Genetic techniques articles within Nature Communications

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  • Article
    | Open Access

    CRISPR/Cas9 and transcription activator-like effector nuclease (TALEN) are becoming major tools for genome editing. Here, Song et al. show that RS-1, a small-molecule enhancer for homology directed repair, increases the CRISPR/Cas9 and TALEN mediated knock-in efficiency both in vitro and in vivowith rabbit.

    • Jun Song
    • , Dongshan Yang
    •  & Jifeng Zhang

  • Article
    | Open Access

    The domestic dog is an important model organism for our understanding of cancer and other diseases. Here the authors conduct a genome-wide association study across multiple breeds and identify novel loci significantly associated with several complex diseases and morphological traits.

    • Jessica J. Hayward
    • , Marta G. Castelhano
    •  & Adam R. Boyko

  • Article
    | Open Access

    CRISPR-Cas9 is a powerful genome engineering tool but gene knock-in is limited by fragment size and efficiency of recombination. Here the authors used a modified strategy employing single-strand oligonucleotides to efficiently knock-in large DNA fragments and humanise native rat loci.

    • Kazuto Yoshimi
    • , Yayoi Kunihiro
    •  & Tomoji Mashimo

  • Article
    | Open Access

    Drosophila RNAi libraries are commonly used to perform large-scale functional genetics screens in vivo. Here the authors find that a subset of lines from the VDRC KK RNAi line cause false-positive enhancement of the Hippo pathway, and provide a strain that can test whether a genetic screen of interest will be affected by this technical artefact.

    • Joseph H.A. Vissers
    • , Samuel A. Manning
    •  & Kieran F. Harvey

  • Article
    | Open Access

    CRISPR-Cas9 has greatly enhanced genome engineering however gene tagging can still be cumbersome due to a requirement for homology donors. Here the authors introduce a generic system for gene tagging that does not require homology between the donor and the genomic target site.

    • Daniel H. Lackner
    • , Alexia Carré
    •  & Tilmann Bürckstümmer

  • Article
    | Open Access

    A key step for the use of CRISPR-Cas9 in any study is the design of the guide RNA, however the underlying principles are still poorly understood. Here the authors show that multiple protospacer adjacent motif sequences are refractory to efficient targeting and repair.

    • Abba Malina
    • , Christopher J. F. Cameron
    •  & Jerry Pelletier

  • Article
    | Open Access

    Adenosine-to-inosine (A-to-I) RNA editing plays an important role in neurological functions. Here, by a quantitative trait loci (QTL) mapping approach in 131 Drosophila melanogasterstrains, the authors identify 545 QTLs associated with differences in RNA editing.

    • Gokul Ramaswami
    • , Patricia Deng
    •  & Jin Billy Li

  • Article
    | Open Access

    Butterflies are a promising system to study the genetics and evolution of morphological diversification, yet genomic and technological resources are limited. Here, the authors sequence genomes of two Papiliobutterflies and develop a CRISPR/Cas9 gene editing method for these species.

    • Xueyan Li
    • , Dingding Fan
    •  & Wen Wang

  • Article
    | Open Access

    CRISPR-Cas9 is a powerful tool for genome editing; however, difficulties in generating pools of paired guide RNAs limit its applicability to large-scale screening experiments. Here the authors report a one-step method for rapid and efficient generation of pooled libraries of guide RNA pairs.

    • Joana A. Vidigal
    •  & Andrea Ventura

  • Article
    | Open Access

    The shape of the pinna varies widely in the general human population but the genetic basis of this variation is unknown. Here Adhikari et al. conduct a genome-wide association study in Latin Americans and discover seven gene regions influencing pinna morphology, including EDAR and TBX15.

    • Kaustubh Adhikari
    • , Guillermo Reales
    •  & Andrés Ruiz-Linares

  • Article
    | Open Access

    Group O/RhD− blood can be safely transfused to any recipient and methods for converting other blood groups into this group hold therapeutic potential. By using programmable nucleases, here the authors edit the gene that determines the RhD blood group and convert the RhD+ into RhD− erythroid progenitor cells.

    • Young-Hoon Kim
    • , Hyun O. Kim
    •  & Hyongbum Kim

  • Article
    | Open Access

    TALE proteins are popular tools for genome engineering because they can recognize specific DNA sequences, however off-target effects are a routine problem. Here Rogers and Barrera et al. comprehensively map TALE–DNA interactions to develop a computational model to predict binding specificity.

    • Julia M. Rogers
    • , Luis A. Barrera
    •  & Martha L. Bulyk

  • Article
    | Open Access

    Zebrafish is a model system for which for no reliable heritable gene silencing method is available. Here the authors provide a system for heritable miRNA-mediated knockdown and demonstrate tunable silencing of the smn1gene that recapitulate different forms of spinal muscular atrophy.

    • Jean Giacomotto
    • , Silke Rinkwitz
    •  & Thomas S. Becker

  • Article
    | Open Access

    Diabetes is associated with aberrations in glucose metabolism. Here the authors perform a genomic screen in fruit flies to identify new regulators of fly glucose metabolism, and show that mice lacking the murine homologue of one of their hits, the protein kinase CK1alpha, in the adipose lineage develop diabetes.

    • Rupali Ugrankar
    • , Eric Berglund
    •  & Jonathan M. Graff

  • Article
    | Open Access

    The ability to contain and destroy synthetically engineered microorganisms is an important consideration with environmental, industrial and intellectual property implications. Here Caliando et al. design and demonstrate a stably integrated CRISPR-based system for targeted DNA destruction.

    • Brian J. Caliando
    •  & Christopher A. Voigt

  • Article |

    Expression quantitative trait loci (eQTLs) may provide insight into the functional mechanisms underlying disease risk variants. Here the authors characterize INDEL-specific eQTLs in several tissues and show that these can have both tissue-specific and tissue-consistent effects.

    • Jinyan Huang
    • , Jun Chen
    •  & Liming Liang

  • Article
    | Open Access

    Structural variations in crop genomes are thought to be responsible for significant differences in phenotype and they can be well-represented by a ‘pan-genome’. Here, Lu et al.develop an approach to genetically map pan-genome sequence anchors using 14,129 inbred lines of maize, showing structural variation is a significant source of adaptive variation.

    • Fei Lu
    • , Maria C. Romay
    •  & Edward S. Buckler

  • Article |

    Duchenne muscular dystrophy is caused by mutations in the dystrophin gene. Here, Ousterout et al. use multiplexed CRISPR/Cas9 genome editing to excise a large portion of the gene that carries over 60% of known dystrophin mutations. They show that this excision restores dystrophin expression in patient-derived cells.

    • David G. Ousterout
    • , Ami M. Kabadi
    •  & Charles A. Gersbach

  • Article
    | Open Access

    Psoriatic arthritis (PsA) is a chronic inflammatory arthritis with a significant genetic component. Here, the authors analyse immune-related genetic markers in 1,962 PsA patients and 8,923 controls to identify novel PsA risk loci and highlight distinct genetic differences between psoriasis and PsA.

    • John Bowes
    • , Ashley Budu-Aggrey
    •  & Anne Barton

  • Article
    | Open Access

    One of the biggest bottlenecks in large-scale DNA synthesis is the retrieval of target clonal DNA from high-density sequencing platforms. Here, the authors present a method called ‘Sniper Cloning’ that allows for precise mapping of target clone features and rapid retrieval of targets for full utilization of DNA clones.

    • Howon Lee
    • , Hyoki Kim
    •  & Sunghoon Kwon

  • Article
    | Open Access

    The microbial RNA-guided CRISPR/Cas9 system has robust genome-editing activities, but the off-target effects of the Cas9 nuclease have only recently begun to be analysed. Here the authors provide evidence for high specificity of the Cas9 nuclease on targeting of the Tafazzin gene in human-induced pluripotent stem cells and demonstrate the impact of single-nucleotide variations of the human genome on Cas9 specificity.

    • Luhan Yang
    • , Dennis Grishin
    •  & George Church

  • Article
    | Open Access

    One challenge facing the use of programmable nucleases in genome engineering is the requirement for homologous recombination. Here, Nakade et al.harness microhomology-mediated end-joining as a means of inserting exogenous coding sequences into the genome using both TALEN and CRISPR/Cas9 technologies.

    • Shota Nakade
    • , Takuya Tsubota
    •  & Ken-ichi T. Suzuki

  • Article |

    The fission yeast, Schizosaccharomyces pombe, is a valuable model organism, but the lack of a portable RNA Pol III promoter has prevented the implementation of the CRISPR/Cas9 system. Here the authors develop a CRISPR/Cas9 system that achieves selection-free specific mutagenesis with very high efficiencies in S. pombe.

    • Jake Z. Jacobs
    • , Keith M. Ciccaglione
    •  & Mikel Zaratiegui

  • Article
    | Open Access

    Next-generation sequencing technology has made the generation of huge amounts of genetic data possible, but phenotype characterization remains slow and difficult. Here the authors develop a high-throughput phenotyping facility for rice that is able to accurately identify and characterize traits related to morphology, biomass and yield.

    • Wanneng Yang
    • , Zilong Guo
    •  & Lizhong Xiong

  • Article |

    The essential nature of replicative polymerases has hampered the study of polymerase-δ mutations found in colorectal cancer cells. Here, using polymerase-δ mutations as a proof of principle, the authors present an inducible single vector system that replaces any endogenous gene with an RNAi-resistant mutant version.

    • Medini Manohar Ghodgaonkar
    • , Patrick Kehl
    •  & Josef Jiricny

  • Article |

    Current CRISPR-mediated genome-editing methods are limited by the requirement for a specific +1 nucleotide when using the U6 promoter to drive guide RNA synthesis. Now, Ranganathan et al.report a modification of the CRISPR–Cas9 system that more than doubles the number of targetable CRISPR sites within the human genome.

    • Vinod Ranganathan
    • , Karl Wahlin
    •  & Donald J. Zack

  • Article |

    Genomic rearrangements have important functional consequences for cancer. Here, Choi and Meyerson use CRISPR/Cas technology to generate translocations and inversions that are known drivers of lung cancer, and demonstrate the utility of this technology for studying the role of genomic rearrangements in disease.

    • Peter S. Choi
    •  & Matthew Meyerson

  • Article |

    Transcription activator-like effectors (TALEs) of pathogenic bacteria activate target genes in host plants to support infection. Here, the authors show that TALEs with single natural repeats of aberrant length tolerate one base pair deletions and may enable the bacteria to overcome natural plant resistance.

    • Annekatrin Richter
    • , Jana Streubel
    •  & Jens Boch

  • Article |

    Cas9 RNA-guided engineered nucleases (RGENs) induce site-specific DNA cleavages in cultured cells and organisms and are used widely as genome-editing tools. Here, the authors develop an RGEN-based technology to genotype both RGEN-induced mutations and cancer-associated mutations in human cell lines.

    • Jong Min Kim
    • , Daesik Kim
    •  & Jin-Soo Kim

  • Article |

    Genetically engineered mice are an important aspect of human disease research. Here, the authors use artificial transcription activator-like effector-nucleases to generate a mouse line with a conditionally targeted allele and suggest that this method can be easily adapted to any gene in the mouse genome.

    • Daniel Sommer
    • , Annika E. Peters
    •  & Marc Beyer

  • Article |

    Immunosequencing enables cost-effective sequencing of repertoires of immune cells, but it often suffers from amplification biases when attempting cell quantification. Here, the authors present a powerful multiplex PCR assay that allows for quantitative and unbiased analysis of frequency of different T cell receptors.

    • Christopher S. Carlson
    • , Ryan O. Emerson
    •  & Harlan Robins

  • Article
    | Open Access

    Transcription activator-like effector nucleases (TALENs) are dimeric 'molecular scissors' that can be readily engineered for gene-targeting applications. Beurdeley et al. develop a single-chain TALEN architecture having significant in vivoactivity in yeast, plant and mammalian systems.

    • Marine Beurdeley
    • , Fabian Bietz
    •  & George H. Silva

  • Article |

    RNA detection is important in biomedical research and largely relies on the reverse transcription–PCR reaction. Zhao et al.report an isothermal reaction, which involves cleavage by a DNAzyme and signal amplification, to simultaneously amplify and detect RNA.

    • Yongyun Zhao
    • , Li Zhou
    •  & Zhuo Tang

  • Article
    | Open Access

    Hemimetabolous insects comprise many pests but introducing targeted mutations into these species has been difficult. This paper reports efficient targeted mutagenesis, and the generation of homozygous knockouts, in crickets based on zinc finger nucleases or transcription activator-like effector nucleases.

    • Takahito Watanabe
    • , Hiroshi Ochiai
    •  & Taro Mito

  • Article |

    The generation of human cell lines using somatic cell nuclear transfer has been difficult to achieve. In this study, Egliet al. show that while mouse eggs reprogram somatic cells within hours, human eggs arrest after nuclear transfer which may be due to a lack of genome transcription.

    • Dieter Egli
    • , Alice E. Chen
    •  & Kevin Eggan

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