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Transcription activator-like effectors

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https://www.readbyqxmd.com/read/27926841/broken-tales-transcription-activator-like-effectors-populate-partly-folded-states
#1
Kathryn Geiger-Schuller, Doug Barrick
Transcription activator-like effector proteins (TALEs) contain large numbers of repeats that bind double-stranded DNA, wrapping around DNA to form a continuous superhelix. Since unbound TALEs retain superhelical structure, it seems likely that DNA binding requires a significant structural distortion or partial unfolding. In this study, we use nearest-neighbor "Ising" analysis of consensus TALE (cTALE) repeat unfolding to quantify intrinsic folding free energies, coupling energies between repeats, and the free energy distribution of partly unfolded states, and to determine how those energies depend on the sequence that determines DNA-specificity (called the "RVD")...
December 6, 2016: Biophysical Journal
https://www.readbyqxmd.com/read/27917188/crispr-cas9-tool-for-qualitative-and-quantitative-plant-genome-editing
#2
REVIEW
Ali Noman, Muhammad Aqeel, Shuilin He
Recent developments in genome editing techniques have aroused substantial excitement among agricultural scientists. These techniques offer new opportunities for developing improved plant lines with addition of important traits or removal of undesirable traits. Increased adoption of genome editing has been geared by swiftly developing Clustered regularly interspaced short palindromic repeats (CRISPR). This is appearing as driving force for innovative utilization in diverse branches of plant biology. CRISPR-Cas9 mediated genome editing is being used for rapid, easy and efficient alteration of genes among diverse plant species...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27913634/comparative-analysis-highlights-variable-genome-content-of-wheat-rusts-and-divergence-of-the-mating-loci
#3
Christina A Cuomo, Guus Bakkeren, Hala Badr Khalil, Vinay Panwar, David Joly, Rob Linning, Sharadha Sakthikumar, Xiao Song, Xian Adiconis, Lin Fan, Jonathan M Goldberg, Joshua Z Levin, Sarah Young, Qiandong Zeng, Yehoshua Anikster, Myron Bruce, Meinan Wang, Chuntao Yin, Brent McCallum, Les J Szabo, Scot Hulbert, Xiaming Chen, John P Fellers
Three members of the Puccinia genus, P. triticina (Pt), P. striiformis f.sp. tritici (Pst), and P. graminis f.sp. tritici (Pgt), cause the most common and often most significant foliar diseases of wheat. While similar in biology and life cycle, each species is uniquely adapted and specialized. The genomes of Pt and Pst were sequenced and compared to that of Pgt to identify common and distinguishing gene content, to determine gene variation among wheat rust pathogens, other rust fungi and basidiomycetes, and to identify genes of significance for infection...
December 2, 2016: G3: Genes—Genomes—Genetics
https://www.readbyqxmd.com/read/27908936/genome-editing-technologies-principles-and-applications
#4
REVIEW
Thomas Gaj, Shannon J Sirk, Sai-Lan Shui, Jia Liu
Targeted nucleases have provided researchers with the ability to manipulate virtually any genomic sequence, enabling the facile creation of isogenic cell lines and animal models for the study of human disease, and promoting exciting new possibilities for human gene therapy. Here we review three foundational technologies-clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein 9 (Cas9), transcription activator-like effector nucleases (TALENs), and zinc-finger nucleases (ZFNs)...
December 1, 2016: Cold Spring Harbor Perspectives in Biology
https://www.readbyqxmd.com/read/27906829/evidence-for-cd16a-mediated-nk-cell-stimulation-in-antibody-mediated-kidney-transplant-rejection
#5
Michael D Parkes, Philip F Halloran, Luis G Hidalgo
BACKGROUND: Natural killer (NK) cells localize in the microcirculation in antibody-mediated rejection (ABMR) and have been postulated to be activated by donor-specific anti-HLA antibodies triggering their CD16a Fc receptors. However, direct evidence for NK cell CD16a triggering in ABMR is lacking. We hypothesized that CD16a-inducible NK cell-selective transcripts would be expressed in human ABMR biopsies and would offer evidence for CD16a triggering. METHODS: We stimulated human NK cells through CD16a in vitro, characterized CD16a-inducible transcripts, and studied their expression in human kidney transplant biopsies with ABMR and in an extended human cell panel to determine their selectivity...
December 1, 2016: Transplantation
https://www.readbyqxmd.com/read/27905217/to-crispr-and-beyond-the-evolution-of-genome-editing-in-stem-cells
#6
Kuang-Yui Chen, Paul S Knoepfler
The goal of editing the genomes of stem cells to generate model organisms and cell lines for genetic and biological studies has been pursued for decades. There is also exciting potential for future clinical impact in humans. While recent, rapid advances in targeted nuclease technologies have led to unprecedented accessibility and ease of gene editing, biology has benefited from past directed gene modification via homologous recombination, gene traps and other transgenic methodologies. Here we review the history of genome editing in stem cells (including via zinc finger nucleases, transcription activator-like effector nucleases and CRISPR-Cas9), discuss recent developments leading to the implementation of stem cell gene therapies in clinical trials and consider the prospects for future advances in this rapidly evolving field...
December 2016: Regenerative Medicine
https://www.readbyqxmd.com/read/27899639/histone-demethylase-phf8-promotes-epithelial-to-mesenchymal-transition-and-breast-tumorigenesis
#7
Peng Shao, Qi Liu, Peterson Kariuki Maina, Jiayue Cui, Thomas B Bair, Tiandao Li, Shaikamjad Umesalma, Weizhou Zhang, Hank Heng Qi
Histone demethylase PHF8 is upregulated and plays oncogenic roles in various cancers; however, the mechanisms underlying its dysregulation and functions in carcinogenesis remain obscure. Here, we report the novel functions of PHF8 in EMT (epithelial to mesenchymal transition) and breast cancer development. Genome-wide gene expression analysis revealed that PHF8 overexpression induces an EMT-like process, including the upregulation of SNAI1 and ZEB1. PHF8 demethylates H3K9me1, H3K9me2 and sustains H3K4me3 to prime the transcriptional activation of SNAI1 by TGF-β signaling...
November 29, 2016: Nucleic Acids Research
https://www.readbyqxmd.com/read/27899266/dna-aptamers-against-foki-nuclease-domain-for-genome-editing-applications
#8
Maui Nishio, Daisuke Matsumoto, Yoshio Kato, Koichi Abe, Jinhee Lee, Kaori Tsukakoshi, Ayana Yamagishi, Chikashi Nakamura, Kazunori Ikebukuro
Genome editing with site-specific nucleases (SSNs) can modify only the target gene and may be effective for gene therapy. The main limitation of genome editing for clinical use is off-target effects; excess SSNs in the cells and their longevity can contribute to off-target effects. Therefore, a controlled delivery system for SSNs is necessary. FokI nuclease domain (FokI) is a common DNA cleavage domain in zinc finger nuclease (ZFN) and transcription activator-like effector nuclease. Previously, we reported a zinc finger protein delivery system that combined aptamer-fused, double-strand oligonucleotides and nanoneedles...
November 22, 2016: Biosensors & Bioelectronics
https://www.readbyqxmd.com/read/27898394/mef2-transcription-factors-are-key-regulators-of-sprouting-angiogenesis
#9
Natalia Sacilotto, Kira M Chouliaras, Leonid L Nikitenko, Yao Wei Lu, Martin Fritzsche, Marsha D Wallace, Svanhild Nornes, Fernando García-Moreno, Sophie Payne, Esther Bridges, Ke Liu, Daniel Biggs, Indrika Ratnayaka, Shane P Herbert, Zoltán Molnár, Adrian L Harris, Benjamin Davies, Gareth L Bond, George Bou-Gharios, John J Schwarz, Sarah De Val
Angiogenesis, the fundamental process by which new blood vessels form from existing ones, depends on precise spatial and temporal gene expression within specific compartments of the endothelium. However, the molecular links between proangiogenic signals and downstream gene expression remain unclear. During sprouting angiogenesis, the specification of endothelial cells into the tip cells that lead new blood vessel sprouts is coordinated by vascular endothelial growth factor A (VEGFA) and Delta-like ligand 4 (Dll4)/Notch signaling and requires high levels of Notch ligand DLL4...
October 15, 2016: Genes & Development
https://www.readbyqxmd.com/read/27888407/targeting-the-rhesus-macaque-trim5%C3%AE-gene-to-enhance-the-susceptibility-of-cd4-t-cells-to-hiv-1-infection
#10
Xiaoli Wang, Qing Yu, Yahong Yuan, Zhiping Teng, Dongsheng Li, Yi Zeng
The host range of human immunodeficiency virus type 1 (HIV-1) is extremely narrow, which has hampered the establishment of non-human primate models for HIV-1 infection. The species-specific innate immune factor tripartite motif 5 alpha (TRIM5α) is a key molecule that confers potent resistance against HIV-1 infection. In this study, we targeted the TRIM5α gene of rhesus macaques (rhTRIM5α) using the transcription activator-like effector nuclease (TALEN) to study the effect on HIV-1 infection. CD4(+) T cells were separated from the peripheral blood of rhesus macaques by magnetic cell sorting, and the positive rate was greater than 99%...
November 25, 2016: Archives of Virology
https://www.readbyqxmd.com/read/27884961/therapeutic-silencing-of-fat-specific-protein-27-improves-glycemic-control-in-mouse-models-of-obesity-and-insulin-resistance
#11
Cédric Langhi, Noemí Arias, Ananthi Rajamoorthi, Jeannine Basta, Richard G Lee, Ángel Baldán
Obesity is a component of the metabolic syndrome, mechanistically linked to diabetes, fatty liver disease, and cardiovascular disease. Proteins that regulate the metabolic fate of intracellular lipid droplets are potential therapeutic candidates to treat obesity and its related consequences. CIDEC (cell death-inducing DFFA-like effector C), also known in mice as Fsp27 (fat-specific protein 27), is a lipid droplet-associated protein that prevents lipid mobilization and promotes intracellular lipid storage. The consequences of complete loss of FSP27 on hepatic metabolism and on insulin resistance are controversial, as both healthy and deleterious lipodystrophic phenotypes have been reported in Fsp27-/- mice...
November 24, 2016: Journal of Lipid Research
https://www.readbyqxmd.com/read/27883072/non-rvd-mutations-that-enhance-the-dynamics-of-the-tal-repeat-array-along-the-superhelical-axis-improve-talen-genome-editing-efficacy
#12
Naoya Tochio, Kohei Umehara, Jun-Ichi Uewaki, Holger Flechsig, Masaharu Kondo, Takehisa Dewa, Tetsushi Sakuma, Takashi Yamamoto, Takashi Saitoh, Yuichi Togashi, Shin-Ichi Tate
Transcription activator-like effector (TALE) nuclease (TALEN) is widely used as a tool in genome editing. The DNA binding part of TALEN consists of a tandem array of TAL-repeats that form a right-handed superhelix. Each TAL-repeat recognises a specific base by the repeat variable diresidue (RVD) at positions 12 and 13. TALEN comprising the TAL-repeats with periodic mutations to residues at positions 4 and 32 (non-RVD sites) in each repeat (VT-TALE) exhibits increased efficacy in genome editing compared with a counterpart without the mutations (CT-TALE)...
November 24, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27876605/role-of-zebrafish-nlrc5-in-antiviral-response-and-transcriptional-regulation-of-mhc-related-genes
#13
Xiao Man Wu, Yi Wei Hu, Na Na Xue, Shi Si Ren, Shan Nan Chen, Pin Nie, Ming Xian Chang
Intracellular NOD-like receptors (NLRs) are emerging as critical regulators of innate and adaptive immune responses. Although the NLR family member NLRC5 is functionally defined, the role of NLRC5 in regulating innate immune signaling has been controversial in mammals, and is poorly understood in teleost fish. In the present study, we report the functional characterization of zebrafish NLRC5. The cloned NLRC5 consists of 6435 bp which encodes 1746 amino acids. The N-terminal effector-binding domain of zebrafish NLRC5 is absent which is different from all other human NLRs...
November 20, 2016: Developmental and Comparative Immunology
https://www.readbyqxmd.com/read/27872906/sequence-specific-recognition-of-methylated-dna-by-an-engineered-transcription-activator-like-effector-protein
#14
Shogo Tsuji, Shiroh Futaki, Miki Imanishi
A 5mC-selective TALE-repeat was created by screening a TALE repeat library containing randomized amino acids at repeat variable diresidues and their neighboring residues. The new repeat showed high 5mC discrimination ability. An artificial TALE containing the new repeat activated an endogenous gene in a genomic methylation status-dependent manner.
December 6, 2016: Chemical Communications: Chem Comm
https://www.readbyqxmd.com/read/27855160/transcription-factors-encoded-on-core-and-accessory-chromosomes-of-fusarium-oxysporum-induce-expression-of-effector-genes
#15
H Charlotte van der Does, Like Fokkens, Ally Yang, Sarah M Schmidt, Léon Langereis, Joanna M Lukasiewicz, Timothy R Hughes, Martijn Rep
Proteins secreted by pathogens during host colonization largely determine the outcome of pathogen-host interactions and are commonly called 'effectors'. In fungal plant pathogens, coordinated transcriptional up-regulation of effector genes is a key feature of pathogenesis and effectors are often encoded in genomic regions with distinct repeat content, histone code and rate of evolution. In the tomato pathogen Fusarium oxysporum f. sp. lycopersici (Fol), effector genes reside on one of four accessory chromosomes, known as the 'pathogenicity' chromosome, which can be exchanged between strains through horizontal transfer...
November 2016: PLoS Genetics
https://www.readbyqxmd.com/read/27852650/multiparameter-functional-diversity-of-human-c2h2-zinc-finger-proteins
#16
Frank W Schmitges, Ernest Radovani, Hamed S Najafabadi, Marjan Barazandeh, Laura F Campitelli, Yimeng Yin, Arttu Jolma, Guoqing Zhong, Hongbo Guo, Tharsan Kanagalingam, Wei F Dai, Jussi Taipale, Andrew Emili, Jack F Greenblatt, Timothy R Hughes
C2H2 zinc finger proteins represent the largest and most enigmatic class of human transcription factors. Their C2H2-ZF arrays are highly variable, indicating that most will have unique DNA binding motifs. However, most of the binding motifs have not been directly determined. In addition, little is known about whether or how these proteins regulate transcription. Most of the ∼700 human C2H2-ZF proteins also contain at least one KRAB, SCAN, BTB, or SET domain, suggesting that they may have common interacting partners and/or effector functions...
November 16, 2016: Genome Research
https://www.readbyqxmd.com/read/27837487/a-tal-based-reporter-assay-for-monitoring-type-iii-dependent-protein-translocation-in-xanthomonas
#17
Sabine Drehkopf, Jens Hausner, Michael Jordan, Felix Scheibner, Ulla Bonas, Daniela Büttner
Gram-negative plant- and animal-pathogenic bacteria use type III secretion (T3S) systems to translocate effector proteins into eukaryotic host cells. Type III-dependent delivery of effector proteins depends on a secretion and translocation signal, which is often located in the N-terminal protein region and is not conserved on the amino acid level. Translocation signals in effector proteins have been experimentally confirmed by employing reporter proteins, which are specifically activated inside eukaryotic cells...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27837107/rac2-functions-in-both-neutrophils-and-macrophages-to-mediate-motility-and-host-defense-in-larval-zebrafish
#18
Emily E Rosowski, Qing Deng, Nancy P Keller, Anna Huttenlocher
Leukocyte motility is required for host defense responses. Rac-family Rho GTPases are implicated in leukocyte function; however, the distinct roles of different Rac isoforms in host defense in vivo have remained unclear. In this study, we generated Rac2-deficient zebrafish using transcription activator-like effector nucleases to directly compare the role of Rac2 in vivo in neutrophils and macrophages in motility and the response to infection. This zebrafish larval model is highly amenable to live imaging of leukocyte behavior, and we report that in rac2(-/-) larvae both neutrophils and macrophages are defective in basic motility, leading to impaired responses to localized wounds or infections...
December 15, 2016: Journal of Immunology: Official Journal of the American Association of Immunologists
https://www.readbyqxmd.com/read/27826306/transcription-activator-like-effector-nucleases-talen-mediated-targeted-dna-insertion-in-potato-plants
#19
Adrienne Forsyth, Troy Weeks, Craig Richael, Hui Duan
Targeted DNA integration into known locations in the genome has potential advantages over the random insertional events typically achieved using conventional means of genetic modification. Specifically integrated transgenes are guaranteed to co-segregate, and expression level is more predictable, which makes downstream characterization and line selection more manageable. Because the site of DNA integration is known, the steps to deregulation of transgenic crops may be simplified. Here we describe a method that combines transcription activator-like effector nuclease (TALEN)-mediated induction of double strand breaks (DSBs) and non-autonomous marker selection to insert a transgene into a pre-selected, transcriptionally active region in the potato genome...
2016: Frontiers in Plant Science
https://www.readbyqxmd.com/read/27822736/cisgenesis-and-intragenesis-in-microalgae-promising-advancements-towards-sustainable-metabolites-production
#20
REVIEW
Janeth I Galarza, Ninoska Delgado, Vitalia Henríquez
Microalgae are an economically important source of biomolecules and metabolites that can be exploited as feed, nutraceuticals and, potentially, as biofuels, among other biotechnological applications. Microalgae biotechnology involves both culture and metabolic pathways manipulation to obtain high-value products, such as omega-3 fatty acids and carotenoids. However, the introduction of genes and/or foreign regulatory sequences has caused public concern about the effect of genetically modified microalgae to achieve greater secondary metabolite accumulations...
November 7, 2016: Applied Microbiology and Biotechnology
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