Genetic engineering articles within Nature Communications

Featured

  • Article
    | Open Access

    The inclusion of base Z has the potential to heighten the binding affinity between complementary nucleic acids. Here, the authors integrated base Z into CRISRP-Cas12a crRNA to augment the interaction between the crRNA and the target DNA, resulting in a significant enhancement of editing efficiency.

    • Guanhua Xun
    • , Zhixin Zhu
    •  & Huimin Zhao

  • Article
    | Open Access

    The unification of decision-making, communication, and memory would enable the programming of intelligent biotic systems. Here, the authors achieve this goal by engineering E. coli chassis cells with an array of inducible recombinases that mediate diverse genetic programs.

    • Brian D. Huang
    • , Dowan Kim
    •  & Corey J. Wilson

  • Article
    | Open Access

    Fungi have the potential to produce sustainable foods for a growing population, but current products are based on a small number of strains with inherent limitations. Here, the authors develop genetic tools for an edible fungus and engineer its nutritional value and sensory appeal for alternative meat applications.

    • Vayu Maini Rekdal
    • , Casper R. B. van der Luijt
    •  & Jay D. Keasling

  • Article
    | Open Access

    Bacteriophages have great potential in both medicine and biotechnology. Here the authors present PHEIGES, a cell-free method for phage genome engineering, synthesis and selection based on T7, which allows direct selection of engineered and mutant phages without compartmentalization.

    • Antoine Levrier
    • , Ioannis Karpathakis
    •  & Vincent Noireaux

  • Article
    | Open Access

    Current gene silencing tools can have drawbacks. Here the authors report CRISPRδ, an approach for translational silencing, harnessing catalytically inactive Cas13 proteins (dCas13): they also show that fusion of a translational repressor to dCas13 further improved the performance.

    • Antonios Apostolopoulos
    • , Naohiro Kawamoto
    •  & Shintaro Iwasaki

  • Article
    | Open Access

    Engineered biosensing bacteria can potentially probe the human gut microbiome to prevent, diagnose, or treat disease. Here the authors present a robust biocontainment assisted by Cas9 and an engineered gene expression control combined in a genetically engineered human commensal bacterium that successfully functioned in a mouse intestinal tract as well as cell culture condition.

    • Naoki Hayashi
    • , Yong Lai
    •  & Timothy K. Lu

  • Article
    | Open Access

    All natural AAV serotypes transduce murine hepatocytes more efficiently than their human counterparts in human liver chimeric mouse models. Here the authors developed a novel humanized mouse were human transduction of AAV can be studied.

    • Mercedes Barzi
    • , Tong Chen
    •  & Karl-Dimiter Bissig

  • Article
    | Open Access

    The delivery of CRISPR RNPs has potential advantages over other genome editing approaches, including reduced off-target editing and reduced immunogenicity. Here the authors report self-deliverable Cas9 RNPs capable of robustly editing cultured cells in vitro and the mouse brain upon direct injections.

    • Kai Chen
    • , Elizabeth C. Stahl
    •  & Jennifer A. Doudna

  • Article
    | Open Access

    Recent protein design methods rely on large neural networks, yet it is unclear which dependencies are critical for determining function. Here, authors show that learning the per residue mutation preferences, without considering interactions, enables design of functional and diverse protein variants.

    • David Ding
    • , Ada Y. Shaw
    •  & Debora S. Marks

  • Article
    | Open Access

    The most recent class of base editors utilize DddAtox, a deaminase domain that can act upon double-stranded DNA. Here the authors target DddAtox fragments and a FokI-based nickase to the human CIITA gene by fusing these domains to arrays of engineered zinc fingers; they also identify a variety of DddAtox orthologues.

    • Friedrich Fauser
    • , Bhakti N. Kadam
    •  & Jeffrey C. Miller

  • Article
    | Open Access

    Site-specific recombinases such as the Cre-LoxP system are routinely used for genome engineering in both prokaryotes and eukaryotes. Here the authors develop 63 symmetrical LoxP variants and test 1192 pairwise combinations to determine their cross-reactivity and specificity upon Cre activation.

    • Charlotte Cautereels
    • , Jolien Smets
    •  & Kevin J. Verstrepen

  • Article
    | Open Access

    Prime editing in bacteria is currently inefficient. Here the authors report BacPE, a versatile prime editing platform in Escherichia coli that works by inhibiting 3′→5′ DNA exonucleases, highlighting the intrinsic genetic factors that are adverse to efficient prime editing.

    • Hongyuan Zhang
    • , Jiacheng Ma
    •  & Quanjiang Ji

  • Article
    | Open Access

    Synthetic Chromosome Rearrangement and Modification by LoxP-mediated Evolution (SCRaMbLE) is a promising tool to study genomic rearrangements. Here the authors present an engineered yeast strain with 83 sparsely distributed loxPsym sites across the genome can genrerate large-scale genomic rearrangements, which benefits cell fitness under stress and boosts the SCRaMbLE system when combined with synthetic chromosomes.

    • Li Cheng
    • , Shijun Zhao
    •  & Junbiao Dai

  • Article
    | Open Access

    Homing-based gene drives are novel interventions promising the area-wide, species-specific genetic control of harmful insect populations. Here the authors demonstrate the feasibility of a gene drive approach for the genetic control of the agricultural pest, the medfly, based on complete female-to-male sex conversion.

    • Angela Meccariello
    • , Shibo Hou
    •  & Nikolai Windbichler

  • Article
    | Open Access

    Building synthetic chromosomes from natural components is an unexplored alternative to de novo chromosome synthesis that may have many potential applications. In this paper, the authors report CReATiNG, a method for constructing synthetic chromosomes from natural components in yeast.

    • Alessandro L. V. Coradini
    • , Christopher Ne Ville
    •  & Ian M. Ehrenreich

  • Article
    | Open Access

    Ddd-Aderived cytosine base editors (DdCBEs) are important for research of mitochondrial DNA mutation diseases. Here the authors report a strategy for screening and characterising dsDNA cytidine deaminases, and identify 7 DddA homologs which they optimise to minimise nuclear and mitochondrial off-target editing.

    • Haifeng Sun
    • , Zhaojun Wang
    •  & Bin Shen

  • Article
    | Open Access

    Exogenous control of genes in vivo is important. Here the authors report a system that can be inducibly activated through thermal energy produced by ultrasound absorption and use this to control induction of gene activation and base editing: they apply this in cell lines and in a mouse model.

    • Pei Liu
    • , Josquin Foiret
    •  & Lei S. Qi

  • Article
    | Open Access

    Designing promoters with desired properties is crucial in synthetic biology. Here, authors introduce DeepSEED, an AI-aided flanking sequence optimisation framework which combines expert knowledge with deep learning techniques to efficiently design promoters in both eukaryotic and prokaryotic cells.

    • Pengcheng Zhang
    • , Haochen Wang
    •  & Xiaowo Wang

  • Article
    | Open Access

    Small Cas enzymes are required for therapeutic use. Here the authors report an Interaction, Dynamics and Conservation (IDC) strategy for protein miniaturisation and use this to generate five compact variants of Cas13 based on a combination of IDC strategy and AlphaFold2.

    • Feiyu Zhao
    • , Tao Zhang
    •  & Zhanjun Li

  • Article
    | Open Access

    Regulatory T cells, and to certain extent other T cell subsets, limit the immune response to avoid harmful inflammation and tissue damage. Here authors identify a surface molecule, Lrig1, that is directly responsible for the suppressive function in regulatory T cells and in Il-17-producing helper T cells.

    • Jae-Seung Moon
    • , Chun-Chang Ho
    •  & Sang-Kyou Lee

  • Article
    | Open Access

    Memory is a basic tenet of intelligent biological systems. Here the authors engineered a programmable and expandable iteration of recombinase-based synthetic memory (interception) that functions post-translation, resulting in faster recombination.

    • Andrew E. Short
    • , Dowan Kim
    •  & Corey J. Wilson

  • Article
    | Open Access

    The challenge of designing chimeric antigen receptor (CAR)-T cells for cancer therapy is not limited to finding targetable cellular proteins, but also in optimising the effector properties. Here authors show that single-chain variable fragment targeting moieties could unpredictably prompt spontaneous CAR-T cell activation via CAR clustering, which argues for empirical screening for tonic signalling.

    • Tina Sarén
    • , Giulia Saronio
    •  & Magnus Essand

  • Article
    | Open Access

    Although diagnosis of urinary tract infections has improved through the use of point-of-care molecular technologies, they are however limited by poor specificity and / or sensitivity, and requirement of laboratory resources. In this work, the authors develop a bacteriophage-based diagnostic assay for the detection of prevalent uropathogens.

    • Susanne Meile
    • , Jiemin Du
    •  & Samuel Kilcher

  • Article
    | Open Access

    Retrotransposons replicate their genetic information through target-primed reverse transcription (TPRT). Here the authors report a template-jumping prime editor (TJ-PE) to act similarly to TPRT and achieve insertions of large DNA fragments at endogenous sites: they rewrite a mutated exon in the mouse liver.

    • Chunwei Zheng
    • , Bin Liu
    •  & Wen Xue

  • Article
    | Open Access

    The role of DNA methylation in early embryo development has been difficult to determine due to the functional redundancy of DNA methyltransferases. Here they develop an efficient base editing system that enables one-step generation of Dnmt-null embryos and show that DNA methylation-related miRNA suppression may be involved in gastrulation.

    • Qing Li
    • , Jiansen Lu
    •  & Jinsong Li

  • Article
    | Open Access

    An in-depth understanding of the molecular pathogenesis of fibrolamellar carcinoma (FLC) is hampered due to limited human preclinical models. Here the authors engineer human organoids to reflect different FLC genetic backgrounds and show that hepatocytes can be a cell-of-origin of FLC that transdifferentiate into ductal/progenitor like cells due to combined BAP1 and PRKAR2A loss.

    • Laura Rüland
    • , Francesco Andreatta
    •  & Benedetta Artegiani

  • Article
    | Open Access

    Using synthetic sRNAs to knockdown target genes has been restricted to a limited number of bacteria. Here, the authors develop a broad-host-range synthetic sRNA platform and show its application in 16 bacterial species, including mitigating virulence-associated phenotypes in pathogens and production of chemicals via metabolic engineering.

    • Jae Sung Cho
    • , Dongsoo Yang
    •  & Sang Yup Lee

  • Article
    | Open Access

    The scarcity of qualified RNA-binding proteins hinders the development of artificial translational regulators and synthetic gene circuits. Here, the authors repurposed CRISPR-Cas proteins as translational regulators to build synthetic circuits.

    • Shunsuke Kawasaki
    • , Hiroki Ono
    •  & Hirohide Saito

  • Article
    | Open Access

    Antimicrobial peptides (AMPs) are next-generation antibiotics that can be used to combat drugresistant pathogens. Here, the authors report efficient production of bioactive amidated AMPs by transient expression in Nicotiana benthamiana line expressing the mammalian enzyme peptidylglycine α-amidating mono-oxygenase.

    • Shahid Chaudhary
    • , Zahir Ali
    •  & Magdy Mahfouz

  • Article
    | Open Access

    The generation of CRISPR-mediated transcriptional activation (CRISPRa)-competent cell lines pose significant technical challenges. Here the authors report a platform for production of CRISPRa-ready cell populations which they combine with optimised expressed and synthetic gRNA scaffolds to enhance functionality.

    • Amy J. Heidersbach
    • , Kristel M. Dorighi
    •  & Benjamin Haley

  • Article
    | Open Access

    Properties of cytidine and adenosine deaminases lead to off-target effects for cytosine base editors (CBEs) and adenine base editors (ABEs). Here the authors report that 25 TadA orthologs could be engineered to generate functional ABEs, CBEs or ACBEs via single/double mutations with minimised off-targets.

    • Shuqian Zhang
    • , Bo Yuan
    •  & Tian-Lin Cheng

  • Article
    | Open Access

    It is still a challenge to accurately identify off-target endonuclease edits. Here the authors report PEAC-seq using a Prime Editor to insert a tag to the editing sites and enrich the tagged regions with site-specific primers for sequencing: they show that PEAC-seq could identify DNA translocations.

    • Zhenxing Yu
    • , Zhike Lu
    •  & Lijia Ma

  • Article
    | Open Access

    Artificial receptors targeted to the secretory pathway often fail to exhibit the expected activity due to post-translational modifications and/or improper folding. Here, the authors engineer diverse synthetic receptors that reside in the cytoplasm, inside the endoplasmic reticulum, or on the plasma membrane through orientation adjustment of the receptor parts and by elimination of dysfunctional PTMs sites.

    • Mohamed Mahameed
    • , Pengli Wang
    •  & Martin Fussenegger

  • Article
    | Open Access

    Zinc finger (ZF) arrays are programmable DNA-binding proteins. Here the authors report ZF-DddA-derived cytosine base editors (DdCBEs) and optimise their architectures to improve targeting; they apply these variants in vitro and in vivo to mitochondrial base editing and show higher editing than ZF deaminases.

    • Julian C. W. Willis
    • , Pedro Silva-Pinheiro
    •  & David R. Liu

  • Article
    | Open Access

    CRISPR/Cas gene drives can bias transgene inheritance through different mechanisms. Here the authors use gene linkage to show that in males inheritance bias of wGDe did not occur by homing, rather through increased propagation of the donor drive element.

    • Sebald A. N. Verkuijl
    • , Estela Gonzalez
    •  & Luke Alphey

Browse broader subjects

Browse Genetic engineering across other nature.com journals