Molecular biology articles within Nature Communications

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  • 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

  • Article |

    Chemical modifications of CpG dinucleotides form part of the epigenetic code and various methods for the detection of modified CpG sites exist. Here Kriukiene and colleagues report a complementary method that allows the profiling of unmodified CpG sites within the genome, which they call the 'unmethylome'.

    • Edita Kriukienė
    • , Viviane Labrie
    •  & Saulius Klimašauskas

  • Article |

    Inhibition of the p53–p21 axis increases reprogramming efficiency of somatic cells into induced pluripotent stem cells (iPSCs). Here the authors show that depletion of the pro-apoptotic factor PUMA, acting downstream of p53, increases reprogramming efficiency, providing new insights into the roles of p53 in reprogramming.

    • Yanxin Li
    • , Haizhong Feng
    •  & Tao Cheng

  • Article
    | Open Access

    Cancer-associated mutations in isocitrate dehydrogenase are proposed to impair TET2-dependent DNA demethylation. By comparing the methylomes of IDH-mutant cancers, the authors identify the transcription factor EBF1 as a partner of TET2, suggesting a possible means for targeting TET2 to specific DNA sequences.

    • Paul Guilhamon
    • , Malihe Eskandarpour
    •  & Stephan Beck

  • Article
    | Open Access

    The fidelity of DNA polymerases depends on conformational changes that promote the rejection of incorrect nucleotides. Here, by using an intramolecular single-molecule FRET assay, the authors establish and characterize the partially closed conformation as a crucial fidelity checkpoint.

    • Johannes Hohlbein
    • , Louise Aigrain
    •  & Achillefs N. Kapanidis

  • Article
    | Open Access

    DNA double-strand breaks commonly occur in all replicating cells. Wimberly and colleagues show that in non-replicating cells, aborted transcription/translation forms RNA/DNA hybrid R-loops that prime origin-independent replication, leading to DNA breakage, point mutations and chromosomal rearrangements.

    • Hallie Wimberly
    • , Chandan Shee
    •  & P. J. Hastings

  • Article
    | Open Access

    The thermodynamics of unwinding polynucleotide duplexes can be determined from energy changes for DNA and mRNA interactions. Here the authors show that the ratio between mRNA/DNA and DNA/DNA duplex stability upstream of the 3′- spice sites is a characteristic that can contribute to intron–exon recognition.

    • Marina N. Nedelcheva-Veleva
    • , Mihail Sarov
    •  & Stoyno S. Stoynov

  • Article |

    The XY body is a structure required for silencing of sex chromosomes, which is enriched in DNA damage response proteins during meiosis in male germ cells. Here, the authors identify differences between the regulation of the DNA damage response at the XY body and in somatic cells.

    • Lin-Yu Lu
    • , Yi Xiong
    •  & Xiaochun Yu

  • Article
    | Open Access

    RecQ helicases are enzymes that play a central role in maintaining genome stability in the DNA repair cascade. Klaue et al. show that RecQ2 and RecQ3 from Arabidopsis thalianaprocess DNA by, respectively, unwinding and rewinding forked DNA substrates, using a frequent strand switching mechanism.

    • Daniel Klaue
    • , Daniela Kobbe
    •  & Ralf Seidel

  • Article |

    Changes in DNA methylation during mammalian spermatogenesis are poorly understood. The authors show that the content of 5-hydroxymethylcytosine, a stable intermediate of DNA demethylation, changes dynamically during mouse spermatogenesis and is associated with functional genomic regions and transcription.

    • Haiyun Gan
    • , Lu Wen
    •  & Fuchou Tang

  • Article |

    Erm methyltransferases confer antimicrobial drug resistance and their expression is induced by macrolides. Gupta et al.show that Erm-catalysed modification of rRNA affects synthesis of some proteins and reduces cell fitness, explaining why expression of Erm is deleterious in the absence of antibiotics.

    • Pulkit Gupta
    • , Shanmugapriya Sothiselvam
    •  & Alexander S. Mankin

  • Article
    | Open Access

    Tracking single molecules on long stretches of single-stranded DNA poses technical challenges due to its propensity to form hairpin structures. To solve this problem, the authors combine TIRF microscopy with optical tweezers to stretch the DNA and capture the dynamics of DNA unwinding by UvrD DNA helicase.

    • Kyung Suk Lee
    • , Hamza Balci
    •  & Taekjip Ha

  • Article |

    GATA simple sequence repeats (SSRs) are located throughout vertebrate genomes in a non-random fashion. The authors show that these act as enhancer blocker elements in both human cells and Drosophila, indicating a conserved function of GATA SSRs.

    • Ram P. Kumar
    • , Jaya Krishnan
    •  & Rakesh K. Mishra

  • Article
    | Open Access

    The organized initiation of DNA replication at sites throughout the genome must be carefully choreographed to maintain genome stability. Bonne-Andrea and colleagues show that protein SUMOylation controls the density of origin firing, and identify cyclin E as an important substrate in this context.

    • Catherine Bonne-Andrea
    • , Malik Kahli
    •  & Olivier Coux

  • Article
    | Open Access

    The affinity of antibodies for their targets is enhanced by somatic hypermutation, in which the cytidine deaminase AID is recruited to immunoglobulin variable region genes in B cells. Here the authors show that the nuclear protein GANP has an important role in this process by modifying chromatin structure and enhancing AID recruitment.

    • Shailendra Kumar Singh
    • , Kazuhiko Maeda
    •  & Nobuo Sakaguchi

  • Article |

    RecA/Rad51 proteins catalyse the recognition and exchange between two homologous DNA strands during homologous recombination. Sasanuma et al. now demonstrate that Rad51 association with ssDNA is mediated by a complex consisting of Psy3, Csm2, Shu1 and Shu2 proteins.

    • Hiroyuki Sasanuma
    • , Maki S. Tawaramoto
    •  & Akira Shinohara

  • Article
    | Open Access

    CAND1 promotes the activity of Cullin–RING ubiquitin ligases, but binds exclusively to inactive unneddylated forms of the enzyme. By identifying a simple means to reversibly activate this complex in budding yeast, Zemla et al. resolve this paradox and show that CAND1 acts as an exchange factor for substrate adaptors.

    • Aleksandra Zemla
    • , Yann Thomas
    •  & Thimo Kurz

  • Article |

    Macromolecular crowding significantly affects interactions between macromolecules such as proteins, DNA and RNA. Akabayov and colleagues use a SAXS reconstitution assay to show that the effect of macromolecular crowding on T7 DNA replication causes structural changes of the replisome.

    • Barak Akabayov
    • , Sabine R. Akabayov
    •  & Charles C. Richardson

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