Molecular biology articles within Nature Communications

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  • Article
    | Open Access

    Mitochondrial ribosomes are uniquely affected by mutations in the mitochondrial genome. By mapping the position of ribosomes on transcripts, the authors here reveal functional differences between mitochondrial and cytosolic ribosomes, and show that mutations in mitochondrial tRNAs induce ribosome stalling.

    • Koos Rooijers
    • , Fabricio Loayza-Puch
    •  & Reuven Agami

  • Article
    | Open Access

    The micro-RNA miR-33 is encoded by an intron of the gene encoding sterol regulatory-binding protein 2 (SREBP-2) and controls cholesterol homoeostasis. Here, Horie et al.identify SREBP-1 as a target of miR-33 and show that deletion of miR-33 promotes diet-induced obesity and liver steatosis in mice.

    • Takahiro Horie
    • , Tomohiro Nishino
    •  & Koh Ono

  • Article |

    Whether microRNA processing mediated by Dicer is regulated in a cell-cycle-dependent manner is unknown. Here, Chen et al.show that Cyclin D1, which is important in the control of the cell cycle, regulates the expression of Dicer, and that Cyclin D1 and Dicer expression levels correlate in breast cancer.

    • Zuoren Yu
    • , Liping Wang
    •  & Richard G. Pestell

  • Article
    | Open Access

    mRNA transport contributes to the proper localization of its cognate proteins. Here the authors report a correlation between the physicochemical properties of mRNAs and their cognate proteins, suggesting that these properties of mRNAs can predict the subcellular localization of their cognate proteins.

    • Anton A. Polyansky
    • , Mario Hlevnjak
    •  & Bojan Zagrovic

  • Article |

    Toxin–antitoxin systems have been implicated in the pathogenicity of Mycobacterium tuberculosis. Here, the authors study the function of the M. tuberculosistoxin VapC20 and show that it can impair protein translation and inhibit bacterial growth by cleaving the Sarcin–Ricin loop of 23S rRNA

    • Kristoffer S. Winther
    • , Ditlev E. Brodersen
    •  & Kenn Gerdes

  • Article |

    The Hoppel transposable element mediates heterochromatin formation in Drosophila. Here Savva et al. report that the RNA-editing enzyme, ADAR, edits a long double-stranded RNA generated by the Hoppeltransposon, thereby regulating heterochromatin formation and gene expression.

    • Yiannis A. Savva
    • , James E. C. Jepson
    •  & Robert A. Reenan

  • Article |

    The miR-372-3 cluster has a role in oncogenesis. In this study, by utilizing parthenogenetic induced pluripotent stem cells, that lack the paternal genome, Stelzer et al.report that these miR-372-3 are negatively regulated by a paternally imprinted antisense transcript and that loss of its expression promotes oncogenesis.

    • Yonatan Stelzer
    • , Ido Sagi
    •  & Nissim Benvenisty

  • Article |

    APOBEC3F is a DNA cytosine deaminase involved in restriction of HIV-1, but its activity can be suppressed by the viral protein Vif. Here, the authors provide insights into the interaction between these two proteins by determining the structure of the APOBEC3F Vif-binding domain.

    • Karen K. Siu
    • , Azmiri Sultana
    •  & Jeffrey E. Lee

  • Article |

    Semiconductor-based, non-optical DNA sequencing technologies such as Ion Torrent sequencing offer speed and cost advantages compared with alternative techniques. Cheng et al. demonstrate a protocol allowing the use of Ion Torrent technology to sequence DNA from chromatin immunoprecipitation experiments.

    • Christine S. Cheng
    • , Kunal Rai
    •  & Ido Amit

  • Article
    | Open Access

    The chemotherapeutic drug 5-fluorouracil causes cell toxicity by inducing DNA lesions. Here, SenGupta et al. use C. elegansto show that components of the base excision repair and the mismatch repair pathways function together in the response to 5-fluorouracil, resulting in activation of the DNA damage checkpoint and induction of autophagy.

    • Tanima SenGupta
    • , Maria Lyngaas Torgersen
    •  & Hilde Nilsen

  • Article
    | Open Access

    PALB2 is a BRCA1-/BRCA2-interacting protein and heterozygous mutations in PALB2 are associated with hereditary breast cancer predisposition. Here the authors show that human lymphoblastoid cells from heterozygous PALB2mutation carriers display abnormal DNA replication dynamics and DNA damage response.

    • Jenni Nikkilä
    • , Ann Christin Parplys
    •  & Robert Winqvist

  • Article |

    Histone H2A-H2B heterodimers are lost from nucleosomes during transcription by RNA polymerase II. Here Sheinin et al. investigate the behaviour of single nucleosomes subjected to DNA supercoiling and observe a loss of these heterodimers under positive supercoiling, which might have implications for histone turnover during transcription in vivo.

    • Maxim Y. Sheinin
    • , Ming Li
    •  & Michelle D. Wang

  • Article |

    MicroRNAs are thought to confer robustness to biological processes, but clear experimental evidence is still needed. Here, Siciliano et al. construct a toggle-switch in mammalian cells to show that microRNAs buffer fluctuations in protein levels, thereby providing phenotypic robustness to gene regulatory networks.

    • Velia Siciliano
    • , Immacolata Garzilli
    •  & Diego di Bernardo

  • Article |

    Topoisomerase 2α (Top2α) has essential roles during DNA replication, whereas its isoform Top2β is implicated in gene expression. Thakurela et al.show that Top2α is also required for stem-cell transcriptome regulation and primes developmental genes for activation by Top2β upon terminal differentiation.

    • Sudhir Thakurela
    • , Angela Garding
    •  & Vijay K. Tiwari

  • Article
    | Open Access

    During the initiation of bacterial DNA replication, loader proteins transfer the hexameric helicase ring onto replication origin DNA. Liu et al.report the crystal structure of a 570-kDa prepriming complex and suggest that the release of loader proteins is associated with the transition of the helicase ring to a spiral configuration.

    • Bin Liu
    • , William K. Eliason
    •  & Thomas A. Steitz

  • Article
    | Open Access

    Hydrogenosomes and mitosomes are mitochondria-related organelles with distinct properties. Here the authors find that the mitochondria-related organelle of the salmon parasite Spironucleus salmonicidahas characteristics of both diplomonad mitosomes and of parabasalid hydrogenosomes, suggesting the presence of hydrogenosomes in the last common ancestor.

    • Jon Jerlström-Hultqvist
    • , Elin Einarsson
    •  & Staffan G. Svärd

  • Article |

    The microRNA-200 family members have a role in regulating tumour angiogenesis but the underlying mechanism is unclear. In this study, Pecot et al.demonstrate that miR-200 affects angiogenesis by altering endothelial and cancer cell cytokine secretion.

    • Chad V. Pecot
    • , Rajesha Rupaimoole
    •  & Anil K. Sood

  • Article
    | Open Access

    The helicases UvsW and RecG have both unwinding and rewinding activities and are involved in the rescue of stalled DNA replication forks. Here Manosas et al. use single-molecule techniques to characterize the rewinding activities of the two helicases, concluding that rewinding is actively catalysed.

    • Maria Manosas
    • , Senthil K. Perumal
    •  & Vincent Croquette

  • Article |

    The nuclear protein HMGB1 is involved in muscle fibre formation. Here, Dormoy-Raclet et al. show that during muscle cell differentiation, the RNA-binding protein HuR promotes HMGB1mRNA translation by preventing its repression by miR-1192.

    • Virginie Dormoy-Raclet
    • , Anne Cammas
    •  & Imed-Eddine Gallouzi

  • Article
    | Open Access

    Artificial genetic circuits have been designed to enable precise control of cellular behaviour and phenotypes. Saito and colleagues present a new RNA module that can invert the function of a translational OFF to an ON switch and demonstrate its utility in mammalian cells.

    • Kei Endo
    • , Karin Hayashi
    •  & Hirohide Saito

  • Article |

    Protein deacetylases of the sirtuin family have important roles in aging and metabolism. Using peptide microarrays displaying physiological lysine acetylation sites, the authors map the substrate preferences of all seven human sirtuin isoforms, revealing enzyme specificities and identifying new sirtuin substrates.

    • David Rauh
    • , Frank Fischer
    •  & Clemens Steegborn

  • Article |

    Absence of Brca2 or Rad51 paralogues biases homologous recombination towards the error-prone outcome of long-tract gene conversion. Here, the authors report that BRCA1, together with the end resection protein CtIP, controls the balance between short- and long-tract gene conversion, thereby affecting the fidelity of homologous recombination.

    • Gurushankar Chandramouly
    • , Amy Kwok
    •  & Ralph Scully

  • Article
    | Open Access

    Horizontal gene transfer of mobile genetic elements contributes to bacterial evolution and emergence of new pathogens. Here the authors demonstrate that the highly diverse structure of wall teichoic acid polymers governs horizontal gene transfer among Gram-positive pathogens, even across long phylogenetic distances.

    • Volker Winstel
    • , Chunguang Liang
    •  & Guoqing Xia

  • Article
    | Open Access

    Bacterial endonuclease V enzymes are characterized as DNA repair proteins. Here the authors show that human endonuclease V is an inosine-specific ribonuclease, indicating a role for this enzyme in normal RNA metabolism rather than DNA repair.

    • Erik Sebastian Vik
    • , Meh Sameen Nawaz
    •  & Ingrun Alseth

  • Article
    | Open Access

    In Escherichia coli, the highly conserved enzyme endonuclease V has a role in DNA repair. Here the authors show that human endonuclease V is an inosine 3' endoribonuclease and that Tudor Staphylococcal nuclease enhances this activity, suggesting a role for human endonuclease V in RNA metabolism.

    • Yoko Morita
    • , Toshihiro Shibutani
    •  & Isao Kuraoka

  • Article |

    H3K64 trimethylation on the nucleosome lateral surface marks pericentric heterochromatin. Here Lange et al.show that H3K64me3 enrichment ensures heterochromatin integrity and occurs in an H3K9me3-dependent, but an H4K20me3- and heterochromatin protein 1-independent manner.

    • Ulrike C. Lange
    • , Stéphanie Siebert
    •  & Robert Schneider

  • Article |

    A central, imperfect duplex RNA secondary structure is generally required for site-specific adenosine-to-inosine RNA editing by ADAR enzymes. Rieder et al. show in Drosophila that conserved and complex long-range RNA tertiary structures form in vivoand can also regulate specific RNA-editing events by ADAR enzymes.

    • Leila E. Rieder
    • , Cynthia J. Staber
    •  & Robert A. Reenan

  • Article |

    Genetic effects on gene expression by variants at expression quantitative trait loci (eQTLs), can contribute to human genetic diseases. Here, Liet al. present a method to study eQTLs with effects on protein translation on a transcriptome-wide scale.

    • Quan Li
    • , Angeliki Makri
    •  & Hui-Qi Qu

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