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Transcription activator-like effectors

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https://www.readbyqxmd.com/read/28643257/genome-editing-mediated-by-primordial-germ-cell-in-chicken
#1
Jae Yong Han, Hong Jo Lee
Rapid development of genome editing technology has facilitated the studies on exploring specific gene functions and establishment of model animals. In livestock, the technology has contributed to create high value in industry fields, e.g., enhancing productivity or acquiring the resistance against disease. Meanwhile, genome editing in avian species has been emphasized because of their applicable possibilities in terms of highly productive chickens, disease-controlled avian lines, and development of novel biological models...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28643253/genome-editing-of-rat
#2
Takehito Kaneko
Many genetically engineered rat strains have been produced for biomedical research. The simple and quick production of knock-out and knock-in rats is currently possible using genome editing techniques incorporating zinc finger nuclease (ZFN), transcription activator-like effector nuclease (TALEN), or clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9. Genome-edited animals have been produced by the introduction of endonucleases into embryos using conventional microinjection and a new electroporation method named Technique for Animal Knockout system by Electroporation (TAKE)...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28643251/genome-editing-in-mouse-and-rat-by-electroporation
#3
Takehito Kaneko
Many knock-out/knock-in mouse and rat strains have been produced by genome editing techniques using engineered endonucleases, including zinc finger nuclease (ZFN), transcription activator-like effector nuclease (TALEN), or clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9. Microinjection of engineered endonucleases into pronuclear-stage embryos is required to produce genome-edited rodents and the development of easy, rapid, and high-efficiency methods that do not require special skills such as microinjection is needed...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28643246/current-overview-of-talen-construction-systems
#4
Tetsushi Sakuma, Takashi Yamamoto
Transcription activator-like effector (TALE) nuclease (TALEN) is the second-generation genome editing tool consisting of TALE protein containing customizable DNA-binding repeats and nuclease domain of FokI enzyme. Each DNA-binding repeat recognizes one base of double-strand DNA, and functional TALEN can be created by a simple modular assembly of these repeats. To easily and efficiently assemble the highly repetitive DNA-binding repeat arrays, various construction systems such as Golden Gate assembly, serial ligation, and ligation-independent cloning have been reported...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28642062/lrh-1-senses-signaling-from-phosphatidylcholine-to-regulate-the-expansion-growth-of-digestive-organs-via-synergy-with-wnt-%C3%AE-catenin-signaling-in-zebrafish
#5
Gang Zhai, Jia Song, Tingting Shu, Junjun Yan, Xia Jin, Jiangyan He, Zhan Yin
Liver receptor homolog-1 (LRH-1) is an orphan nuclear receptor that is critical for the growth and proliferation of cancer cells and other biological processes, including lipid transportation and metabolism, sexual determination and steroidogenesis. However, because homozygous lrh-1(-/-) mice die in utero, the regulatory mechanisms involved in embryonic development mediated by this receptor are poorly understood. In the present study, we performed transcription activator-like effector nuclease (TALEN)-mediated loss-of-function assays, taking advantage of zebrafish external fertilization, to investigate the function of lrh-1...
April 27, 2017: Journal of Genetics and Genomics, Yi Chuan Xue Bao
https://www.readbyqxmd.com/read/28639422/medaka-and-zebrafish-contactin1-mutants-as-a-model-for-understanding-neural-circuits-for-motor-coordination
#6
Miki Takeuchi, Chikako Inoue, Akiko Goshima, Yusuke Nagao, Koichi Shimizu, Hiroki Miyamoto, Takashi Shimizu, Hisashi Hashimoto, Shigenobu Yonemura, Atsuo Kawahara, Yutaka Hirata, Masayuki Yoshida, Masahiko Hibi
A spontaneous medaka ro mutant shows abnormal wobbling and rolling swimming behaviors. By positional cloning, we mapped the ro locus to a region containing the gene encoding Contactin1b (Cntn1b), which is an immunoglobulin (Ig)-superfamily domain-containing membrane-anchored protein. The ro mutant had a deletion in the cntn1b gene that introduced a premature stop codon. Furthermore, cntn1b mutants generated by the CRISPR/Cas9 system and trans-heterozygotes of the CRISPR mutant allele and ro had abnormal swimming behavior, indicating that the cntn1b gene was responsible for the ro-mutant phenotype...
June 22, 2017: Genes to Cells: Devoted to Molecular & Cellular Mechanisms
https://www.readbyqxmd.com/read/28637323/evolution-of-transcription-activator-like-effectors-in-xanthomonas-oryzae
#7
Annett Erkes, Maik Reschke, Jens Boch, Jan Grau
Transcription activator-like effectors (TALEs) are secreted by plant-pathogenic Xanthomonas bacteria into plant cells where they act as transcriptional activators and, hence, are major drivers in reprogramming the plant for the benefit of the pathogen. TALEs possess a highly repetitive DNA-binding domain of typically 34 amino acid tandem repeats, where amino acid 12 and 13, termed repeat variable di-residue (RVD), determine target specificity. Different Xanthomonas strains possess different repertoires of TALEs...
June 14, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28628927/curcumin-promotes-apoptosis-of-activated-hepatic-stellate-cells-by-inhibiting-protein-expression-of-the-myd88-pathway
#8
Ya-Jun He, Kenny Kuchta, Yan-Mei Deng, Silke Cameron, Yu Lin, Xu-You Liu, Guo-Ron Ye, Xia Lv, Yuta Kobayashi, Jian-Chang Shu
Activation and proliferation of hepatic stellate cells (HSC) play an important role in the progress of liver fibrosis. HSC activation occurs in response to inflammatory cytokines, cellular interactions with immune cells, and morphogenetic signals. The literature hints to a role of the adaptor protein MyD88 in fibrosis. Although curcumin has been shown to exert inhibitory effects on the proliferation of HSC in vitro, its influence on the MyD88 pathway in HSC has remained unclear. Here, we investigated whether curcumin accelerates apoptosis of HSC through the MyD88 pathway...
June 19, 2017: Planta Medica
https://www.readbyqxmd.com/read/28625977/p300-mediated-acetylation-of-the-notch-effector-transcription-factor-maml-1-recruits-nack-to-initiate-notch-dependent-transcription
#9
Ke Jin, Wen Zhou, Xiaoqing Han, Zhiqiang Wang, Bin Li, Shawn Jeffries, Wensi Tao, David J Robbins, Anthony J Capobianco
Although it has long been appreciated that p300 acts as a critical Notch coactivator, the mechanistic details of p300 in Notch-mediated transcription remain unclear. We previously demonstrated that PEAK1-related kinase activating pseudokinase 1 (NACK) is a critical co-activator of Notch signaling and binds to the Notch1 ternary complex. Herein we report that p300 and CBP acetylate mastermind-like transcriptional coactivator 1 (Maml1) on amino acid residues K188 and K189 to recruit NACK to the Notch1 ternary complex, which results in the recruitment of RNA polymerase II to initiate transcription...
June 16, 2017: Cancer Research
https://www.readbyqxmd.com/read/28623876/developmental-history-and-application-of-crispr-in-human-disease
#10
REVIEW
Puping Liang, Xiya Zhang, Yuxi Chen, Junjiu Huang
Genome editing tools are programmable artificial nucleases, mainly including zinc-finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs) and clustered regularly interspaced short palindromic repeat (CRISPR). By recognizing and cleaving specific DNA sequences, genome editing tools make it possible to generate site-specific DNA double-strand breaks (DSBs) in the genome. DSBs will then be repaired by either error-prone non-homologous end joining (NHEJ) or high-fidelity homologous recombination (HR) mechanisms...
June 17, 2017: Journal of Gene Medicine
https://www.readbyqxmd.com/read/28623587/generation-of-dtales-and-libraries-of-synthetic-tale-activated-promoters-for-engineering-of-gene-regulatory-networks-in-plants
#11
Tom Schreiber, Alain Tissier
Transcription factors with programmable DNA-binding specificity constitute valuable tools for the design of orthogonal gene regulatory networks for synthetic biology. Transcription activator-like effectors (TALEs), as natural transcription regulators, were used to design, build, and test libraries of synthetic TALE-activated promoters (STAPs) that show a broad range of expression levels in plants. In this chapter, we present protocols for the construction of artificial TALEs and corresponding STAPs.
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28622433/research-on-genodermatoses-using-novel-genome-editing-tools
#12
REVIEW
Janin Lehmann, Christina Seebode, Steffen Emmert
Genodermatoses comprise a clinically heterogeneous group of mostly devastating disorders affecting the skin. To date, treatment options have in general been limited to symptom relief. However, the recent technical evolution in genome editing has ushered in a new era in the development of causal therapies for rare monogenetic diseases such as genodermatoses. The present review revisits the advantages and drawbacks of engineered nuclease tools currently available: zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), meganucleases, and - the most innovative - clustered regularly interspaced short palindromic repeats (CRISPR)-associated (Cas) nuclease 9 (CRISPR/Cas9) system...
June 16, 2017: Journal der Deutschen Dermatologischen Gesellschaft, Journal of the German Society of Dermatology: JDDG
https://www.readbyqxmd.com/read/28617832/a-tale-inspired-computational-screen-for-proteins-that-contain-approximate-tandem-repeats
#13
Malgorzata Perycz, Joanna Krwawicz, Matthias Bochtler
TAL (transcription activator-like) effectors (TALEs) are bacterial proteins that are secreted from bacteria to plant cells to act as transcriptional activators. TALEs and related proteins (RipTALs, BurrH, MOrTL1 and MOrTL2) contain approximate tandem repeats that differ in conserved positions that define specificity. Using PERL, we screened ~47 million protein sequences for TALE-like architecture characterized by approximate tandem repeats (between 30 and 43 amino acids in length) and sequence variability in conserved positions, without requiring sequence similarity to TALEs...
2017: PloS One
https://www.readbyqxmd.com/read/28605407/recent-advances-in-functional-perturbation-and-genome-editing-techniques-in-studying-sea-urchin-development
#14
Miao Cui, Che-Yi Lin, Yi-Hsien Su
Studies on the gene regulatory networks (GRNs) of sea urchin embryos have provided a basic understanding of the molecular mechanisms controlling animal development. The causal links in GRNs have been verified experimentally through perturbation of gene functions. Microinjection of antisense morpholino oligonucleotides (MOs) into the egg is the most widely used approach for gene knockdown in sea urchin embryos. The modification of MOs into a membrane-permeable form (vivo-MOs) has allowed gene knockdown at later developmental stages...
June 12, 2017: Briefings in Functional Genomics
https://www.readbyqxmd.com/read/28601904/disease-modeling-in-genetic-kidney-diseases-mice
#15
REVIEW
Andreas F Hofmeister, Martin Kömhoff, Stefanie Weber, Ivica Grgic
The mouse still represents arguably the most important mammal organism in research for modeling human genetic kidney diseases in vivo. Compared with many other mammal species, the breeding and maintenance of mice in the laboratory is relatively simple and cheap and reproduction cycles are short. In addition to classic gene knockout mouse lines, new molecular biological technologies have led to the development of a plethora of other, more sophisticated, mouse models, allowing the targeting of genes or gene function in a cell-specific, tissue-specific and time-dependent fashion...
July 2017: Cell and Tissue Research
https://www.readbyqxmd.com/read/28591671/mille-viae-in-eukaryotic-mrna-decapping
#16
REVIEW
Eugene Valkov, Stefanie Jonas, Oliver Weichenrieder
Cellular mRNA levels are regulated via rates of transcription and decay. Since the removal of the mRNA 5'-cap by the decapping enzyme DCP2 is generally an irreversible step towards decay, it requires regulation. Control of DCP2 activity is likely effected by two interdependent means: by conformational control of the DCP2-DCP1 complex, and by assembly control of the decapping network, an array of mutually interacting effector proteins. Here, we compare three recent and conformationally distinct crystal structures of the DCP2-DCP1 decapping complex in the presence of substrate analogs and decapping enhancers and we discuss alternative substrate recognition modes for the catalytic domain of DCP2...
June 4, 2017: Current Opinion in Structural Biology
https://www.readbyqxmd.com/read/28590408/tdrd12-is-essential-for-germ-cell-development-and-maintenance-in-zebrafish
#17
Xiangyan Dai, Yuqin Shu, Qiyong Lou, Qiang Tian, Gang Zhai, Jia Song, Suxiang Lu, Hong Yu, Jiangyan He, Zhan Yin
The regularity of Piwi-interacting RNA (piRNA) biogenesis is crucial to germline development. Functioning as Piwi-interacting proteins, Tudor domain-related proteins (Tdrds) have been demonstrated to be involved in spermatogenesis and the piRNA pathway. In this study, zebrafish tdrd12 was identified, and the maternal and germ cell-specific expression patterns of zebrafish tdrd12 were observed. Utilizing TALEN (transcription activator-like effector nuclease) techniques, two independent tdrd12 mutant zebrafish lines were generated...
June 7, 2017: International Journal of Molecular Sciences
https://www.readbyqxmd.com/read/28589393/a-history-of-genome-editing-in-mammals
#18
Almudena Fernández, Santiago Josa, Lluis Montoliu
Genome editing is now a routine procedure in many mammalian genetics laboratories. The ostensibly short but intense history of genome-editing approaches illustrates how a disruptive technology can universally colonize a field when this new methodology, conceived to alter mammalian genomes at specific locations, is found to efficiently and robustly deliver results. This review summarizes the early development of genome editing using nucleases, from the pioneering experiments using yeast meganucleases, to the latest prokaryotic nucleases used for precise genome manipulation...
June 6, 2017: Mammalian Genome: Official Journal of the International Mammalian Genome Society
https://www.readbyqxmd.com/read/28585817/production-of-medium-chain-fatty-acids-by-yarrowia-lipolytica-combining-molecular-design-and-talen-to-engineer-the-fatty-acid-synthase
#19
Coraline Rigouin, Marc Gueroult, Christian Croux, Gwendoline Dubois, Vinciane Borsenberger, Sophie Barbe, Alain Marty, Fayza Daboussi, Isabelle André, Florence Bordes
Yarrowia lipolytica is a promising organism for the production of lipids of biotechnological interest and particularly for biofuel. In this study, we engineered the key enzyme involved in lipid biosynthesis, the giant multifunctional fatty acid synthase (FAS), to shorten chain length of the synthesized fatty acids. Taking as starting point that the ketoacyl synthase (KS) domain of Yarrowia lipolytica FAS is directly involved in chain length specificity, we used molecular modeling to investigate molecular recognition of palmitic acid (C16 fatty acid) by the KS...
June 21, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28585197/human-protein-kinases-and-obesity
#20
Atilla Engin
The action of protein kinases and protein phosphatases is essential for multiple physiological responses. Each protein kinase displays its own unique substrate specificity, and a regulatory mechanism that may be modulated by association with other proteins. Protein kinases are classified by the target amino acid in their substrates. Some protein kinases can phosphorylate both serine/threonine, as well as tyrosine residues. This group of kinases has been known as dual specificity kinases. Unlike the dual specificity kinases, a heterogeneous group of protein phosphatases are known as dual-specificity phosphatases...
2017: Advances in Experimental Medicine and Biology
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