keyword
MENU ▼
Read by QxMD icon Read
search

dCas9

keyword
https://www.readbyqxmd.com/read/28730450/crispr-cas-rna-scaffolds-for-transcriptional-programming-in-yeast
#1
Jesse G Zalatan
CRISPR scaffold RNAs (scRNAs) provide a modular system for locus-specific transcriptional programming. scRNAs are generated by extending CRISPR guide RNA sequences with domains that recruit RNA-binding proteins, thus physically linking DNA binding and protein recruitment activities. A single scRNA molecule encodes information about the target locus and instructions about what regulatory function to execute at that locus. Sets of scRNA constructs can be used to generate synthetic multigene transcriptional programs in which some genes are activated and others are repressed...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28712493/crispr-cas9-enabled-multiplex-genome-editing-and-its-application
#2
Bastian Minkenberg, Matthew Wheatley, Yinong Yang
The CRISPR/Cas9 system is a prevalent and versatile genome-editing tool of choice for basic and applied biological research. An exchange of a 20-bp spacer sequence in the gRNA can easily reprogram Cas9 to target a different DNA site. By expressing or providing multiple gRNAs, the system also enables multiplex genome editing at high efficiencies. Current approaches for providing multiple gRNAs in vivo include the use of multigene cassettes to express several gRNAs, Csy4-based excision, arrays of crRNAs, ribozyme-flanked gRNAs, tRNA-dependent cleavage of gRNAs, and direct introduction of Cas9 proteins preloaded with different gRNAs...
2017: Progress in Molecular Biology and Translational Science
https://www.readbyqxmd.com/read/28703221/manipulation-of-nuclear-architecture-through-crispr-mediated-chromosomal-looping
#3
Stefanie L Morgan, Natasha C Mariano, Abel Bermudez, Nicole L Arruda, Fangting Wu, Yunhai Luo, Gautam Shankar, Lin Jia, Huiling Chen, Ji-Fan Hu, Andrew R Hoffman, Chiao-Chain Huang, Sharon J Pitteri, Kevin C Wang
Chromatin looping is key to gene regulation, yet no broadly applicable methods to selectively modify chromatin loops have been described. We have engineered a method for chromatin loop reorganization using CRISPR-dCas9 (CLOuD9) to selectively and reversibly establish chromatin loops. We demonstrate the power of this technology to selectively modulate gene expression at targeted loci.
July 13, 2017: Nature Communications
https://www.readbyqxmd.com/read/28700213/enabling-graded-and-large-scale-multiplex-of-desired-genes-using-a-dual-mode-dcas9-activator-in-saccharomyces-cerevisiae
#4
Matthew Deaner, Julio Mejia, Hal S Alper
Standard approaches for dCas9-based modification of gene expression are limited in the ability to multiplex targets, establish streamlined cassettes, and utilize commonly studied Pol II promoters. In this work, we re-purpose the dCas9-VPR activator to act as a dual-mode activator/repressor that can be programmed based solely on target position at gene loci. Furthermore, we implement this approach using a streamlined Pol II-ribozyme system that allows expression of many sgRNAs from a single transcript. By "stepping" dCas9-VPR within the promoter region and ORF we create graded activation and repression (respectively) of target genes, allowing precise control over multiplexed gene modulation...
July 12, 2017: ACS Synthetic Biology
https://www.readbyqxmd.com/read/28695892/targeted-dna-methylation-in-vivo-using-an-engineered-dcas9-mq1-fusion-protein
#5
Yong Lei, Xiaotian Zhang, Jianzhong Su, Mira Jeong, Michael C Gundry, Yung-Hsin Huang, Yubin Zhou, Wei Li, Margaret A Goodell
Comprehensive studies have shown that DNA methylation plays vital roles in both loss of pluripotency and governance of the transcriptome during embryogenesis and subsequent developmental processes. Aberrant DNA methylation patterns have been widely observed in tumorigenesis, ageing and neurodegenerative diseases, highlighting the importance of a systematic understanding of DNA methylation and the dynamic changes of methylomes during disease onset and progression. Here we describe a facile and convenient approach for efficient targeted DNA methylation by fusing inactive Cas9 (dCas9) with an engineered prokaryotic DNA methyltransferase MQ1...
July 11, 2017: Nature Communications
https://www.readbyqxmd.com/read/28683826/identification-and-characterization-of-a-foxa2-regulated-transcriptional-enhancer-at-a-type-2-diabetes-intronic-locus-that-controls-gckr-expression-in-liver-cells
#6
Maykel López Rodríguez, Dorota Kaminska, Kati Lappalainen, Jussi Pihlajamäki, Minna U Kaikkonen, Markku Laakso
BACKGROUND: Genome-wide association studies (GWAS) have identified more than 100 genetic loci associated with type 2 diabetes (T2D). However, the underlying biological mechanisms for many of these associations remain unknown. GWAS signals close to the glucokinase regulatory protein gene (GCKR) have been reported for lipid and glucose metabolism traits and the risk of T2D. We investigated the regulatory function of an intronic locus at GCKR represented by the lead single nucleotide polymorphism (SNP) rs780094...
July 6, 2017: Genome Medicine
https://www.readbyqxmd.com/read/28666380/comparative-analysis-of-chimeric-zfp-tale-and-cas9-piggybac-transposases-for-integration-into-a-single-locus-in-human-cells
#7
Wentian Luo, Daniel L Galvan, Lauren E Woodard, Dan Dorset, Shawn Levy, Matthew H Wilson
Integrating DNA delivery systems hold promise for many applications including treatment of diseases; however, targeted integration is needed for improved safety. The piggyBac (PB) transposon system is a highly active non-viral gene delivery system capable of integrating defined DNA segments into host chromosomes without requiring homologous recombination. We systematically compared four different engineered zinc finger proteins (ZFP), four transcription activator-like effector proteins (TALE), CRISPR associated protein 9 (SpCas9) and the catalytically inactive dSpCas9 protein fused to the amino-terminus of the transposase enzyme designed to target the hypoxanthine phosphoribosyltransferase (HPRT) gene located on human chromosome X...
June 29, 2017: Nucleic Acids Research
https://www.readbyqxmd.com/read/28649363/genetic-and-epigenetic-control-of-gene-expression-by-crispr-cas-systems
#8
REVIEW
Albert Lo, Lei Qi
The discovery and adaption of bacterial clustered regularly interspaced short palindromic repeats (CRISPR)-CRISPR-associated (Cas) systems has revolutionized the way researchers edit genomes. Engineering of catalytically inactivated Cas variants (nuclease-deficient or nuclease-deactivated [dCas]) combined with transcriptional repressors, activators, or epigenetic modifiers enable sequence-specific regulation of gene expression and chromatin state. These CRISPR-Cas-based technologies have contributed to the rapid development of disease models and functional genomics screening approaches, which can facilitate genetic target identification and drug discovery...
2017: F1000Research
https://www.readbyqxmd.com/read/28639197/repurposing-crispr-system-for-transcriptional-activation
#9
Meng Chen, Lei Stanley Qi
In recent years, Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) system has become the most popular one for genome editing. When the nuclease domains of Cas9 protein are mutated into deactivated form (dCas9), CRISPR/dCas9 still retains the ability to bind the targeted DNA sequence, but loses the endonuclease cleavage activity. Taking advantage of the characteristics of this engineered nuclease inactive Cas9, the CRISPR/dCas system has been repurposed into versatile RNA-guided, DNA-targeting platforms, such as genome imaging, gene regulation, and epigenetic modification...
2017: Advances in Experimental Medicine and Biology
https://www.readbyqxmd.com/read/28623586/multiplexed-transcriptional-activation-or-repression-in-plants-using-crispr-dcas9-based-systems
#10
Levi G Lowder, Joseph W Paul, Yiping Qi
Novel tools and methods for regulating in vivo plant gene expression are quickly gaining popularity and utility due to recent advances in CRISPR-dCas9 chimeric effector regulators, otherwise known as CRISPR artificial transcription factors (CRISPR-ATFs). These tools are especially useful for studying gene function and interaction within various regulatory networks. First generation CRISPR-ATFs are nuclease-deactivated (dCas9) CRISPR systems where dCas9 proteins are fused to known transcriptional activator domains (VP64) or repressor domains (SRDX)...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/28623229/zebrafish-znfl1s-control-the-expression-of-hoxb1b-in-the-posterior-neuroectoderm-by-acting-upstream-of-pou5f3-and-sall4
#11
Xiaohua Dong, Jingyun Li, Luqingqing He, Chun Gu, Wenshuang Jia, Yunyun Yue, Jun Li, Qinxin Zhang, Lele Chu, Qingshun Zhao
Transcription factors play crucial roles in patterning posterior neuroectoderm. Previously, zinc finger transcription factor znfl1 was reported to express in the posterior neuroectoderm of zebrafish embryos. However, its roles remain unknown. Here, we report that there are 13 copies of znfl1 in zebrafish genome and all the paralogues share highly identical protein sequences and cDNA sequences. When znfl1s are knocked down by using morpholino to inhibit their translations or dCas9-Eve to inhibit their transcriptions, the zebrafish gastrula displays reduced expression of hoxb1b, the maker gene for the posterior neuroectoderm...
June 16, 2017: Journal of Biological Chemistry
https://www.readbyqxmd.com/read/28622347/rna-guided-transcriptional-activation-via-crispr-dcas9-mimics-overexpression-phenotypes-in-arabidopsis
#12
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/28607761/multiplex-gene-regulation-by-crispr-ddcpf1
#13
Xiaochun Zhang, Jingman Wang, Qiuxiang Cheng, Xuan Zheng, Guoping Zhao, Jin Wang
The clustered regularly interspaced short palindromic repeats (CRISPR)/dCas9 system has been widely applied in both transcriptional regulation and epigenetic studies. However, for multiple targets, independent expression of multiple single guide RNAs (sgRNAs) is needed, which is less convenient. To address the problem, we employed a DNase-dead Cpf1 mutant (ddCpf1) for multiplex gene regulation. We demonstrated that ddCpf1 alone could be employed for gene repression in Escherichia coli, and the repression was more effective with CRISPR RNAs (crRNAs) specifically targeting to the template strand of its target genes, which was different from that of dCas9...
2017: Cell Discovery
https://www.readbyqxmd.com/read/28603699/crispr-interference-crispri-inhibition-of-luxs-gene-expression-in-e-coli-an-approach-to-inhibit-biofilm
#14
Azna Zuberi, Lama Misba, Asad U Khan
Biofilm is a sessile bacterial accretion embedded in self-producing matrix. It is the root cause of about 80% microbial infections in human. Among them, E. coli biofilms are most prevalent in medical devices associated nosocomial infections. The objective of this study was to inhibit biofilm formation by targeting gene involved in quorum sensing, one of the main mechanisms of biofilm formation. Hence we have introduced the CRISPRi, first time to target luxS gene. luxS is a synthase, involved in the synthesis of Autoinducer-2(AI-2), which in turn guides the initial stage of biofilm formation...
2017: Frontiers in Cellular and Infection Microbiology
https://www.readbyqxmd.com/read/28557624/rna-guided-activation-of-pluripotency-genes-in-human-fibroblasts
#15
Kai Xiong, Yan Zhou, Kristian Aabo Blichfeld, Poul Hyttel, Lars Bolund, Kristine Karla Freude, Yonglun Luo
Specific activation of endogenous genes can be achieved by programmable artificial transcription factors (ATFs). In this study, we compared two artificial, programmable, clustered regularly interspaced short palindromic repeats (CRISPR)-based, ubiquitous transcription factors: deficient CRISPR-associated protein 9 (dCas9)-VP64 (CRISPRa) alone, or a combination of dCas9-VP64 and MS2-P65-HSF1 [synergistic activation mediator (SAM) system] mediated activation of five pluripotency genes: KLF4 (K), LIN28 (L), MYC (M), OCT4 (O), and SOX2 (S) in human cells (HEK293T, HeLa, HepG2, and primary fibroblasts)...
June 2017: Cellular Reprogramming
https://www.readbyqxmd.com/read/28547585/aio-casilio-a-robust-crispr-cas9-pumilio-system-for-chromosome-labeling
#16
Shuxian Zhang, Zhan Song
The biological function of chromatin bases on its spatial organization and dynamic activities in different situations. Labeling and tracing of genomic sequences has been a huge challenge in studying the spatial dynamics of chromatin. We reported the development of 'all-in-one Casilio system (Aio-Casilio)', a new system that enables the labeling of endogenous genomic loci. The Aio-Casilio system consists of the dCas9 protein, mClover fused with the Pumilio and FBF proteins RNA-binding domain (PUF domain) and an U6-sgRNA appended with multiple PUF-binding site(s)...
August 2017: Journal of Molecular Histology
https://www.readbyqxmd.com/read/28542388/targeted-dna-methylation-in-pericentromeres-with-genome-editing-based-artificial-dna-methyltransferase
#17
Taiga Yamazaki, Yu Hatano, Tetsuya Handa, Sakiko Kato, Kensuke Hoida, Rui Yamamura, Takashi Fukuyama, Takayuki Uematsu, Noritada Kobayashi, Hiroshi Kimura, Kazuo Yamagata
To study the impact of epigenetic changes on biological functions, the ability to manipulate the epigenetic status of certain genomic regions artificially could be an indispensable technology. "Epigenome editing" techniques have gradually emerged that apply TALE or CRISPR/Cas9 technologies with various effector domains isolated from epigenetic code writers or erasers such as DNA methyltransferase, 5-methylcytosine oxidase, and histone modification enzymes. Here we demonstrate that a TALE recognizing a major satellite, consisting of a repeated sequence in pericentromeres, could be fused with the bacterial CpG methyltransferase, SssI...
2017: PloS One
https://www.readbyqxmd.com/read/28541304/digital-logic-circuits-in-yeast-with-crispr-dcas9-nor-gates
#18
Miles W Gander, Justin D Vrana, William E Voje, James M Carothers, Eric Klavins
Natural genetic circuits enable cells to make sophisticated digital decisions. Building equally complex synthetic circuits in eukaryotes remains difficult, however, because commonly used components leak transcriptionally, do not arbitrarily interconnect or do not have digital responses. Here, we designed dCas9-Mxi1-based NOR gates in Saccharomyces cerevisiae that allow arbitrary connectivity and large genetic circuits. Because we used the chromatin remodeller Mxi1, our gates showed minimal leak and digital responses...
May 25, 2017: Nature Communications
https://www.readbyqxmd.com/read/28534478/complementary-information-derived-from-crispr-cas9-mediated-gene-deletion-and-suppression
#19
Joseph Rosenbluh, Han Xu, William Harrington, Stanley Gill, Xiaoxing Wang, Francisca Vazquez, David E Root, Aviad Tsherniak, William C Hahn
CRISPR-Cas9 provides the means to perform genome editing and facilitates loss-of-function screens. However, we and others demonstrated that expression of the Cas9 endonuclease induces a gene-independent response that correlates with the number of target sequences in the genome. An alternative approach to suppressing gene expression is to block transcription using a catalytically inactive Cas9 (dCas9). Here we directly compare genome editing by CRISPR-Cas9 (cutting, CRISPRc) and gene suppression using KRAB-dCas9 (CRISPRi) in loss-of-function screens to identify cell essential genes...
May 23, 2017: Nature Communications
https://www.readbyqxmd.com/read/28522389/crispr-dcas9-mediated-inhibition-of-gene-expression-in-staphylococcus-aureus
#20
Xiaoyun Dong, Yingli Jin, Di Ming, Bangbang Li, Haisi Dong, Lin Wang, Tiedong Wang, Dacheng Wang
The understanding of the genetic mechanism of Staphylococcus aureus requires efficient tools, however, genetic manipulation in S. aureus is always laborious and time-consuming. Here we proposed a novel CRISPR/dCas9 interference method for the rapid knockdown of target genes. Furthermore, multiple genes can be repressed simultaneously by using this method.
May 15, 2017: Journal of Microbiological Methods
keyword
keyword
70359
1
2
Fetch more papers »
Fetching more papers... Fetching...
Read by QxMD. Sign in or create an account to discover new knowledge that matter to you.
Remove bar
Read by QxMD icon Read
×

Search Tips

Use Boolean operators: AND/OR

diabetic AND foot
diabetes OR diabetic

Exclude a word using the 'minus' sign

Virchow -triad

Use Parentheses

water AND (cup OR glass)

Add an asterisk (*) at end of a word to include word stems

Neuro* will search for Neurology, Neuroscientist, Neurological, and so on

Use quotes to search for an exact phrase

"primary prevention of cancer"
(heart or cardiac or cardio*) AND arrest -"American Heart Association"