RNA modification articles within Nature Communications

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  • Comment
    | Open Access

    A controversial discussion on the occurrence of the RNA modification m1A in mRNA takes a new turn, as an antibody with a central role in modification mapping was shown to also bind mRNA cap structures.

    • Mark Helm
    • , Frank Lyko
    •  & Yuri Motorin

  • Article
    | Open Access

    Bacterial tRNA is modified by thiolation of nucleosides. Here the authors identify 2-methylthiocytidine in bacterial tRNA using nucleic acid isotope labeling coupled mass spectrometry. Exposure to methylating agents converts 2-thiocytidine to 2-methylthiocytidine, which is repaired by demethylase AlkB in vivo.

    • Valentin F. Reichle
    • , Dimitar P. Petrov
    •  & Stefanie Kellner

  • Article
    | Open Access

    E. coli and human tRNAs contain 3-(3-amino-3-carboxypropyl)uridine (acp3U) modification. Here the authors identify E. coli TapT and human DTWD1/2 as tRNA aminocarboxypropyltransferases responsible for acp3U formation. Inhibition of acp3U modification results in genome instability in heat-stressed E. coli and growth defects in human cells.

    • Mayuko Takakura
    • , Kensuke Ishiguro
    •  & Tsutomu Suzuki

  • Article
    | Open Access

    N1-methyladenosine (m1A) was recently reported as a new mRNA modification but its prevalence has been controversial. Here the authors showed that m1A, if present in mRNA, is at very low stoichiometry, with the notable exception of MT-ND5. Further, they show that the previously reported enrichment of m1A near the start of transcripts are false-positive identifications due to cross-reactivity of the commonly used m1A antibody with mRNA caps.

    • Anya V. Grozhik
    • , Anthony O. Olarerin-George
    •  & Samie R. Jaffrey

  • Article
    | Open Access

    We currently lack generic methods to map RNA modifications across the entire transcriptome. Here, the authors demonstrate that m6A RNA modifications can be detected with high accuracy using nanopore direct RNA sequencing.

    • Huanle Liu
    • , Oguzhan Begik
    •  & Eva Maria Novoa

  • Article
    | Open Access

    The biosynthesis of N6-threonylcarbamoylated adenosine 37 in tRNA (t6A) involves the YRDC enzyme and the KEOPS complex. Here, the authors report mutations in YRDC and the KEOPS component GON7 in Galloway-Mowat syndrome and determine the crystal structure of a GON7-containg subcomplex that suggests a role in KEOPS complex stability.

    • Christelle Arrondel
    • , Sophia Missoury
    •  & Géraldine Mollet

  • Article
    | Open Access

    Ime4p is a yeast N6-methyladenosine (m6A) methyltransferase with an unknown role in meiosis. Rme1p is a repressor of meiosis. Here the authors show that Ime4p methylates RME1 3′ UTR to reduce its expression and enable meiosis, thus providing an example of an m6A site with a physiological role.

    • G. Guy Bushkin
    • , David Pincus
    •  & Gerald R. Fink

  • Article
    | Open Access

    Transfer RNA (tRNA) is regulated by RNA modifications. Here the authors employ time-resolved NMR to monitor modifications of yeast tRNAPhe in cellular extracts, revealing a sequential order and cross-talk between modifications.

    • Pierre Barraud
    • , Alexandre Gato
    •  & Carine Tisné

  • Article
    | Open Access

    5-carboxymethoxyuridine (cmo5U) is one of the RNA modifications found in bacterial tRNA anticodons. Here the authors show that the first step of cmo5U biosynthesis from uridine is mediated by either one of two parallel factors, TrhP or TrhO, and that cmo5U modification is required for efficient translation.

    • Yusuke Sakai
    • , Satoshi Kimura
    •  & Tsutomu Suzuki

  • Article
    | Open Access

    Terminal uridylyltransferase 4/7 (TUT4/7) binds to Lin28 and modifies let-7 precursor (pre-let-7) to regulate cell differentiation and proliferation. Here the authors report the crystal structure of the N-terminal Lin28-interacting module of TUT4, showing a role of the N-terminal zinc finger domain in stabilizing the Lin28:pre-let-7:TUT4 ternary complex.

    • Seisuke Yamashita
    • , Takashi Nagaike
    •  & Kozo Tomita

  • Article
    | Open Access

    Mutations in mitochondrially-encoded tRNA genes can lead to mitochondrial disorders. Here the authors use next generation RNA sequencing to reveal the role of a N1 -methyladenosine modification in tRNALys MERR patients for translation elongation and the stability of selected nascent chains.

    • Uwe Richter
    • , Molly E. Evans
    •  & Brendan J. Battersby

  • Article
    | Open Access

    Mutations in the RNA component TERC can cause telomerase dysfunction but the underlying mechanisms are largely unknown. Here, the authors show that RNA-binding protein HuR regulates telomerase function by enhancing the methylation of TERC, which is impaired by several disease-relevant TERC mutations.

    • Hao Tang
    • , Hu Wang
    •  & Wengong Wang

  • Article
    | Open Access

    Transfer RNA modifications play critical roles in protein synthesis. Here the authors reveal the t6A37 tRNA modification is dynamically regulated by sensing intracellular CO2 concentration in mitochondria, implying metabolic regulation of protein synthesis.

    • Huan Lin
    • , Kenjyo Miyauchi
    •  & Tsutomu Suzuki

  • Article
    | Open Access

    Methylated RNA bases influence many life processes, but current detection methods lack the ability to detect individual methylations in single cells. Here, the authors use fluorescence hybridization probes sensitive to methylation to detect specific epitranscriptomic modifications at the single-cell level.

    • Rohan T. Ranasinghe
    • , Martin R. Challand
    •  & David Klenerman

  • Article
    | Open Access

    N6-methyladenosine (m6A) is a conserved RNA modification that has recently emerged as an important regulator of messenger RNA processing and activity. Here, the authors provide evidence that m6A pathway facilitates female-specific splicing of Sxl, regulating sex determination in Drosophila.

    • Lijuan Kan
    • , Anya V. Grozhik
    •  & Eric C. Lai

  • Article |

    Modification of mRNA with N6-methyladenosine (m6A) is proposed to regulate transcript stability. Here, Jia et al. uncover plant-specific features in the m6A methylome of Arabidopsis, such as methylation enrichment around the start codon, and suggest a positive role in gene expression.

    • Guan-Zheng Luo
    • , Alice MacQueen
    •  & Chuan He

  • Article |

    The use of alternative polyadenylation sites can potentially result in mRNA being more or less susceptible to interaction with modulators of translation or stability. Here Gruber et al. find that the shortening of 3′UTRs observed in proliferating T cells does not significantly impact protein abundance.

    • Andreas R. Gruber
    • , Georges Martin
    •  & Mihaela Zavolan

  • Article
    | Open Access

    Phosphorylation of the carboxy-terminal domain of RNA polymerase II is important for controlling gene transcription. In this study, the transcription elongation factor Tefb is shown to phosphorylate serine-5 and its activity is enhanced when the polymerase is already phosphorylated on serine-7.

    • Nadine Czudnochowski
    • , Christian A. Bösken
    •  & Matthias Geyer

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