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https://www.readbyqxmd.com/read/28634160/high-throughput-characterization-of-cascade-type-i-e-crispr-guide-efficacy-reveals-unexpected-pam-diversity-and-target-sequence-preferences
#1
Becky Xu Hua Fu, Michael Wainberg, Anshul Kundaje, Andrew Z Fire
Interactions between Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) RNAs and CRISPR-associated (Cas) proteins form an RNA-guided adaptive immune system in prokaryotes. The adaptive immune system utilizes segments of the genetic material of invasive foreign elements in the CRISPR locus. The loci are transcribed and processed to produce small CRISPR RNAs (crRNAs), with degradation of invading genetic material directed by a combination of complementarity between RNA and DNA and in some cases recognition of adjacent motifs called PAMs (Protospacer Adjacent Motifs)...
June 20, 2017: Genetics
https://www.readbyqxmd.com/read/28633080/disruptive-non-disruptive-applications-of-crispr-cas9
#2
REVIEW
Jonathan L Schmid-Burgk
The bacterial type II Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-CRISPR Associated (Cas) systems, and in particular Streptococcus pyogenes CRISPR-Cas9, have been broadly applied to edit the genome of bacterial and eukaryotic cells. Cas9, which is an RNA-guided programmable nuclease, is a powerful tool for disrupting protein-coding genes. Cas9 cleaves target sites to generate a double-strand break (DSB) that is repaired via an error-prone repair process, leading to insertion/deletion mutations and gene knockouts...
June 17, 2017: Current Opinion in Biotechnology
https://www.readbyqxmd.com/read/28631377/state-of-the-art-technologies-to-explore-long-non-coding-rnas-in-cancer
#3
REVIEW
Saeede Salehi, Mohammad Naser Taheri, Negar Azarpira, Abdolhossein Zare, Abbas Behzad-Behbahani
Long non-coding RNAs (lncRNAs) comprise a vast repertoire of RNAs playing a wide variety of crucial roles in tissue physiology in a cell-specific manner. Despite being engaged in myriads of regulatory mechanisms, many lncRNAs have still remained to be assigned any functions. A constellation of experimental techniques including single-molecule RNA in situ hybridization (sm-RNA FISH), cross-linking and immunoprecipitation (CLIP), RNA interference (RNAi), Clustered regularly interspaced short palindromic repeats (CRISPR) and so forth has been employed to shed light on lncRNA cellular localization, structure, interaction networks and functions...
June 19, 2017: Journal of Cellular and Molecular Medicine
https://www.readbyqxmd.com/read/28630140/three-dimensional-structure-of-the-3-x-tail-of-hepatitis-c-virus-rna-in-monomeric-and-dimeric-states
#4
Angel Cantero-Camacho, Lixin Fan, Yun-Xing Wang, José Gallego
The 3'X domain is a 98-nucleotide region located at the 3' end of hepatitis C virus genomic RNA that plays essential functions in the viral life cycle. It contains an absolutely conserved, 16-base palindromic sequence that promotes viral RNA dimerization, overlapped with a 7-nucleotide tract implicated in a distal contact with a nearby functional sequence. Using small angle X-ray scattering measurements combined with model building guided by NMR spectroscopy, we have studied the stoichiometry, structure and flexibility of domain 3'X and two smaller subdomain sequences as a function of ionic strength, and obtained a three-dimensional view of the full-length domain in its monomeric and dimeric states...
June 19, 2017: RNA
https://www.readbyqxmd.com/read/28627488/diversity-of-veronaea-botryosa-from-different-hosts-and-evaluation-of-laboratory-challenge-models-for-phaeohyphomycosis-in-acipenser-transmontanus
#5
Esteban Soto, Christine Richey, Stephen R Reichley, Brittany Stevens, Kirsten V Kenelty, Janiee Lewis, Barbara Byrne, Nathan P Wiederhold, Thomas B Waltzek, Matthew F Sheley, Alvin C Camus, Matt J Griffin
Veronaea botryosa has been identified as a pathogen of cultured white sturgeon Acipenser transmontanus. In 2015, samples from 19 white sturgeon were received for diagnosis, of which 14 cultured positive for V. botryosa. Intraspecific variability among V. botryosa isolates from different clinically affected hosts and geographic regions was investigated using repetitive extragenic palindromic PCR fingerprinting (rep-PCR). The rep-PCR profiles of 16 V. botryosa isolates from a human, sea turtles, and cultured fish were distinct from those of other phaeoid fungi belonging to the genera Cladophialophora and Exophiala...
June 19, 2017: Diseases of Aquatic Organisms
https://www.readbyqxmd.com/read/28625564/crispr-system-in-filamentous-fungi-current-achievements-and-future-directions
#6
REVIEW
Huaxiang Deng, Ruijie Gao, Xiangru Liao, Yujie Cai
As eukaryotes, filamentous fungi share many features with humans, and they produce numerous active metabolites, some of which are toxic. Traditional genetic approaches are generally inefficient, but the clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 system that has been widely used for basic research on bacteria, mammals and plants offers a simple, fast, versatile technology for systemic research on filamentous fungi. In this review, we summarized the current knowledge on Cas9 and its variants, different ways used to detect off-target, and different approaches used to express and transform the CRISPR complex...
June 15, 2017: Gene
https://www.readbyqxmd.com/read/28624224/optimizing-the-dna-donor-template-for-homology-directed-repair-of-double-strand-breaks
#7
Fei Song, Knut Stieger
The CRISPR-Cas (clustered regularly interspaced short palindromic repeats-associated proteins) technology enables rapid and precise genome editing at any desired genomic position in almost all cells and organisms. In this study, we analyzed the impact of different repair templates on the frequency of homology-directed repair (HDR) and non-homologous end joining (NHEJ). We used a stable HEK293 cell line expressing the traffic light reporter (TLR-3) system to quantify HDR and NHEJ events following transfection with Cas9, eight different guide RNAs, and a 1,000 bp donor template generated either as circular plasmid, as linearized plasmid with long 3' or 5' backbone overhang, or as PCR product...
June 16, 2017: Molecular Therapy. Nucleic Acids
https://www.readbyqxmd.com/read/28624187/correction-of-the-exon-2-duplication-in-dmd-myoblasts-by-a-single-crispr-cas9-system
#8
Annalisa Lattanzi, Stephanie Duguez, Arianna Moiani, Araksya Izmiryan, Elena Barbon, Samia Martin, Kamel Mamchaoui, Vincent Mouly, Francesco Bernardi, Fulvio Mavilio, Matteo Bovolenta
Exonic duplications account for 10%-15% of all mutations in Duchenne muscular dystrophy (DMD), a severe hereditary neuromuscular disorder. We report a CRISPR (clustered regularly interspaced short palindromic repeat)/Cas9-based strategy to correct the most frequent (exon 2) duplication in the DMD gene by targeted deletion, and tested the efficacy of such an approach in patient-derived myogenic cells. We demonstrate restoration of wild-type dystrophin expression at transcriptional and protein level in myotubes derived from genome-edited myoblasts in the absence of selection...
June 16, 2017: Molecular Therapy. Nucleic Acids
https://www.readbyqxmd.com/read/28623876/developmental-history-and-application-of-crispr-in-human-disease
#9
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/28622433/research-on-genodermatoses-using-novel-genome-editing-tools
#10
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/28622347/rna-guided-transcriptional-activation-via-crispr-dcas9-mimics-overexpression-phenotypes-in-arabidopsis
#11
Jong-Jin Park, Emma Dempewolf, Wenzheng Zhang, Zeng-Yu Wang
Clustered regularly interspaced short palindromic repeats (CRISPR) and the CRISPR associated protein 9 (Cas9) system allows effective gene modification through RNA-guided DNA targeting. The Cas9 has undergone a series of functional alterations from the original active endonuclease to partially or completely deactivated Cas9. The catalytically deactivated Cas9 (dCas9) offers a platform to regulate transcriptional expression with the addition of activator or repressor domains. We redesigned a CRISPR/Cas9 activation system by adding the p65 transactivating subunit of NF-kappa B and a heat-shock factor 1 (HSF) activation domain to dCas9 bound with the VP64 (tetramer of VP16) activation domain for application in plants...
2017: PloS One
https://www.readbyqxmd.com/read/28620688/controlling-microbial-phb-synthesis-via-crispri
#12
Dan Li, Li Lv, Jin-Chun Chen, Guo-Qiang Chen
Microbial polyhydroxyalkanoates (PHA) are a family of biopolyesters with properties similar to petroleum plastics such as polyethylene (PE) or polypropylene (PP). Polyhydroxybutyrate (PHB) is the most common PHA known so far. Clustered regularly interspaced short palindromic repeats interference (CRISPRi), a technology recently developed to control gene expression levels in eukaryotic and prokaryotic genomes, was employed to regulate PHB synthase activity influencing PHB synthesis. Recombinant Escherichia coli harboring an operon of three PHB synthesis genes phaCAB cloned from Ralstonia eutropha, was transformed with various single guided RNA (sgRNA with its guide sequence of 20-23 bases) able to bind to various locations of the PHB synthase PhaC, respectively...
June 15, 2017: Applied Microbiology and Biotechnology
https://www.readbyqxmd.com/read/28619505/application-of-crispr-cas9-in-eye-disease
#13
REVIEW
Wenyi Wu, Luosheng Tang, Patricia A D'Amore, Hetian Lei
The system of clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated nuclease (Cas)9 is an effective instrument for revising the genome with great accuracy. This system has been widely employed to generate mutants in genomes from plants to human cells. Rapid improvements in Cas9 specificity in eukaryotic cells have opened great potential for the use of this technology as a therapeutic. Herein, we summarize the recent advancements of CRISPR-Cas9 use in research on human cells and animal models, and outline a basic and clinical pipeline for CRISPR-Cas9-based treatments of genetic eye diseases...
June 12, 2017: Experimental Eye Research
https://www.readbyqxmd.com/read/28619172/genetic-analysis-of-salmonella-enterica-serovar-gallinarum-biovar-pullorum-based-on-characterization-and-evolution-of-crispr-sequence
#14
Xiaolei Xie, Yachen Hu, Yaohui Xu, Kequan Yin, Yang Li, Yun Chen, Jie Xia, Lijuan Xu, Zijian Liu, Shizhong Geng, Qiuchun Li, Xinan Jiao, Xiang Chen, Zhiming Pan
Salmonella enterica serovar Gallinarum biovar Pullorum (S. Pullorum) is the cause of pullorum disease, characterized by white diarrhea, which leads to high mortality in poultry. In this study, we aimed to assess the genetic diversity of 655 S. Pullorum strains from 1962 to 2015 in China, Europe, and South America. A sequence typing scheme based on clustered regularly interspaced short palindromic repeats (CRISPR) was used to reveal the genetic relationships among these strains in this study. Overall, a total of 20 Pullorum sequence types (PSTs) of CRISPR were identified in the 655 isolates with PST7 (74%, 486/655) and PST3 (13%, 86/655) to be the most two frequent PSTs belonging to two different lineages, which confirmed the genetic conservation of S...
May 2017: Veterinary Microbiology
https://www.readbyqxmd.com/read/28619109/type-ii-crispr-cas9-approach-in-the-oncological-therapy
#15
REVIEW
A Biagioni, A Chillà, E Andreucci, A Laurenzana, F Margheri, S Peppicelli, M Del Rosso, G Fibbi
CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) is a prokaryotic adaptable immune mechanism used by many bacteria and archaea to protect themselves from foreign nucleic acids. This complex system can recognize and cut non-self DNA in order to provide the prokaryotic organisms a strong defense against foreign viral or plasmid attacks and make the cell immune from further assaults. Today, it has been adapted to be used in vitro and in vivo in eukaryotic cells to perform a complete and highly selective gene knockout or a specific gene editing...
June 15, 2017: Journal of Experimental & Clinical Cancer Research: CR
https://www.readbyqxmd.com/read/28619044/differing-specificities-and-isotypes-of-anti-citrullinated-peptide-protein-antibodies-in-palindromic-rheumatism-and-rheumatoid-arthritis
#16
Sonia Cabrera-Villalba, María José Gomara, Juan D Cañete, Julio Ramírez, Georgina Salvador, Virginia Ruiz-Esquide, Maria Victoria Hernández, José Inciarte-Mundo, Isabel Haro, Raimon Sanmartí
BACKGROUND: To analyze differences in the recognition of anti-citrullinated peptide/protein antibody (ACPA) citrullinated epitopes and isotypes in patients with palindromic rheumatism (PR) and rheumatoid arthritis (RA). METHODS: ACPA fine specificities (citrullinated peptides of enolase, fibrin, and vimentin) and isotypes (IgG, IgM, and IgA) were analyzed in 54 patients with longstanding PR and 54 patients with established RA. RESULTS: CCP2 tested positive in 66...
June 15, 2017: Arthritis Research & Therapy
https://www.readbyqxmd.com/read/28618222/de-novo-biosynthesis-of-glutarate-via-%C3%AE-keto-acid-carbon-chain-extension-and-decarboxylation-pathway-in-escherichia-coli
#17
Jian Wang, Yifei Wu, Xinxiao Sun, Qipeng Yuan, Yajun Yan
Microbial based bioplastics are promising alternatives to petroleum based synthetic plastics due to their renewability and economic feasibility. Glutarate is one of the most potential building blocks for bioplastics. The recent biosynthetic routes for glutarate were mostly based on the L-lysine degradation pathway from Pseudomonas putida that required lysine either by feeding or lysine overproduction via genetic manipulations. Herein, we established a novel glutarate biosynthetic pathway by incorporation of a "+1" carbon chain extension pathway from α-ketoglutarate (α-KG) in combination with α-keto acid decarboxylation pathway in Escherichia coli...
June 15, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28616968/crispri-srna-transcriptional-translational-regulation-of-extracellular-electron-transfer-in-shewanella-oneidensis
#18
Yingxiu Cao, Xiaofei Li, Feng Li, Hao Song
Extracellular electron transfer (EET) in Shewanella oneidensis MR-1, which is one of the most well-studied exoelectrogens, underlies many microbial electrocatalysis processes, including microbial fuel cells, microbial electrolysis cells, and microbial electrosynthesis. However, regulating the efficiency of EET remains challenging due to the lack of efficient genome regulation tools that regulate gene expression levels in S. oneidensis. Here, we systematically established a transcriptional regulation technology, i...
June 15, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28616376/genome-editing-and-muscle-stem-cells-as-a-therapeutic-tool-for-muscular-dystrophies
#19
REVIEW
Veronica Pini, Jennifer E Morgan, Francesco Muntoni, Helen C O'Neill
PURPOSE OF REVIEW: Muscular dystrophies are a group of severe degenerative disorders characterized by muscle fiber degeneration and death. Therapies designed to restore muscle homeostasis and to replace dying fibers are being experimented, but none of those in clinical trials are suitable to permanently address individual gene mutation. The purpose of this review is to discuss genome editing tools such as CRISPR/Cas (clustered regularly interspaced short palindromic repeats/CRISPR-associated), which enable direct sequence alteration and could potentially be adopted to correct the genetic defect leading to muscle impairment...
2017: Current Stem Cell Reports
https://www.readbyqxmd.com/read/28614576/the-hope-and-hype-of-crispr-cas9-genome-editing-a-review
#20
Kiran Musunuru
Importance: Clustered regularly interspaced short palindromic repeats (CRISPR) CRISPR-associated protein 9 (CRISPR-Cas9) has garnered a great degree of attention since its first reported uses in mammalian cells in early 2013 due to its perceived impact with respect to potential research applications and, especially, therapeutic applications. Observations: CRISPR-Cas9 is being widely used in the laboratory and has greatly improved the ability to generate genetically modified animal models of human diseases...
June 14, 2017: JAMA Cardiology
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