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clustered regularly interspaced short palindromic repeats

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https://www.readbyqxmd.com/read/28527665/therapeutic-editing-of-hepatocyte-genome-in-vivo
#1
REVIEW
Marina Ruiz de Galarreta, Amaia Lujambio
The recent development of gene editing platforms enables making precise changes in the genome of eukaryotic cells. Programmable nucleases, such as meganucleases, zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and clustered regularly interspaced short palindromic repeat (CRISPR)-associated nucleases, have revolutionized the way research is conducted as they facilitate the rapid production of mutant or knock-out cellular and animal models. These same genetic tools can potentially be applied to cure or alleviate a variety of diseases, including genetic diseases that lack an efficient therapy...
May 17, 2017: Journal of Hepatology
https://www.readbyqxmd.com/read/28527117/non-viral-and-viral-delivery-systems-for-crispr-cas9-technology-in-the-biomedical-field
#2
REVIEW
Zhi-Yao He, Ke Men, Zhou Qin, Yang Yang, Ting Xu, Yu-Quan Wei
The clustered regularly interspaced short palindromic repeats (CRISPR)-associated protein 9 (CRISPR-Cas9) system provides a novel genome editing technology that can precisely target a genomic site to disrupt or repair a specific gene. Some CRISPR-Cas9 systems from different bacteria or artificial variants have been discovered or constructed by biologists, and Cas9 nucleases and single guide RNAs (sgRNA) are the major components of the CRISPR-Cas9 system. These Cas9 systems have been extensively applied for identifying therapeutic targets, identifying gene functions, generating animal models, and developing gene therapies...
May 2, 2017: Science China. Life Sciences
https://www.readbyqxmd.com/read/28522157/antiviral-goes-viral-harnessing-crispr-cas9-to-combat-viruses-in-humans
#3
REVIEW
Jasper Adriaan Soppe, Robert Jan Lebbink
The clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated (Cas) systems are RNA-guided sequence-specific prokaryotic antiviral immune systems. In prokaryotes, small RNA molecules guide Cas effector endonucleases to invading foreign genetic elements in a sequence-dependent manner, resulting in DNA cleavage by the endonuclease upon target binding. A rewired CRISPR/Cas9 system can be used for targeted and precise genome editing in eukaryotic cells. CRISPR/Cas has also been harnessed to target human pathogenic viruses as a potential new antiviral strategy...
May 15, 2017: Trends in Microbiology
https://www.readbyqxmd.com/read/28521637/the-receptor-like-cytoplasmic-kinase-bsr1-mediates-chitin-induced-defense-signaling-in-rice-cells
#4
Yasukazu Kanda, Naoki Yokotani, Satoru Maeda, Yoko Nishizawa, Takashi Kamakura, Masaki Mori
Broad-Spectrum Resistance 1 (BSR1) encodes a rice receptor-like cytoplasmic kinase, and enhances disease resistance when overexpressed. Rice plants overexpressing BSR1 are highly resistant to diverse pathogens, including rice blast fungus. However, the mechanism responsible for this resistance has not been fully characterized. To analyze the BSR1 function, BSR1-knockout (BSR1-KO) plants were generated using a clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated protein 9 (Cas9) system...
May 18, 2017: Bioscience, Biotechnology, and Biochemistry
https://www.readbyqxmd.com/read/28515773/building-a-multipurpose-insertional-mutant-library-for-forward-and-reverse-genetics-in-chlamydomonas
#5
Xi Cheng, Gai Liu, Wenting Ke, Lijuan Zhao, Bo Lv, Xiaocui Ma, Nannan Xu, Xiaoling Xia, Xuan Deng, Chunlei Zheng, Kaiyao Huang
BACKGROUND: The unicellular green alga, Chlamydomonas reinhardtii, is a classic model for studying flagella and biofuel. However, precise gene editing, such as Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) and CRISPR-associated protein (Cas9) system, is not widely used in this organism. Screening of random insertional mutant libraries by polymerase chain reaction provides an alternate strategy to obtain null mutants of individual gene. But building, screening, and maintaining such a library was time-consuming and expensive...
2017: Plant Methods
https://www.readbyqxmd.com/read/28513735/highly-efficient-genome-editing-of-human-hematopoietic-stem-cells-via-a-nano-silicon-blade-delivery-approach
#6
Yuan Ma, Xin Han, Oscar Quintana Bustamante, Ricardo Bessa de Castro, Kai Zhang, Pengchao Zhang, Ying Li, Zongbin Liu, Xuewu Liu, Mauro Ferrari, Zhongbo Hu, José Carlos Segovia, Lidong Qin
Recently, the clustered regularly interspaced short palindromic repeats (CRISPR)-Cas9 bacterial immunity system has opened a promising avenue to treat genetic diseases that affect the human hematopoietic stem cells (HSCs). Therefore, finding a highly efficient delivery method capable of modifying the genome in the hard-to-transfect HSCs, combined with the advanced CRISPR-Cas9 system, may meet the challenges for dissecting the hematologic disease mechanisms and facilitate future clinical applications. Here, we developed an effective HSC-specified delivery microfluidic chip to disrupt the cell membrane transiently by inducing rapid mechanical deformation that allowed the delivery of biomaterials into the cytoplasm from the surrounding matrix...
May 17, 2017: Integrative Biology: Quantitative Biosciences From Nano to Macro
https://www.readbyqxmd.com/read/28508063/the-long-noncoding-rna-sprightly-acts-as-an-intranuclear-organizing-hub-for-pre-mrna-molecules
#7
Bongyong Lee, Anupama Sahoo, John Marchica, Erwin Holzhauser, Xiaoli Chen, Jian-Liang Li, Tatsuya Seki, Subramaniam Shyamala Govindarajan, Fatu Badiane Markey, Mona Batish, Sonali J Lokhande, Shaojie Zhang, Animesh Ray, Ranjan J Perera
Molecular mechanisms by which long noncoding RNA (lncRNA) molecules may influence cancerous condition are poorly understood. The aberrant expression of SPRIGHTLY lncRNA, encoded within the drosophila gene homolog Sprouty-4 intron, is correlated with a variety of cancers, including human melanomas. We demonstrate by SHAPE-seq and dChIRP that SPRIGHTLY RNA secondary structure has a core pseudoknotted domain. This lncRNA interacts with the intronic regions of six pre-mRNAs: SOX5, SMYD3, SND1, MEOX2, DCTN6, and RASAL2, all of which have cancer-related functions...
May 2017: Science Advances
https://www.readbyqxmd.com/read/28505256/crispr-cas-system-for-yeast-genome-engineering-advances-and-applications
#8
Vratislav Stovicek, Carina Holkenbrink, Irina Borodina
The methods based on the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/CRISPR-associated (Cas) system have quickly gained popularity for genome editing and transcriptional regulation in many organisms, including yeast. This review aims to provide a comprehensive overview of CRISPR application for different yeast species: from basic principles and genetic design to applications.
May 15, 2017: FEMS Yeast Research
https://www.readbyqxmd.com/read/28503441/applications-of-crispr-cas9-in-retinal-degenerative-diseases
#9
REVIEW
Ying-Qian Peng, Luo-Sheng Tang, Shigeo Yoshida, Ye-Di Zhou
Gene therapy is a potentially effective treatment for retinal degenerative diseases. Clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) system has been developed as a new genome-editing tool in ophthalmic studies. Recent advances in researches showed that CRISPR/Cas9 has been applied in generating animal models as well as gene therapy in vivo of retinitis pigmentosa (RP) and leber congenital amaurosis (LCA). It has also been shown as a potential attempt for clinic by combining with other technologies such as adeno-associated virus (AAV) and induced pluripotent stem cells (iPSCs)...
2017: International Journal of Ophthalmology
https://www.readbyqxmd.com/read/28503202/stabilization-of-foxp3-expression-by-crispr-dcas9-based-epigenome-editing-in-mouse-primary-t-cells
#10
Masahiro Okada, Mitsuhiro Kanamori, Kazue Someya, Hiroko Nakatsukasa, Akihiko Yoshimura
BACKGROUND: Epigenome editing is expected to manipulate transcription and cell fates and to elucidate the gene expression mechanisms in various cell types. For functional epigenome editing, assessing the chromatin context-dependent activity of artificial epigenetic modifier is required. RESULTS: In this study, we applied clustered regularly interspaced short palindromic repeats (CRISPR)-dCas9-based epigenome editing to mouse primary T cells, focusing on the Forkhead box P3 (Foxp3) gene locus, a master transcription factor of regulatory T cells (Tregs)...
2017: Epigenetics & Chromatin
https://www.readbyqxmd.com/read/28501380/crispri-mediated-phosphoenolpyruvate-carboxylase-regulation-to-enhance-the-production-of-lipid-in-chlamydomonas-reinhardtii
#11
Pei-Hsun Kao, I-Son Ng
In this study, CRISPRi (clustered regularly interspaced short palindromic repeats interference) was used for the first time to regulate expression of exogenously supplied rfp gene as a proof-of-concept, and endogenous PEPC1 gene as a proof-of-function in Chlamydomonas reinhardtii. The efficiency of 94% and stability of 7 generations via CRISPRi mediated gene regulation in C. reinhardtii have been demonstrated by RFP. Gene PEPC1 encoding proteins are essential for controlling the carbon flux that enters the TCA cycle and plays a crucial role in carbon partitioning of substrates in competition with lipid synthesis...
May 4, 2017: Bioresource Technology
https://www.readbyqxmd.com/read/28499063/high-efficient-multi-sites-genome-editing-in-allotetraploid-cotton-gossypium-hirsutum-using-crispr-cas9-system
#12
Pengcheng Wang, Jun Zhang, Lin Sun, Yizan Ma, Jiao Xu, Sijia Liang, Jinwu Deng, Jiafu Tan, Qinghua Zhang, Lili Tu, Henry Daniell, Shuangxia Jin, Xianlong Zhang
Gossypium hirsutum is an allotetraploid with a complex genome. Most genes have multiple copies that belong to At and Dt subgenomes. Sequence similarity is also very high between gene homologs. To efficiently achieve site/gene-specific mutation is quite needed. Due to its high efficiency and robustness, the CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)/Cas9 system has exerted broad site-specific genome editing from prokaryotes to eukaryotes. In this study, we utilized a CRISPR/Cas9 system to generate two sgRNAs in a single vector to conduct multiple sites genome editing in allotetraploid cotton...
May 12, 2017: Plant Biotechnology Journal
https://www.readbyqxmd.com/read/28497115/an-efficient-rapid-and-recyclable-system-for-crispr-mediated-genome-editing-in-candida-albicans
#13
Namkha Nguyen, Morgan M F Quail, Aaron D Hernday
Candida albicans is the most common fungal pathogen of humans. Historically, molecular genetic analysis of this important pathogen has been hampered by the lack of stable plasmids or meiotic cell division, limited selectable markers, and inefficient methods for generating gene knockouts. The recent development of clustered regularly interspaced short palindromic repeat(s) (CRISPR)-based tools for use with C. albicans has opened the door to more efficient genome editing; however, previously reported systems have specific limitations...
March 2017: MSphere
https://www.readbyqxmd.com/read/28496941/chromosomal-features-of-escherichia-coli-serotype-o2-k2-an-avian-pathogenic-e-coli
#14
Steffen L Jørgensen, Egle Kudirkiene, Lili Li, Jens P Christensen, John E Olsen, Lisa Nolan, Rikke H Olsen
Escherichia coli causing infection outside the gastrointestinal system are referred to as extra-intestinal pathogenic E. coli. Avian pathogenic E. coli is a subgroup of extra-intestinal pathogenic E. coli and infections due to avian pathogenic E. coli have major impact on poultry production economy and welfare worldwide. An almost defining characteristic of avian pathogenic E. coli is the carriage of plasmids, which may encode virulence factors and antibiotic resistance determinates. For the same reason, plasmids of avian pathogenic E...
2017: Standards in Genomic Sciences
https://www.readbyqxmd.com/read/28494568/-the-research-advances-and-applications-of-genome-editing-in-hereditary-eye-diseases
#15
S W Cai, Y Zhang, M Z Hou, Y Liu, X R Li
Genome editing is a cutting-edge technology that generates DNA double strand breaks at the specific genomic DNA sequence through nuclease recognition and cleavage, and then achieves insertion, replacement, or deletion of the target gene via endogenous DNA repair mechanisms, such as non-homologous end joining, homology directed repair, and homologous recombination. So far, more than 600 human hereditary eye diseases and systemic hereditary diseases with ocular phenotypes have been found. However, most of these diseases are of incompletely elucidated pathogenesis and without effective therapies...
May 11, 2017: [Zhonghua Yan Ke za Zhi] Chinese Journal of Ophthalmology
https://www.readbyqxmd.com/read/28493337/cas6-processes-tight-and-relaxed-repeat-rna-via-multiple-mechanisms-a-hypothesis
#16
REVIEW
Jana Sefcikova, Mitchell Roth, Ge Yu, Hong Li
RNA molecules are flexible yet foldable. Proteins must cope with this structural duality when forming biologically active complexes with RNA. Recent studies of the Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs)-mediated RNA immunity illustrate some remarkable mechanisms with which proteins interact with RNA. Currently known structures of CRISPR-Cas6 endoribonucleases bound with RNA suggest a conserved protein recognition mechanism mediated by RNA stem-loops. However, a survey of CRISPR RNA reveals that many repeats either lack a productive stem-loop (Relaxed) or possess stable but inhibitory structures (Tight), which raises the question of how the enzyme processes structurally diverse RNA...
May 11, 2017: BioEssays: News and Reviews in Molecular, Cellular and Developmental Biology
https://www.readbyqxmd.com/read/28493126/application-of-crispr-cas9-genome-editing-to-improve-recombinant-protein-production-in-cho-cells
#17
Lise Marie Grav, Karen Julie la Cour Karottki, Jae Seong Lee, Helene Faustrup Kildegaard
Genome editing has become an increasingly important aspect of Chinese Hamster Ovary (CHO ) cell line engineering for improving production of recombinant protein therapeutics. Currently, the focus is directed toward expanding the product diversity, controlling and improving product quality and yields. In this chapter, we present our protocol on how to use the genome editing tool Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR)/CRISPR-associated protein 9 (Cas9) to knockout engineering target genes in CHO cells...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28489428/a-single-molecule-view-of-genome-editing-proteins-biophysical-mechanisms-for-tales-and-crispr-cas9
#18
Luke Cuculis, Charles M Schroeder
Exciting new advances in genome engineering have unlocked the potential to radically alter the treatment of human disease. In this review, we discuss the application of single-molecule techniques to uncover the mechanisms behind two premier classes of genome editing proteins: transcription activator-like effector nucleases (TALENs) and the clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated system (Cas). These technologies have facilitated a striking number of gene editing applications in a variety of organisms; however, we are only beginning to understand the molecular mechanisms governing the DNA editing properties of these systems...
May 10, 2017: Annual Review of Chemical and Biomolecular Engineering
https://www.readbyqxmd.com/read/28487442/crispr-cas9-at-the-cutting-edge-of-hepatology
#19
REVIEW
Francis P Pankowicz, Kelsey E Jarrett, William R Lagor, Karl-Dimiter Bissig
Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/Cas9 genome engineering has revolutionised biomedical science and we are standing on the cusp of medical transformation. The therapeutic potential of this technology is tremendous, however, its translation to the clinic will be challenging. In this article, we review recent progress using this genome editing technology and explore its potential uses in studying and treating diseases of the liver. We discuss the development of new research tools and animal models as well as potential clinical applications, strategies and challenges...
May 9, 2017: Gut
https://www.readbyqxmd.com/read/28487431/different-roles-of-mitochondrial-calcium-uniporter-complex-subunits-in-growth-and-infectivity-of-trypanosoma-cruzi
#20
Miguel A Chiurillo, Noelia Lander, Mayara S Bertolini, Melissa Storey, Anibal E Vercesi, Roberto Docampo
Trypanosoma cruzi is the agent of Chagas disease, and the finding that this parasite possesses a mitochondrial calcium uniporter (TcMCU) with characteristics similar to that of mammalian mitochondria was fundamental for the discovery of the molecular nature of MCU in eukaryotes. We report here that ablation of TcMCU, or its paralog TcMCUb, by clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9 led to a marked decrease in mitochondrial Ca(2+) uptake without affecting the membrane potential of these cells, whereas overexpression of each gene caused a significant increase in the ability of mitochondria to accumulate Ca(2+) While TcMCU-knockout (KO) epimastigotes were viable and able to differentiate into trypomastigotes, infect host cells, and replicate normally, ablation of TcMCUb resulted in epimastigotes having an important growth defect, lower rates of respiration and metacyclogenesis, more pronounced autophagy changes under starvation, and significantly reduced infectivity...
May 9, 2017: MBio
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