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https://www.readbyqxmd.com/read/28941336/-the-new-generation-tool-for-crispr-genome-editing-crispr-cpf1
#1
Fan Yang, Yin Li
Almost all archaea and many bacteria achieve adaptive immunity through a diverse set of CRISPR-Cas systems. From 2012, Cas9 has been harnessed by thousands of laboratories for genome editing applications in a variety of experimental model systems. Cas9 is driving innovative applications from basic biology to biotechnology and medicine. However, numerous challenges still remain, such as limited targeting range, toxicity, and potential for off-target mutagenesis. Cpf1 represents a class 2/type V CRISPR RNA-guided endonuclease that is distinct from the type II CRISPR Cas9 nuclease...
March 25, 2017: Sheng Wu Gong Cheng Xue Bao, Chinese Journal of Biotechnology
https://www.readbyqxmd.com/read/28938651/positive-transcription-elongation-factor-b-p-tefb-is-a-therapeutic-target-in-human-multiple-myeloma
#2
Yu Zhang, Liang Zhou, Yun Leng, Yun Dai, Robert Z Orlowski, Steven Grant
The role of the positive RNA Pol II regulator, P-TEFb (positive transcription elongation factor b), in maintenance of the anti-apoptotic protein Mcl-1 and bortezomib (btz) resistance was investigated in human multiple myeloma (MM) cells. Mcl-1 was up-regulated in all MM lines tested, including bortezomib-resistant lines, human MM xenograft mouse models, and primary CD138(+) MM cells. Mcl-1 over-expression significantly reduced bortezomib lethality, indicating a functional role for Mcl-1 in bortezomib resistance...
August 29, 2017: Oncotarget
https://www.readbyqxmd.com/read/28937734/discovery-of-oligonucleotide-signaling-mediated-by-crispr-associated-polymerases-solves-two-puzzles-but-leaves-an-enigma
#3
Eugene V Koonin, Kira S Makarova
The signature component of type III CRISPR-Cas systems is the Cas10 protein that consists of two Palm domains homologous to those of DNA and RNA polymerases, and nucleotide cyclases, and an HD nuclease domain. However, until very recently, the activity of the Palm domains and their role in CRISPR function have not been experimentally established. Most of the type III CRISPR-Cas systems and some type I systems also encompass proteins containing the CARF (CRISPR-associated Rossmann fold) domain that has been predicted to regulate CRISPR functions via nucleotide binding but its function in CRISPR-Cas remained obscure...
September 22, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/28936671/use-of-the-cas9-orthologs-from-streptococcus-thermophilus-and-staphylococcus-aureus-for-non-homologous-end-joining-mediated-site-specific-mutagenesis-in-arabidopsis-thaliana
#4
Jeannette Steinert, Carla Schmidt, Holger Puchta
Since the discovery of the CRISPR/Cas system and its in vivo application for site-specific targeted mutagenesis, this technique is wildly used in a great variety of organisms, such as many plant species. Commonly used for this application is the Cas9 enzyme from Streptococcus pyogenes. Here, we describe the application of two Cas9 orthologs from Streptococcus thermophilus and Staphylococcus aureus for targeted non-homologous end-joining mediated mutagenesis in Arabidopsis thaliana. With both orthologs, we could show efficient inheritance of the induced mutations...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28934377/the-environmental-acinetobacter-baumannii-isolate-dsm30011-reveals-clues-into-the-preantibiotic-era-genome-diversity-virulence-potential-and-niche-range-of-a-predominant-nosocomial-pathogen
#5
Guillermo D Repizo, Alejandro M Viale, Vítor Borges, María M Cameranesi, Najwa Taib, Martín Espariz, Céline Brochier-Armanet, João Paulo Gomes, Suzana P Salcedo
Acinetobacter baumannii represents nowadays an important nosocomial opportunistic pathogen whose reservoirs outside the clinical setting are obscure. Here, we traced the origins of the collection strain A. baumannii DSM30011 to an isolate first reported in 1944, obtained from the enriched microbiota responsible of the aerobic decomposition of the resinous desert shrub guayule. Whole-genome sequencing and phylogenetic analysis based on core genes confirmed DSM30011 affiliation to A. baumannii. Comparative studies with 32 complete A...
September 1, 2017: Genome Biology and Evolution
https://www.readbyqxmd.com/read/28932209/the-mobilome-a-major-contributor-to-escherichia-coli-stx2-positive-o26-h11-strains-intra-serotype-diversity
#6
Sabine Delannoy, Patricia Mariani-Kurkdjian, Hattie E Webb, Stephane Bonacorsi, Patrick Fach
Shiga toxin-producing Escherichia coli of serotype O26:H11/H- constitute a diverse group of strains and several clones with distinct genetic characteristics have been identified and characterized. Whole genome sequencing was performed using Illumina and PacBio technologies on eight stx2-positive O26:H11 strains circulating in France. Comparative analyses of the whole genome of the stx2-positive O26:H11 strains indicate that several clones of EHEC O26:H11 are co-circulating in France. Phylogenetic analysis of the French strains together with stx2-positive and stx-negative E...
2017: Frontiers in Microbiology
https://www.readbyqxmd.com/read/28932198/progress-and-prospects-of-crispr-cas-systems-in-insects-and-other-arthropods
#7
REVIEW
Dan Sun, Zhaojiang Guo, Yong Liu, Youjun Zhang
Clustered regularly interspaced short palindromic repeats (CRISPR) and the CRISPR-associated gene Cas9 represent an invaluable system for the precise editing of genes in diverse species. The CRISPR/Cas9 system is an adaptive mechanism that enables bacteria and archaeal species to resist invading viruses and phages or plasmids. Compared with zinc finger nucleases and transcription activator-like effector nucleases, the CRISPR/Cas9 system has the advantage of requiring less time and effort. This efficient technology has been used in many species, including diverse arthropods that are relevant to agriculture, forestry, fisheries, and public health; however, there is no review that systematically summarizes its successful application in the editing of both insect and non-insect arthropod genomes...
2017: Frontiers in Physiology
https://www.readbyqxmd.com/read/28928211/the-crispr-spacer-space-is-dominated-by-sequences-from-species-specific-mobilomes
#8
Sergey A Shmakov, Vassilii Sitnik, Kira S Makarova, Yuri I Wolf, Konstantin V Severinov, Eugene V Koonin
Clustered regularly interspaced short palindromic repeats and CRISPR-associated protein (CRISPR-Cas) systems store the memory of past encounters with foreign DNA in unique spacers that are inserted between direct repeats in CRISPR arrays. For only a small fraction of the spacers, homologous sequences, called protospacers, are detectable in viral, plasmid, and microbial genomes. The rest of the spacers remain the CRISPR "dark matter." We performed a comprehensive analysis of the spacers from all CRISPR-cas loci identified in bacterial and archaeal genomes, and we found that, depending on the CRISPR-Cas subtype and the prokaryotic phylum, protospacers were detectable for 1% to about 19% of the spacers (~7% global average)...
September 19, 2017: MBio
https://www.readbyqxmd.com/read/28926145/a-crispr-reimagining-new-twists-and-turns-of-crispr-beyond-the-genome-engineering-revolution
#9
Robert J Plummer, Yi Guo, Ying Peng
Despite its explosive applications in genome engineering, CRISPR (Clustered Regularly Interspersed Short Palindromic Repeats) has been developed into a versatile tool beyond its well-known nuclease function. In this prospect article, we summarize a few exciting "off-label" applications of CRISPR including manipulating DNA sequences, visualizing chromosomal loci in living cells, and modulating transcription and chromatin structures. These novel applications will likely elevate CRISPR tools into yet another level of sophistication and diversity, leading to many more exciting cell biological discoveries...
September 19, 2017: Journal of Cellular Biochemistry
https://www.readbyqxmd.com/read/28923089/dna-epigenome-editing-using-crispr-cas-suntag-directed-dnmt3a
#10
Yung-Hsin Huang, Jianzhong Su, Yong Lei, Lorenzo Brunetti, Michael C Gundry, Xiaotian Zhang, Mira Jeong, Wei Li, Margaret A Goodell
BACKGROUND: DNA methylation has widespread effects on gene expression during development. However, our ability to assign specific function to regions of DNA methylation is limited by the poor correlation between global patterns of DNA methylation and gene expression. RESULTS: Here, we utilize nuclease-deactivated Cas9 protein fused to repetitive peptide epitopes (SunTag) recruiting multiple copies of antibody-fused de novo DNA methyltransferase 3A (DNMT3A) (dCas9-SunTag-DNMT3A) to amplify the local DNMT3A concentration to methylate genomic sites of interest...
September 18, 2017: Genome Biology
https://www.readbyqxmd.com/read/28922076/crispr-cas-technology-in-viral-therapeutics
#11
David L Woodland
No abstract text is available yet for this article.
September 18, 2017: Viral Immunology
https://www.readbyqxmd.com/read/28918056/the-therapeutic-potential-of-crispr-cas9-systems-in-oncogene-addicted-cancer-types-virally-driven-cancers-as-a-model-system
#12
REVIEW
Luqman Jubair, Nigel A J McMillan
The field of gene editing is undergoing unprecedented growth. The first ex vivo human clinical trial in China started in 2016, more than 1000 US patents have been filed, and there is exponential growth in publications. The ability to edit genes with high fidelity is promising for the development of new treatments for a range of diseases, particularly inherited conditions, infectious diseases, and cancers. For cancer, a major issue is the identification of driver mutations and oncogenes to target for therapeutic effect, and this requires the development of robust models with which to prove their efficacy...
September 15, 2017: Molecular Therapy. Nucleic Acids
https://www.readbyqxmd.com/read/28917058/lineage-tracing-of-genome-edited-alleles-reveals-high-fidelity-axolotl-limb-regeneration
#13
Grant Parker Flowers, Lucas D Sanor, Craig M Crews
Salamanders are unparalleled among tetrapods in their ability to regenerate many structures, including entire limbs, and the study of this ability may provide insights into human regenerative therapies. The complex structure of the limb poses challenges to the investigation of the cellular and molecular basis of its regeneration. Using CRISPR/Cas, we genetically labelled unique cell lineages within the developing axolotl embryo and tracked the frequency of each lineage within amputated and fully regenerated limbs...
September 16, 2017: ELife
https://www.readbyqxmd.com/read/28915012/managing-the-sos-response-for-enhanced-crispr-cas-based-recombineering-in-e-coli-through-transient-inhibition-of-host-reca-activity
#14
Eirik Adim Moreb, Benjamin Hoover, Adam Yaseen, Nisakorn Valyasevi, Zoe Roecker, Romel Menacho-Melgar, Michael Lynch
Phage-derived "recombineering" methods are utilized for bacterial genome editing. Recombineering results in a heterogeneous population of modified and unmodified chromosomes and therefore selection methods, such as CRISPR-Cas9, are required to select for edited clones. Cells can evade CRISPR-Cas-induced cell death through recA-mediated induction of the SOS response. The SOS response increases RecA dependent repair as well mutation rates through the induction of the umuDC error prone polymerase. As a result, CRISPR-Cas selection is more efficient in recA mutants...
September 15, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28913801/targeted-mutagenesis-in-hexaploid-bread-wheat-using-the-talen-and-crispr-cas-systems
#15
Yanpeng Wang, Yuan Zong, Caixia Gao
The use of sequence-specific transcription activator-like effector nucleases (TALENs) and the clustered regularly interspaced short palindromic repeats-associated system (CRISPR/Cas9) have provided powerful reverse genetic approaches to the targeted modification of genomes in numerous organisms. Both systems have been employed to generate loss-of-function alleles in bread wheat, by targeting multiple and single copies of genes. Here we present protocols for modifying the wheat genome using the two systems. The protocols include the design of TALEN and CRISPR/Cas9 target sites and their construction, evaluation of their activities in protoplasts, transformation of plants, and mutation screening...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28911114/coupling-transcriptional-activation-of-crispr-cas-system-and-dna-repair-genes-by-csa3a-in-sulfolobus-islandicus
#16
Tao Liu, Zhenzhen Liu, Qing Ye, Saifu Pan, Xiaodi Wang, Yingjun Li, Wenfang Peng, Yunxiang Liang, Qunxin She, Nan Peng
CRISPR-Cas system provides the adaptive immunity against invading genetic elements in prokaryotes. Recently, we demonstrated that Csa3a regulator mediates spacer acquisition in Sulfolobus islandicus by activating the expression of Type I-A adaptation cas genes. However, links between the activation of spacer adaptation and CRISPR transcription/processing, and the requirement for DNA repair genes during spacer acquisition remained poorly understood. Here, we demonstrated that de novo spacer acquisition required Csa1, Cas1, Cas2 and Cas4 proteins of the Sulfolobus Type I-A system...
September 6, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28910979/crispr-cas9-based-efficient-genome-editing-in-staphylococcus-aureus
#17
Qi Liu, Yu Jiang, Lei Shao, Ping Yang, Bingbing Sun, Sheng Yang, Daijie Chen
Staphylococcus aureus is an important pathogenic bacterium prevalent in nosocomial infections and associated with high morbidity and mortality rates, which arise from the significant pathogenicity and multi-drug resistance. However, the typical genetic manipulation tools used to explore the relevant molecular mechanisms of S. aureus have multiple limitations: leaving a scar in the genome, comparatively low gene-editing efficiency, and prolonged experimental period. Here, we present a single-plasmid based on the clustered regularly interspaced short palindromic repeat (CRISPR)/CRISPR-associated (Cas) system which allows rapid and efficient chromosomal manipulation in S...
September 1, 2017: Acta Biochimica et Biophysica Sinica
https://www.readbyqxmd.com/read/28910631/specialized-weaponry-how-a-type-iii-a-crispr-cas-system-excels-at-combating-phages
#18
Ole Niewoehner, Martin Jinek
CRISPR-Cas-mediated defense against phage invaders usually requires recognition of short sequences, termed protospacer-adjacent motifs (PAMs), in phage DNA. In this issue of Cell Host & Microbe, Pyenson et al. (2017) show that the lack of a PAM requirement in some CRISPR-Cas systems prevents interference evasion and facilitates phage extinction.
September 13, 2017: Cell Host & Microbe
https://www.readbyqxmd.com/read/28905415/hyperactive-mtor-induces-neuroendocrine-differentiation-in-prostate-cancer-cell-with-concurrent-up-regulation-of-irf1
#19
Mayuko Kanayama, Toshiya Hayano, Michinori Koebis, Tatsuya Maeda, Yoko Tabe, Shigeo Horie, Atsu Aiba
BACKGROUND: Neuroendocrine-differentiated prostate cancer (NEPCa) is refractory to androgen deprivation therapy and shows a poor prognosis. The underlying mechanisms responsible for neuroendocrine differentiation (NED) are yet to be clarified. In this study, we investigated the role of mammalian target of rapamycin (mTOR) in NEPCa. METHODS: We utilized a gain-of-function analysis by establishing a human PCa LNCaP stable line that expresses hyperactive mTOR (LNCaP-mTOR)...
September 14, 2017: Prostate
https://www.readbyqxmd.com/read/28900693/complete-genome-sequence-of-geobacillus-thermodenitrificans-t12-a-potential-host-for-biotechnological-applications
#20
Martinus J A Daas, Bastienne Vriesendorp, Antonius H P van de Weijer, John van der Oost, Richard van Kranenburg
In attempt to obtain a thermophilic host for the conversion of lignocellulose derived substrates into lactic acid, Geobacillus thermodenitrificans T12 was isolated from a compost heap. It was selected from over 500 isolates as a genetically tractable hemicellulolytic lactic acid producer, requiring little nutrients. The strain is able to ferment glucose and xylose simultaneously and can produce lactic acid from xylan, making it a potential host for biotechnological applications. The genome of strain T12 consists of a 3...
September 12, 2017: Current Microbiology
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