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https://www.readbyqxmd.com/read/29344851/the-evolution-of-crispr-cas9-and-their-cousins-hope-or-hype
#1
REVIEW
Kulbhushan Chaudhary, Anirudha Chattopadhyay, Dharmendra Pratap
Clustered regularly interspaced short palindromic repeats (CRISPR)/Cas9 system allows biologists to edit genomic DNA of any cell in precise and specific way, entailing great potential for crop improvement, drug development and gene therapy. The system involves a nuclease (Cas9) and a designed guide RNA that are involved in wide range of applications such as genome modification, transcriptional modulation, genomic loci marking and RNA tracking. The limitation of the technique, in view of resistance of thymidine-rich genome to Cas9 cleavage, has now been overcome by the use of Cpf1 nuclease...
January 17, 2018: Biotechnology Letters
https://www.readbyqxmd.com/read/29335559/publisher-correction-fusion-guide-rnas-for-orthogonal-gene-manipulation-with-cas9-and-cpf1
#2
Jiyeon Kweon, An-Hee Jang, Da-Eun Kim, Jin Wook Yang, Mijung Yoon, Ha Rim Shin, Jin-Soo Kim, Yongsub Kim
The originally published version of this Article contained an error in the spelling of the author Da-eun Kim, which was incorrectly given as Da-Eun Kim. Furthermore, in Figure 1a, the Cas9 protein was positioned incorrectly during typesetting. These errors have now been corrected in both the PDF and HTML versions of the Article.
January 16, 2018: Nature Communications
https://www.readbyqxmd.com/read/29304331/rapid-and-scalable-characterization-of-crispr-technologies-using-an-e-%C3%A2-coli-cell-free-transcription-translation-system
#3
Ryan Marshall, Colin S Maxwell, Scott P Collins, Thomas Jacobsen, Michelle L Luo, Matthew B Begemann, Benjamin N Gray, Emma January, Anna Singer, Yonghua He, Chase L Beisel, Vincent Noireaux
CRISPR-Cas systems offer versatile technologies for genome engineering, yet their implementation has been outpaced by ongoing discoveries of new Cas nucleases and anti-CRISPR proteins. Here, we present the use of E. coli cell-free transcription-translation (TXTL) systems to vastly improve the speed and scalability of CRISPR characterization and validation. TXTL can express active CRISPR machinery from added plasmids and linear DNA, and TXTL can output quantitative dynamics of DNA cleavage and gene repression-all without protein purification or live cells...
January 4, 2018: Molecular Cell
https://www.readbyqxmd.com/read/29281823/rna-independent-dna-cleavage-activities-of-cas9-and-cas12a
#4
Ramya Sundaresan, Hari Priya Parameshwaran, S D Yogesha, Mark Walter Keilbarth, Rakhi Rajan
CRISPR-Cas systems provide bacteria and archaea with sequence-specific protection against invading mobile genetic elements. In the presence of divalent metal ions, Cas9 and Cas12a (formerly Cpf1) proteins target and cleave DNA that is complementary to a cognate guide RNA. The recognition of a protospacer adjacent motif (PAM) sequence in the target DNA by Cas9 and Cas12a is essential for cleavage. This RNA-guided DNA targeting is widely used for gene-editing methods. Here, we show that Francisella tularensis novicida (Fno) Cas12a, FnoCas9, and Streptococcus pyogenes Cas9 (SpyCas9) cleave DNA without a guide RNA in the presence of Mn2+ ions...
December 26, 2017: Cell Reports
https://www.readbyqxmd.com/read/29235474/engineering-cell-signaling-using-tunable-crispr-cpf1-based-transcription-factors
#5
Yuchen Liu, Jinghong Han, Zhicong Chen, Hanwei Wu, Hongsong Dong, Guohui Nie
The catalytically dead Cpf1 endonuclease from Acidaminococcus sp. BV3L6 (dAsCpf1) has been used to construct effective transcriptional repressors in bacteria and plants. However, it is still unclear if dAsCpf1 can function in human cells as a transcriptional regulator or a signal conductor. Here, we repurpose the dAsCpf1 system in human cells for a variety of functions, including the activation or repression of gene transcription. Moreover, we construct programmable ligand-controlled dAsCpf1 systems either by coupling crRNAs with engineered riboswitches or by fusing dAsCpf1 proteins with G protein-coupled receptors...
December 13, 2017: Nature Communications
https://www.readbyqxmd.com/read/29222508/crispr-cpf1-mediates-efficient-homology-directed-repair-and-temperature-controlled-genome-editing
#6
Miguel A Moreno-Mateos, Juan P Fernandez, Romain Rouet, Charles E Vejnar, Maura A Lane, Emily Mis, Mustafa K Khokha, Jennifer A Doudna, Antonio J Giraldez
Cpf1 is a novel class of CRISPR-Cas DNA endonucleases, with a wide range of activity across different eukaryotic systems. Yet, the underlying determinants of this variability are poorly understood. Here, we demonstrate that LbCpf1, but not AsCpf1, ribonucleoprotein complexes allow efficient mutagenesis in zebrafish and Xenopus. We show that temperature modulates Cpf1 activity by controlling its ability to access genomic DNA. This effect is stronger on AsCpf1, explaining its lower efficiency in ectothermic organisms...
December 8, 2017: Nature Communications
https://www.readbyqxmd.com/read/29208717/efficient-targeted-dna-editing-and-replacement-in-chlamydomonas-reinhardtii-using-cpf1-ribonucleoproteins-and-single-stranded-dna
#7
Aron Ferenczi, Douglas Euan Pyott, Andromachi Xipnitou, Attila Molnar
The green alga Chlamydomonas reinhardtii is an invaluable reference organism to research fields including algal, plant, and ciliary biology. Accordingly, decades-long standing inefficiencies in targeted nuclear gene editing broadly hinder Chlamydomonas research. Here we report that single-step codelivery of CRISPR/Cpf1 ribonucleoproteins with single-stranded DNA repair templates results in precise and targeted DNA replacement with as much as ∼10% efficiency in C. reinhardtii We demonstrate its use in transgene- and selection-free generation of sequence-specific mutations and epitope tagging at an endogenous locus...
December 5, 2017: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/29189942/the-conspicuity-of-crispr-cpf1-system-as-a-significant-breakthrough-in-genome-editing
#8
REVIEW
Hadi Bayat, Mohammad Hossein Modarressi, Azam Rahimpour
Clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated protein (Cas) is a microbial adaptive immune system. CRISPR-Cas systems are classified into two main classes and six types. Cpf1 is a putative type V (class II) CRISPR effector, which has revolutionized the genome editing approaches through multiple distinct features such as using T-rich protospacer-adjacent motif, applying a short guide RNA lacking trans-activating crRNA, introducing a staggered double-strand break, and possessing RNA processing activity in addition to DNA nuclease activity...
November 30, 2017: Current Microbiology
https://www.readbyqxmd.com/read/29186338/cpf1-database-web-based-genome-wide-guide-rna-library-design-for-gene-knockout-screens-using-crispr-cpf1
#9
Jeongbin Park, Sangsu Bae
Summary: Following the type II CRISPR-Cas9 system, type V CRISPR-Cpf1 endonucleases have been found to be applicable for genome editing in various organisms in vivo. However, there are as yet no web-based tools capable of optimally selecting guide RNAs (gRNAs) among all possible genome-wide target sites. Here, we present Cpf1-Database, a genome-wide gRNA library design tool for LbCpf1 and AsCpf1, which have DNA recognition sequences of 5'-TTTN-3' at the 5' ends of target sites. Cpf1-Database provides a sophisticated but simple way to design gRNAs for AsCpf1 nucleases on the genome scale...
November 27, 2017: Bioinformatics
https://www.readbyqxmd.com/read/29179261/targeted-base-editing-via-rna-guided-cytidine-deaminases-in-xenopus-laevis-embryos
#10
Dong-Seok Park, Mijung Yoon, Jiyeon Kweon, An-Hee Jang, Yongsub Kim, Sun-Cheol Choi
Genome editing using programmable nucleases such as CRISPR/Cas9 or Cpf1 has emerged as powerful tools for gene knock-out or knock-in in various organisms. While most genetic diseases are caused by point mutations, these genome-editing approaches are inefficient in inducing single-nucleotide substitutions. Recently, Cas9-linked cytidine deam-inases, named base editors (BEs), have been shown to convert cytidine to uridine efficiently, leading to targeted single-base pair substitutions in human cells and organisms...
November 20, 2017: Molecules and Cells
https://www.readbyqxmd.com/read/29167440/fusion-guide-rnas-for-orthogonal-gene-manipulation-with-cas9-and-cpf1
#11
Jiyeon Kweon, An-Hee Jang, Da-Eun Kim, Jin Wook Yang, Mijung Yoon, Ha Rim Shin, Jin-Soo Kim, Yongsub Kim
The bacteria-derived clustered regularly interspaced short palindromic repeat (CRISPR)-Cas systems are powerful tools for genome engineering. Recently, in addition to Cas protein engineering, the improvement of guide RNAs are also performed, contributing to broadening the research area of CRISPR-Cas9 systems. Here we develop a fusion guide RNA (fgRNA) that functions with both Cas9 and Cpf1 proteins to induce mutations in human cells. Furthermore, we demonstrate that fgRNAs can be used in multiplex genome editing and orthogonal genome manipulation with two types of Cas proteins...
November 23, 2017: Nature Communications
https://www.readbyqxmd.com/read/29112372/tuning-the-color-palette-of-fluorescent-copper-sensors-through-systematic-heteroatom-substitution-at-rhodol-cores
#12
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
#13
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
#14
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
#15
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...
January 2018: Wiley Interdisciplinary Reviews. Systems Biology and Medicine
https://www.readbyqxmd.com/read/29082718/-recent-progresses-in-crispr-genome-editing-in-plants
#16
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
#17
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
#18
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
#19
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...
November 2, 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
#20
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
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