Genomes and Genes
Summary: Directed modification of the gene complement of a living organism by such techniques as altering the DNA, substituting genetic material by means of a virus, transplanting whole nuclei, transplanting cell hybrids, etc.
- Bedell V, Wang Y, Campbell J, Poshusta T, Starker C, Krug R, et al. In vivo genome editing using a high-efficiency TALEN system. Nature. 2012;491:114-8 pubmed publisher..We further show successful germline transmission of both EcoRV and mloxP engineered chromosomes. This combined approach offers the potential to model genetic variation as well as to generate targeted conditional alleles. ..
- Kang S, Choi O, Lee J, Hwang B, Uhm T, Hong Y. Artificial biosynthesis of phenylpropanoic acids in a tyrosine overproducing Escherichia coli strain. Microb Cell Fact. 2012;11:153 pubmed publisher..This work forms a basis for further improvement in production and opens the possibility of microbial synthesis of more complex plant secondary metabolites derived from phenylpropanoic acids. ..
- Mutalik V, Guimaraes J, Cambray G, Lam C, Christoffersen M, Mai Q, et al. Precise and reliable gene expression via standard transcription and translation initiation elements. Nat Methods. 2013;10:354-60 pubmed publisher..We expect the genetic element definitions validated here can be collectively expanded to create collections of public-domain standard biological parts that support reliable forward engineering of gene expression at genome scales. ..
- Zu Y, Tong X, Wang Z, Liu D, Pan R, Li Z, et al. TALEN-mediated precise genome modification by homologous recombination in zebrafish. Nat Methods. 2013;10:329-31 pubmed publisher..We also successfully targeted two additional genes. Homologous recombination in zebrafish with a dsDNA donor expands the utility of this model organism. ..
- Yang H, Wang H, Shivalila C, Cheng A, Shi L, Jaenisch R. One-step generation of mice carrying reporter and conditional alleles by CRISPR/Cas-mediated genome engineering. Cell. 2013;154:1370-9 pubmed publisher..Finally, we analyzed potential off-targets of five sgRNAs in gene-modified mice and ESC lines and identified off-target mutations in only rare instances. ..
- Friedland A, Tzur Y, Esvelt K, COLAIACOVO M, Church G, Calarco J. Heritable genome editing in C. elegans via a CRISPR-Cas9 system. Nat Methods. 2013;10:741-3 pubmed publisher..Our results demonstrate that targeted, heritable genetic alterations can be achieved in C. elegans, providing a convenient and effective approach for generating loss-of-function mutants. ..
- Shin J, Noireaux V. An E. coli cell-free expression toolbox: application to synthetic gene circuits and artificial cells. ACS Synth Biol. 2012;1:29-41 pubmed publisher..This toolbox is a unique platform to study complex transcription/translation-based biochemical systems in vitro. ..
- Sharma V, Yamamura A, Yokobayashi Y. Engineering artificial small RNAs for conditional gene silencing in Escherichia coli. ACS Synth Biol. 2012;1:6-13 pubmed publisher..We anticipate that the artificial sRNAs will be useful for dynamic control and fine-tuning of endogenous gene expression in bacteria for applications in synthetic biology. ..
- Chen H, Melis A. Marker-free genetic engineering of the chloroplast in the green microalga Chlamydomonas reinhardtii. Plant Biotechnol J. 2013;11:818-28 pubmed publisher..A metabolic pathway for ethanol production is proposed in Chlamydomonas, mediated by the chloroplast-localized CrCpADH1 transgenic enzyme. ..
- Yan Y, Hong N, Chen T, Li M, Wang T, Guan G, et al. p53 gene targeting by homologous recombination in fish ES cells. PLoS ONE. 2013;8:e59400 pubmed publisher..Our results demonstrate that medaka ES cells are proficient for HR-mediated GT, offering a first model organism of lower vertebrates towards the development of full ES cell-based GT technology. ..
- Pushko P, Pumpens P, Grens E. Development of virus-like particle technology from small highly symmetric to large complex virus-like particle structures. Intervirology. 2013;56:141-65 pubmed publisher..Further development of safe and efficient VLP nanotechnology may require a rational combination of both approaches. ..
- Goñi Moreno A, Amos M. A reconfigurable NAND/NOR genetic logic gate. BMC Syst Biol. 2012;6:126 pubmed publisher..The circuit addresses important issues in genetic logic that will have significance for more complex synthetic biology applications. ..
- Valton J, Dupuy A, Daboussi F, Thomas S, Maréchal A, Macmaster R, et al. Overcoming transcription activator-like effector (TALE) DNA binding domain sensitivity to cytosine methylation. J Biol Chem. 2012;287:38427-32 pubmed publisher..Using a combination of biochemical, structural, and cellular approaches, we were able to identify the molecular basis of such sensitivity and propose a simple, drug-free, and universal method to overcome it. ..
- Ramalingam S, London V, Kandavelou K, Cebotaru L, Guggino W, Civin C, et al. Generation and genetic engineering of human induced pluripotent stem cells using designed zinc finger nucleases. Stem Cells Dev. 2013;22:595-610 pubmed publisher..Further genetic engineering of the single-allele CCR5-modified IMR90 hiPSCs was achieved by site-specific addition of the large CFTR ..
- Zhang Y, Zhang F, Li X, Baller J, Qi Y, Starker C, et al. Transcription activator-like effector nucleases enable efficient plant genome engineering. Plant Physiol. 2013;161:20-7 pubmed publisher..The optimized reagents implemented in plant protoplasts should be useful for targeted modification of cells from diverse plant species and using a variety of means for reagent delivery. ..
- Acevedo Rocha C, Fang G, Schmidt M, Ussery D, Danchin A. From essential to persistent genes: a functional approach to constructing synthetic life. Trends Genet. 2013;29:273-9 pubmed publisher..These criteria impose constraints on genome organization, and these are important considerations for engineering cells and for creating cellular life-like forms in SB. ..
- Pfander C, Anar B, Brochet M, Rayner J, Billker O. Recombination-mediated genetic engineering of Plasmodium berghei DNA. Methods Mol Biol. 2013;923:127-38 pubmed..The basic techniques we describe here can be adapted to generate highly efficient vectors for gene deletion, tagging, targeted mutagenesis, or genetic complementation with larger genomic regions...
- Ceres P, Garst A, Marcano Velázquez J, Batey R. Modularity of select riboswitch expression platforms enables facile engineering of novel genetic regulatory devices. ACS Synth Biol. 2013;2:463-72 pubmed publisher..Importantly, this technique does not require selection of device-specific "communication modules" required to transmit ligand binding to the regulatory domain, enabling rapid engineering of novel functional RNAs. ..
- Karas B, Tagwerker C, Yonemoto I, Hutchison C, Smith H. Cloning the Acholeplasma laidlawii PG-8A genome in Saccharomyces cerevisiae as a yeast centromeric plasmid. ACS Synth Biol. 2012;1:22-8 pubmed publisher..laidlawii gene, a surface anchored extracellular endonuclease, was toxic when cloned in yeast. This gene was inactivated in order to clone and stably maintain the A. laidlawii genome as a centromeric plasmid in the yeast cell...
- Riolobos L, Hirata R, Turtle C, Wang P, Gornalusse G, Zavajlevski M, et al. HLA engineering of human pluripotent stem cells. Mol Ther. 2013;21:1232-41 pubmed publisher..Here, we develop two distinct genetic engineering approaches that address this problem...
- Sarov M, Murray J, Schanze K, Pozniakovski A, Niu W, Angermann K, et al. A genome-scale resource for in vivo tag-based protein function exploration in C. elegans. Cell. 2012;150:855-66 pubmed publisher..We illustrate the utility of the resource by systematic chromatin immunopurification and automated 4D imaging, which produced detailed DNA binding and cell/tissue distribution maps for key transcription factor proteins. ..
- Xu P, Vansiri A, Bhan N, Koffas M. ePathBrick: a synthetic biology platform for engineering metabolic pathways in E. coli. ACS Synth Biol. 2012;1:256-66 pubmed publisher..The ePathBrick vectors presented here provide a versatile platform for rapid design and optimization of metabolic pathways in E. coli. ..
- Perez Pinera P, Ousterout D, Brunger J, Farin A, Glass K, Guilak F, et al. Synergistic and tunable human gene activation by combinations of synthetic transcription factors. Nat Methods. 2013;10:239-42 pubmed publisher..These combinations of TALE transcription factors induced substantial gene activation and allowed tuning of gene expression levels that will broadly enable synthetic biology, gene therapy and biotechnology. ..
- Yau Y, Stewart C. Less is more: strategies to remove marker genes from transgenic plants. BMC Biotechnol. 2013;13:36 pubmed publisher..This review discusses the advantages and disadvantages of existing SMG-removal strategies and explores possible future research directions for SMG removal including emerging technologies for increased precision for genome modification. ..
- McIsaac R, Oakes B, Wang X, Dummit K, Botstein D, Noyes M. Synthetic gene expression perturbation systems with rapid, tunable, single-gene specificity in yeast. Nucleic Acids Res. 2013;41:e57 pubmed publisher..These new tools allow for the elucidation of regulatory network elements dynamically, which we demonstrate with a major metabolic regulator, Gcn4p. ..
- Lajoie M, Rovner A, Goodman D, Aerni H, Haimovich A, Kuznetsov G, et al. Genomically recoded organisms expand biological functions. Science. 2013;342:357-60 pubmed publisher..The GRO also exhibited increased resistance to T7 bacteriophage, demonstrating that new genetic codes could enable increased viral resistance. ..
- Dicarlo J, Norville J, Mali P, Rios X, Aach J, Church G. Genome engineering in Saccharomyces cerevisiae using CRISPR-Cas systems. Nucleic Acids Res. 2013;41:4336-43 pubmed publisher..Our approach provides foundations for a simple and powerful genome engineering tool for site-specific mutagenesis and allelic replacement in yeast. ..
- Pattanayak V, Lin S, Guilinger J, Ma E, Doudna J, Liu D. High-throughput profiling of off-target DNA cleavage reveals RNA-programmed Cas9 nuclease specificity. Nat Biotechnol. 2013;31:839-43 pubmed publisher..High concentrations of guide-RNA:Cas9 complexes can cleave off-target sites containing mutations near or within the PAM that are not cleaved when enzyme concentrations are limiting. ..
- Zhu C, Sanahuja G, Yuan D, Farre G, Arjó G, Berman J, et al. Biofortification of plants with altered antioxidant content and composition: genetic engineering strategies. Plant Biotechnol J. 2013;11:129-41 pubmed publisher..In this review, we consider the state of the art in antioxidant biofortification and discuss the challenges that remain to be overcome in the development of nutritionally complete and health-promoting functional foods. ..
- Chen C, Fenk L, de Bono M. Efficient genome editing in Caenorhabditis elegans by CRISPR-targeted homologous recombination. Nucleic Acids Res. 2013;41:e193 pubmed publisher..The possibility to edit the C. elegans genome at selected locations will facilitate the systematic study of gene function in this widely used model organism. ..
- Maeder M, Linder S, Reyon D, Angstman J, Fu Y, Sander J, et al. Robust, synergistic regulation of human gene expression using TALE activators. Nat Methods. 2013;10:243-5 pubmed publisher..These findings will encourage applications of TALE activators for research and therapy, and guide design of monomeric TALE-based fusion proteins. ..
- Xiao A, Wang Z, Hu Y, Wu Y, Luo Z, Yang Z, et al. Chromosomal deletions and inversions mediated by TALENs and CRISPR/Cas in zebrafish. Nucleic Acids Res. 2013;41:e141 pubmed publisher..To facilitate the analyses and application of existing ZFN, TALEN and CRISPR/Cas data, we have updated our EENdb database to provide a chromosomal view of all reported engineered endonucleases targeting human and zebrafish genomes. ..
- Lawlor D. Genetic engineering to improve plant performance under drought: physiological evaluation of achievements, limitations, and possibilities. J Exp Bot. 2013;64:83-108 pubmed publisher..Current evidence is that GM plants may not be better able to cope with drought than selection-bred cultivars. ..
- Jao L, Wente S, Chen W. Efficient multiplex biallelic zebrafish genome editing using a CRISPR nuclease system. Proc Natl Acad Sci U S A. 2013;110:13904-9 pubmed publisher..This CRISPR/Cas9 system represents a highly effective and scalable gene knockout method in zebrafish and has the potential for applications in other model organisms. ..
- Bauer D, Kamran S, Lessard S, Xu J, Fujiwara Y, Lin C, et al. An erythroid enhancer of BCL11A subject to genetic variation determines fetal hemoglobin level. Science. 2013;342:253-7 pubmed publisher..We propose the GWAS-marked BCL11A enhancer represents an attractive target for therapeutic genome engineering for the ?-hemoglobinopathies. ..
- Sainsbury F, Saxena P, Aljabali A, Saunders K, Evans D, Lomonossoff G. Genetic engineering and characterization of Cowpea mosaic virus empty virus-like particles. Methods Mol Biol. 2014;1108:139-53 pubmed publisher..Here we describe methods for the genetic modification and production of CPMV eVLPs and describe techniques useful for their characterization. ..
- Chen K, Gao C. TALENs: customizable molecular DNA scissors for genome engineering of plants. J Genet Genomics. 2013;40:271-9 pubmed publisher..In this article, we review the development of TALENs, and summarize the principles and tools for TALEN-mediated gene targeting in plant cells, as well as current and potential strategies for use in plant research and crop improvement. ..
- Gratz S, Cummings A, Nguyen J, Hamm D, Donohue L, Harrison M, et al. Genome engineering of Drosophila with the CRISPR RNA-guided Cas9 nuclease. Genetics. 2013;194:1029-35 pubmed publisher..This RNA-guided Cas9 system can be rapidly programmed to generate targeted alleles for probing gene function in Drosophila. ..
- Hou Z, Zhang Y, Propson N, Howden S, Chu L, Sontheimer E, et al. Efficient genome engineering in human pluripotent stem cells using Cas9 from Neisseria meningitidis. Proc Natl Acad Sci U S A. 2013;110:15644-9 pubmed publisher..Because of its distinct protospacer adjacent motif, the N. meningitidis CRISPR-Cas machinery increases the sequence contexts amenable to RNA-directed genome editing. ..
- Borgeaud S, Blokesch M. Overexpression of the tcp gene cluster using the T7 RNA polymerase/promoter system and natural transformation-mediated genetic engineering of Vibrio cholerae. PLoS ONE. 2013;8:e53952 pubmed publisher..This provides a proof-of-principle that the T7 RNA polymerase/promoter system is functional in V. cholerae and that genetic engineering of this organism by natural transformation is a straightforward and efficient approach.
- Cho S, Kim S, Kim J, Kim J. Targeted genome engineering in human cells with the Cas9 RNA-guided endonuclease. Nat Biotechnol. 2013;31:230-2 pubmed publisher..We show that complexes of the Cas9 protein and artificial chimeric RNAs efficiently cleave two genomic sites and induce indels with frequencies of up to 33%...
- Lajoie M, Gregg C, Mosberg J, Washington G, Church G. Manipulating replisome dynamics to enhance lambda Red-mediated multiplex genome engineering. Nucleic Acids Res. 2012;40:e170 pubmed publisher..These improvements will facilitate ambitious genome engineering projects by minimizing dependence on time-consuming clonal isolation and screening. ..