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https://www.readbyqxmd.com/read/29112372/tuning-the-color-palette-of-fluorescent-copper-sensors-through-systematic-heteroatom-substitution-at-rhodol-cores
#1
Shang Jia, Karla M Ramos-Torres, Safacan Kolemen, Cheri M Ackerman, Christopher J Chang
Copper is an essential nutrient for sustaining life, and emerging data have expanded the roles of this metal in biology from its canonical functions as a static enzyme cofactor to dynamic functions as a transition metal signal. At the same time, loosely bound, labile copper pools can trigger oxidative stress and damaging events that are detrimental if misregulated. The signal/stress dichotomy of copper motivates the development of new chemical tools to study its spatial and temporal distributions in native biological contexts such as living cells...
November 7, 2017: ACS Chemical Biology
https://www.readbyqxmd.com/read/29106617/fncpf1-a-novel-and-efficient-genome-editing-tool-for-saccharomyces-cerevisiae
#2
Michal A Swiat, Sofia Dashko, Maxime den Ridder, Melanie Wijsman, John van der Oost, Jean-Marc Daran, Pascale Daran-Lapujade
Cpf1 is a new class II family of CRISPR-Cas RNA-programmable endonucleases with unique features that make it a very attractive alternative or complement to Cas9 for genome engineering. Using constitutively expressed Cpf1 from Francisella novicida, the present study demonstrates that FnCpf1 can mediate RNA-guided DNA cleavage at targeted genomic loci in the popular model and industrial yeast Saccharomyces cerevisiae. FnCpf1 very efficiently and precisely promoted repair DNA recombination with efficiencies up to 100%...
November 2, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/29083402/inducible-and-multiplex-gene-regulation-using-crispr-cpf1-based-transcription-factors
#3
Y Esther Tak, Benjamin P Kleinstiver, James K Nuñez, Jonathan Y Hsu, Joy E Horng, Jingyi Gong, Jonathan S Weissman, J Keith Joung
Targeted and inducible regulation of mammalian gene expression is a broadly important capability. We engineered drug-inducible catalytically inactive Cpf1 nuclease fused to transcriptional activation domains to tune the expression of endogenous genes in human cells. Leveraging the multiplex capability of the Cpf1 platform, we demonstrate both synergistic and combinatorial gene expression in human cells. Our work should enable the development of multiplex gene perturbation library screens for understanding complex cellular phenotypes...
October 30, 2017: Nature Methods
https://www.readbyqxmd.com/read/29083112/immunity-to-crispr-cas9-and-cas12a-therapeutics
#4
REVIEW
Wei Leong Chew
Genome-editing therapeutics are poised to treat human diseases. As we enter clinical trials with the most promising CRISPR-Cas9 and CRISPR-Cas12a (Cpf1) modalities, the risks associated with administering these foreign biomolecules into human patients become increasingly salient. Preclinical discovery with CRISPR-Cas9 and CRISPR-Cas12a systems and foundational gene therapy studies indicate that the host immune system can mount undesired responses against the administered proteins and nucleic acids, the gene-edited cells, and the host itself...
October 30, 2017: Wiley Interdisciplinary Reviews. Systems Biology and Medicine
https://www.readbyqxmd.com/read/29082718/-recent-progresses-in-crispr-genome-editing-in-plants
#5
Hong Li, Kabin Xie
In the past 4 years, CRISPR/Cas9-mediated genome editing becomes the revolutionary tool in life sciences. This tool enables us to edit plant genes with unprecedented throughput, scalability, speed and low cost. In addition to targeted knock-in and knock-out applications, CRISPR/Cas9 also provides an efficient platform for targeted gene activation and suppression. At the same time, accuracy, capacity and efficiency of CRISPR/Cas9 genome editing have been improved for sophisticated genetic manipulation. Furthermore, the genome editing toolbox is expanded by new technologies like CRISPR/Cpf1-mediated genome editing and single base editing...
October 25, 2017: Sheng Wu Gong Cheng Xue Bao, Chinese Journal of Biotechnology
https://www.readbyqxmd.com/read/29035385/class-2-crispr-cas-rna-guided-endonucleases-swiss-army-knives-of-genome-editing
#6
REVIEW
Stefano Stella, Pablo Alcón, Guillermo Montoya
CRISPR-Cas is a bacterial defense system against phage infection and nucleic acid invasion. Class 2 type II CRISPR-Cas9 has also been widely used for genome engineering. Here, we review novel insights into the CRISPR class 2 type V enzymes, specifically Cpf1 and C2c1, which display different DNA-recognition and cleavage characteristics than those of Cas9, the best-characterized member of class 2. Recent structures of these ribonucleoprotein complexes that capture several stages of the endonuclease reaction have provided molecular details of recognition, unzipping and cleavage of the target DNA, allowing their comparison with Cas9...
November 2017: Nature Structural & Molecular Biology
https://www.readbyqxmd.com/read/29016997/the-influence-of-a-cryptochrome-on-the-gene-expression-profile-in-the-diatom-phaeodactylum-tricornutum-under-blue-light-and-in-darkness
#7
Sarah König, Marion Eisenhut, Andrea Bräutigam, Samantha Kurz, Andreas P M Weber, Claudia Büchel
Diatoms, albeit being only distantly related with higher plants, harbor a plant-like cryptochrome (CryP) that was proposed to act as a photoreceptor required for the regulation of some photosynthetic proteins. Plant cryptochromes are involved in the regulation of developmental processes relevant only to multicellular organisms. Their role in the unicellular diatoms to date is mostly enigmatic. To elucidate the function of this plant-like cryptochrome in a unicellular species, we examined the role of CryP in the regulation of transcription in the diatom Phaeodactylum tricornutum by comparative RNA-seq of wild type and CryP knock-down mutants, under prolonged darkness and one hour after onset of blue light...
November 1, 2017: Plant & Cell Physiology
https://www.readbyqxmd.com/read/28977650/a-new-lease-of-life-fncpf1-possesses-dna-cleavage-activity-for-genome-editing-in-human-cells
#8
Mengjun Tu, Li Lin, Yilu Cheng, Xiubin He, Huihui Sun, Haihua Xie, Junhao Fu, Changbao Liu, Jin Li, Ding Chen, Haitao Xi, Dongyu Xue, Qi Liu, Junzhao Zhao, Caixia Gao, Zongming Song, Jia Qu, Feng Gu
Cpf1 nucleases were recently reported to be highly specific and programmable nucleases with efficiencies comparable to those of SpCas9. AsCpf1 and LbCpf1 require a single crRNA and recognize a 5'-TTTN-3' protospacer adjacent motif (PAM) at the 5' end of the protospacer for genome editing. For widespread application in precision site-specific human genome editing, the range of sequences that AsCpf1 and LbCpf1 can recognize is limited due to the size of this PAM. To address this limitation, we sought to identify a novel Cpf1 nuclease with simpler PAM requirements...
September 7, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28976642/enhanced-genome-editing-tools-for-multi-gene-deletion-knock-out-approaches-using-paired-crispr-sgrnas-in-cho-cells
#9
Valerie Schmieder, Nina Bydlinski, Richard Strasser, Martina Baumann, Helene Faustrup Kildegaard, Vaibhav Jadhav, Nicole Borth
Since the establishment of clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9, powerful strategies for engineering of CHO cell lines have emerged. Nevertheless, there is still room to expand the scope of the CRISPR tool box for further applications to improve CHO cell factories. Here, we demonstrate activity of the alternative CRISPR endonuclease Cpf1 in CHO-K1 for the first time and that it can be used in parallel to CRISPR/Cas9 without any interference. Both, Cas9 and Cpf1, can be effectively used for multi-gene engineering with a strategy based on paired single guide RNAs (sgRNAs) for full gene deletions...
October 4, 2017: Biotechnology Journal
https://www.readbyqxmd.com/read/28941336/-the-new-generation-tool-for-crispr-genome-editing-crispr-cpf1
#10
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/28932198/progress-and-prospects-of-crispr-cas-systems-in-insects-and-other-arthropods
#11
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/28918044/targeted-disruption-of-v600e-mutant-braf-gene-by-crispr-cpf1
#12
Meijia Yang, Heng Wei, Yuelong Wang, Jiaojiao Deng, Yani Tang, Liangxue Zhou, Gang Guo, Aiping Tong
BRAF-V600E (1799T > A) is one of the most frequently reported driver mutations in multiple types of cancers, and patients with such mutations could benefit from selectively inactivating the mutant allele. Near this mutation site, there are two TTTN and one NGG protospacer-adjacent motifs (PAMs) for Cpf1 and Cas9 CRISPR nucleases, respectively. The 1799T > A substitution also leads to the occurrence of a novel NGNG PAM for the EQR variant of Cas9. We examined the editing efficacy and selectivity of Cpf1, Cas9, and EQR variant to this mutation site...
September 15, 2017: Molecular Therapy. Nucleic Acids
https://www.readbyqxmd.com/read/28912524/precise-insertion-and-guided-editing-of-higher-plant-genomes-using-cpf1-crispr-nucleases
#13
Matthew B Begemann, Benjamin N Gray, Emma January, Gina C Gordon, Yonghua He, Haijun Liu, Xingrong Wu, Thomas P Brutnell, Todd C Mockler, Mohammed Oufattole
Precise genome editing of plants has the potential to reshape global agriculture through the targeted engineering of endogenous pathways or the introduction of new traits. To develop a CRISPR nuclease-based platform that would enable higher efficiencies of precise gene insertion or replacement, we screened the Cpf1 nucleases from Francisella novicida and Lachnospiraceae bacterium ND2006 for their capability to induce targeted gene insertion via homology directed repair. Both nucleases, in the presence of a guide RNA and repairing DNA template flanked by homology DNA fragments to the target site, were demonstrated to generate precise gene insertions as well as indel mutations at the target site in the rice genome...
September 14, 2017: Scientific Reports
https://www.readbyqxmd.com/read/28886218/crispr-cpf1-enables-fast-and-simple-genome-editing-of-saccharomyces-cerevisiae
#14
René Verwaal, Nathalie Buiting-Wiessenhaan, Sacha Dalhuijsen, Johannes A Roubos
Cpf1 represents a novel single RNA-guided CRISPR/Cas endonuclease system suitable for genome editing with distinct features compared to Cas9. We demonstrate the functionality of three Cpf1 orthologues - Acidaminococcus spp. BV3L6 (AsCpf1), Lachnospiraceae bacterium ND2006 (LbCpf1), Francisella novicida U112 (FnCpf1) - for genome editing of Saccharomyces cerevisiae. These Cpf1-based systems enable fast and reliable introduction of donor DNA on the genome using a two plasmid-based editing approach together with linear donor DNA...
September 8, 2017: Yeast
https://www.readbyqxmd.com/read/28840077/engineering-crispr-cpf1-crrnas-and-mrnas-to-maximize-genome-editing-efficiency
#15
Bin Li, Weiyu Zhao, Xiao Luo, Xinfu Zhang, Chenglong Li, Chunxi Zeng, Yizhou Dong
Cpf1, a type-V CRISPR-Cas effector endonuclease, exhibits gene-editing activity in human cells through a single RNA-guided approach. Here, we report the design and assessment of an array of 42 types of engineered Acidaminococcus sp. Cpf1 (AsCpf1) CRISPR RNAs (crRNAs) and 5 types of AsCpf1 mRNAs, and show that the top-performing modified crRNA (cr3'5F, containing five 2'-fluoro ribose at the 3' termini) and AsCpf1 mRNA (full ψ-modification) improved gene-cutting efficiency by, respectively, 127% and 177%, with respect to unmodified crRNA and plasmid-encoding AsCpf1...
May 2017: Nature biomedical engineering
https://www.readbyqxmd.com/read/28781234/structural-basis-for-the-canonical-and-non-canonical-pam-recognition-by-crispr-cpf1
#16
Takashi Yamano, Bernd Zetsche, Ryuichiro Ishitani, Feng Zhang, Hiroshi Nishimasu, Osamu Nureki
The RNA-guided Cpf1 (also known as Cas12a) nuclease associates with a CRISPR RNA (crRNA) and cleaves the double-stranded DNA target complementary to the crRNA guide. The two Cpf1 orthologs from Acidaminococcus sp. (AsCpf1) and Lachnospiraceae bacterium (LbCpf1) have been harnessed for eukaryotic genome editing. Cpf1 requires a specific nucleotide sequence, called a protospacer adjacent motif (PAM), for target recognition. Besides the canonical TTTV PAM, Cpf1 recognizes suboptimal C-containing PAMs. Here, we report four crystal structures of LbCpf1 in complex with the crRNA and its target DNA containing either TTTA, TCTA, TCCA, or CCCA as the PAM...
August 17, 2017: Molecular Cell
https://www.readbyqxmd.com/read/28720252/the-cryptochrome-photolyase-protein-family-in-diatoms
#17
REVIEW
Sarah König, Matthias Juhas, Stefanie Jäger, Tilman Kottke, Claudia Büchel
The cryptochrome - photolyase family (CPF) consists of homologous flavoproteins having completely different functions involving DNA repair, circadian rhythm and/or photoreception. From the original photolyases, working either as (6-4) or cyclobutane pyrimidine dimer photolyases, the animal- and plant-type cryptochromes, respectively, evolved and also the more intermediate DASH cryptochromes. Whereas animal cryptochromes work mostly in clock-related functions, plant cryptochromes are also directly involved in developmental processes such as hypocotyl elongation or flower induction...
July 8, 2017: Journal of Plant Physiology
https://www.readbyqxmd.com/read/28712502/gene-editing-with-talen-and-crispr-cas-in-rice
#18
Honghao Bi, Bing Yang
Engineered, site-specific nucleases induce genomic double-strand DNA breaks and break repair processes enable genome editing in a plethora of eukaryotic genomes. TALENs (transcription activator-like effector nucleases) and CRISPR/Cas (clustered regularly interspaced short palindromic repeats and CRISPR-associated proteins) are potent biotechnological tools used for genome editing. In rice, species-tailored editing tools have proven to be efficient and easy to use. Both tools are capable of generating DNA double-strand breaks (DSBs) in vivo and such breaks can be repaired either by error-prone NHEJ (nonhomologous end joining) that leads to nucleotide insertions or deletions or by HDR (homology-directed repair) if an appropriate exogenous DNA template is provided...
2017: Progress in Molecular Biology and Translational Science
https://www.readbyqxmd.com/read/28695850/assembly-of-francisella-novicida-cpf1-endonuclease-in-complex-with-guide-rna-and-target-dna
#19
Pablo Alcón, Guillermo Montoya, Stefano Stella
Bacteria and archaea use the CRISPR-Cas system as an adaptive response against infection by foreign nucleic acids. Owing to its remarkable flexibility, this mechanism has been harnessed and adopted as a powerful tool for genome editing. The CRISPR-Cas system includes two classes that are subdivided into six types and 19 subtypes according to conservation of the cas gene and loci organization. Recently, a new protein with endonuclease activity belonging to class 2 type V has been identified. This endonuclease, termed Cpf1, in complex with a single CRISPR RNA (crRNA) is able to recognize and cleave a target DNA preceded by a 5'-TTN-3' protospacer-adjacent motif (PAM) complementary to the RNA guide...
July 1, 2017: Acta Crystallographica. Section F, Structural Biology Communications
https://www.readbyqxmd.com/read/28678773/erratum-structure-of-the-cpf1-endonuclease-r-loop-complex-after-target-dna-cleavage
#20
Stefano Stella, Pablo Alcón, Guillermo Montoya
This corrects the article DOI: 10.1038/nature22398.
July 27, 2017: Nature
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