •  & Dina Grohmann

• Article
  30 June 2022 | Open Access

  Simple synthesis of massively parallel RNA microarrays via enzymatic conversion from DNA microarrays

  RNA microarrays have many potential applications, but are difficult to produce. Here, the AUs present a method for converting commercial, customizable DNA microarrays into RNA microarrays using an accessible three-step process involving primer photocrosslinking, extension, and template degradation.

  • Erika Schaudy
  • , Kathrin Hölz
  •  & Mark M. Somoza

• Article
  29 June 2022 | Open Access

  Limited effects of m⁶A modification on mRNA partitioning into stress granules

  Recent studies proposed that m⁶A modification in mammalian mRNAs increases their recruitment to stress granule. However, here the authors observed that m⁶A modification has a limited effect on mRNA entry into stress granules.

  • Anthony Khong
  • , Tyler Matheny
  •  & Roy Parker

• Article
  25 June 2022 | Open Access

  Emergent properties as by-products of prebiotic evolution of aminoacylation ribozymes

  Complex biochemical systems exhibit traits that appear to be highly adapted. Studies of catalytic RNA demonstrate that adaptive traits, such as increased specificity and error tolerance, could originate as evolutionary by-products.

  • Evan Janzen
  • , Yuning Shen
  •  & Irene A. Chen