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Journal articles on the topic 'CRISPR'

Author: Grafiati

Published: 4 June 2021

Last updated: 26 July 2025

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1

Huescas, C. G. Y., R. I. Pereira, J. Prichula, P. A. Azevedo, J. Frazzon, and A. P. G. Frazzon. "Frequency of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPRs) in non-clinical Enterococcus faecalis and Enterococcus faecium strains." Brazilian Journal of Biology 79, no. 3 (2019): 460–65. http://dx.doi.org/10.1590/1519-6984.183375.

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Abstract The fidelity of the genomes is defended by mechanism known as Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR) systems. Three Type II CRISPR systems (CRISPR1- cas, CRISPR2 and CRISPR3-cas) have been identified in enterococci isolates from clinical and environmental samples. The aim of this study was to observe the distribution of CRISPR1-cas, CRISPR2 and CRISPR3-cas in non-clinical strains of Enterococcus faecalis and Enterococcus faecium isolates from food and fecal samples, including wild marine animals. The presence of CRISPRs was evaluated by PCR in 120 enterococ

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2

Horvath, Philippe, Dennis A. Romero, Anne-Claire Coûté-Monvoisin, et al. "Diversity, Activity, and Evolution of CRISPR Loci in Streptococcus thermophilus." Journal of Bacteriology 190, no. 4 (2007): 1401–12. http://dx.doi.org/10.1128/jb.01415-07.

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ABSTRACT Clustered regularly interspaced short palindromic repeats (CRISPR) are hypervariable loci widely distributed in prokaryotes that provide acquired immunity against foreign genetic elements. Here, we characterize a novel Streptococcus thermophilus locus, CRISPR3, and experimentally demonstrate its ability to integrate novel spacers in response to bacteriophage. Also, we analyze CRISPR diversity and activity across three distinct CRISPR loci in several S. thermophilus strains. We show that both CRISPR repeats and cas genes are locus specific and functionally coupled. A total of 124 strai

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3

Isachenko, Nadya, Gayane Aleksanyan, Paul Diehl, and Donato Tedesco. "Abstract 2950: CRISPR/saCas9 and CRISPR/spCas9 systems for combinatorial genetic screens (CRISPR-KO, CRISPRa, CRISPRi)." Cancer Research 84, no. 6_Supplement (2024): 2950. http://dx.doi.org/10.1158/1538-7445.am2024-2950.

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Abstract This study explores the utilization of orthogonal CRISPR-based gene editing/modulation systems for combinatorial genetic screens using CRISPR knockout (CRISPR-KO), CRISPR activation (CRISPRa), and CRISPR interference (CRISPRi) functionalities. S. aureus (sa)Cas9 is an alternative nuclease to S. pyogenes (sp)Cas9 in scenarios where the latter cannot be used, or when multiple independent CRISPR systems need to be simultaneously expressed in the same cell. In this study we set out to explore the feasibility of utilizing different combinations of saCas9 and spCas9 CRISPR systems to achiev

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Toro, Magaly, Guojie Cao, Wenting Ju, et al. "Association of Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) Elements with Specific Serotypes and Virulence Potential of Shiga Toxin-Producing Escherichia coli." Applied and Environmental Microbiology 80, no. 4 (2013): 1411–20. http://dx.doi.org/10.1128/aem.03018-13.

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ABSTRACTShiga toxin-producingEscherichia coli(STEC) strains (n= 194) representing 43 serotypes andE. coliK-12 were examined for clustered regularly interspaced short palindromic repeat (CRISPR) arrays to study genetic relatedness among STEC serotypes. A subset of the strains (n= 81) was further analyzed for subtype I-Ecasand virulence genes to determine a possible association of CRISPR elements with potential virulence. Four types of CRISPR arrays were identified. CRISPR1 and CRISPR2 were present in all strains tested; 1 strain also had both CRISPR3 and CRISPR4, whereas 193 strains displayed a

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Chapman, Brittany, Jeong Hoon Han, Hong Jo Lee, Isabella Ruud, and Tae Hyun Kim. "Targeted Modulation of Chicken Genes In Vitro Using CRISPRa and CRISPRi Toolkit." Genes 14, no. 4 (2023): 906. http://dx.doi.org/10.3390/genes14040906.

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Engineering of clustered regularly interspaced short palindromic repeats (CRISPR) and the CRISPR-associated protein 9 (Cas9) system has enabled versatile applications of CRISPR beyond targeted DNA cleavage. Combination of nuclease-deactivated Cas9 (dCas9) and transcriptional effector domains allows activation (CRISPRa) or repression (CRISPRi) of target loci. To demonstrate the effectiveness of the CRISPR-mediated transcriptional regulation in chickens, three CRISPRa (VP64, VPR, and p300) and three CRISPRi (dCas9, dCas9-KRAB, and dCas9-KRAB-MeCP2) systems were tested in chicken DF-1 cells. By i

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La Russa, Marie F., and Lei S. Qi. "The New State of the Art: Cas9 for Gene Activation and Repression." Molecular and Cellular Biology 35, no. 22 (2015): 3800–3809. http://dx.doi.org/10.1128/mcb.00512-15.

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CRISPR-Cas9 technology has rapidly changed the landscape for how biologists and bioengineers study and manipulate the genome. Derived from the bacterial adaptive immune system, CRISPR-Cas9 has been coopted and repurposed for a variety of new functions, including the activation or repression of gene expression (termed CRISPRa or CRISPRi, respectively). This represents an exciting alternative to previously used repression or activation technologies such as RNA interference (RNAi) or the use of gene overexpression vectors. We have only just begun exploring the possibilities that CRISPR technology

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7

Serbanescu, M. A., M. Cordova, K. Krastel, et al. "Role of the Streptococcus mutans CRISPR-Cas Systems in Immunity and Cell Physiology." Journal of Bacteriology 197, no. 4 (2014): 749–61. http://dx.doi.org/10.1128/jb.02333-14.

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CRISPR-Cas systems provide adaptive microbial immunity against invading viruses and plasmids. The cariogenic bacteriumStreptococcus mutansUA159 has two CRISPR-Cas systems: CRISPR1 (type II-A) and CRISPR2 (type I-C) with several spacers from both CRISPR cassettes matching sequences of phage M102 or genomic sequences of otherS. mutans. The deletion of thecasgenes of CRISPR1 (ΔC1S), CRISPR2 (ΔC2E), or both CRISPR1+2 (ΔC1SC2E) or the removal of spacers 2 and 3 (ΔCR1SP13E) inS. mutansUA159 did not affect phage sensitivity when challenged with virulent phage M102. Using plasmid transformation experi

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8

Achigar, Rodrigo, Martina Scarrone, Geneviève M. Rousseau, et al. "Ectopic Spacer Acquisition in Streptococcus thermophilus CRISPR3 Array." Microorganisms 9, no. 3 (2021): 512. http://dx.doi.org/10.3390/microorganisms9030512.

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Streptococcus thermophilus relies heavily on two type II-A CRISPR-Cas systems, CRISPR1 and CRISPR3, to resist siphophage infections. One hallmark of these systems is the integration of a new spacer at the 5′ end of the CRISPR arrays following phage infection. However, we have previously shown that ectopic acquisition of spacers can occur within the CRISPR1 array. Here, we present evidence of the acquisition of new spacers within the array of CRISPR3 of S. thermophilus. The analysis of randomly selected bacteriophage-insensitive mutants of the strain Uy01 obtained after phage infection, as well

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9

van der Ploeg, Jan R. "Analysis of CRISPR in Streptococcus mutans suggests frequent occurrence of acquired immunity against infection by M102-like bacteriophages." Microbiology 155, no. 6 (2009): 1966–76. http://dx.doi.org/10.1099/mic.0.027508-0.

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Clustered regularly interspaced short palindromic repeats (CRISPR) consist of highly conserved direct repeats interspersed with variable spacer sequences. They can protect bacteria against invasion by foreign DNA elements. The genome sequence of Streptococcus mutans strain UA159 contains two CRISPR loci, designated CRISPR1 and CRISPR2. The aims of this study were to analyse the organization of CRISPR in further S. mutans strains and to investigate the importance of CRISPR in acquired immunity to M102-like phages. The sequences of CRISPR1 and CRISPR2 arrays were determined for 29 S. mutans stra

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10

Yang, Caiting, Yu Lei, Tinglin Ren, and Mingze Yao. "The Current Situation and Development Prospect of Whole-Genome Screening." International Journal of Molecular Sciences 25, no. 1 (2024): 658. http://dx.doi.org/10.3390/ijms25010658.

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High-throughput genetic screening is useful for discovering critical genes or gene sequences that trigger specific cell functions and/or phenotypes. Loss-of-function genetic screening is mainly achieved through RNA interference (RNAi), CRISPR knock-out (CRISPRko), and CRISPR interference (CRISPRi) technologies. Gain-of-function genetic screening mainly depends on the overexpression of a cDNA library and CRISPR activation (CRISPRa). Base editing can perform both gain- and loss-of-function genetic screening. This review discusses genetic screening techniques based on Cas9 nuclease, including Cas

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11

Karlson, Chou Khai Soong, Siti Nurfadhlina Mohd-Noor, Nadja Nolte, and Boon Chin Tan. "CRISPR/dCas9-Based Systems: Mechanisms and Applications in Plant Sciences." Plants 10, no. 10 (2021): 2055. http://dx.doi.org/10.3390/plants10102055.

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RNA-guided genomic transcriptional regulation tools, namely clustered regularly interspaced short palindromic repeats interference (CRISPRi) and CRISPR-mediated gene activation (CRISPRa), are a powerful technology for gene functional studies. Deriving from the CRISPR/Cas9 system, both systems consist of a catalytically dead Cas9 (dCas9), a transcriptional effector and a single guide RNA (sgRNA). This type of dCas9 is incapable to cleave DNA but retains its ability to specifically bind to DNA. The binding of the dCas9/sgRNA complex to a target gene results in transcriptional interference. The C

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Jurić, Ivana, Marko Jelić, Manda Markanović, et al. "CRISPR-Cas Dynamics in Carbapenem-Resistant and Carbapenem-Susceptible Klebsiella pneumoniae Clinical Isolates from a Croatian Tertiary Hospital." Pathogens 14, no. 6 (2025): 604. https://doi.org/10.3390/pathogens14060604.

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(1) Background: CRISPR-Cas systems provide adaptive immunity against mobile genetic elements (MGEs) carrying antimicrobial resistance (AMR) genes. Carbapenem-resistant (CR) Klebsiella pneumoniae is a major public health concern, and the role of CRISPR-Cas in its resistance is understudied. This study explored CRISPR-Cas associations with multidrug resistance in clinical K. pneumoniae. (2) Methods: 400 K. pneumoniae isolates (200 CR and 200 carbapenem susceptible (CS)) were analyzed. Carbapenemase genes (blaOXA-48, blaNDM-1, blaKPC-2), cas1, rpoB, and CRISPR1-3 loci were identified by PCR, whil

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13

Mariam, Mariam, Khizra Ikhlaq, Zulaikha Abid, et al. "Exploring CRISPR Cloning and Beyond Through a Biochemical Lens in Genetic Biotechnology." Scholars Academic Journal of Biosciences 13, no. 07 (2025): 867–76. https://doi.org/10.36347/sajb.2025.v13i07.001.

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By offering a precise, effective, and adaptable method for genome editing, CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats) technology has completely transformed genetic biotechnology. Through a biochemical lens that highlights the molecular complexities behind its methods and discoveries, this review explores the complex field of CRISPR cloning and its emerging frontiers. We examine the molecular underpinnings of target identification, protospacer adjacent motif (PAM) specificity, and Cas nuclease activation, starting with the groundbreaking discovery of CRISPR-Cas systems i

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Yin, Shuang, Mark A. Jensen, Jiawei Bai, Chitrita DebRoy, Rodolphe Barrangou, and Edward G. Dudley. "The Evolutionary Divergence of Shiga Toxin-Producing Escherichia coli Is Reflected in Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) Spacer Composition." Applied and Environmental Microbiology 79, no. 18 (2013): 5710–20. http://dx.doi.org/10.1128/aem.00950-13.

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ABSTRACTThe Shiga toxin-producingEscherichia coli(STEC) strains, including those of O157:H7 and the “big six” serogroups (i.e., serogroups O26, O45, O103, O111, O121, and O145), are a group of pathogens designated food adulterants in the United States. The relatively conserved nature ofclusteredregularlyinterspacedshortpalindromicrepeats (CRISPRs) in phylogenetically relatedE. colistrains makes them potential subtyping markers for STEC detection, and a quantitative PCR (qPCR)-based assay was previously developed for O26:H11, O45:H2, O103:H2, O111:H8, O121:H19, O145:H28, and O157:H7 isolates. T

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15

Lou, Kai-Jye. "Crisper results for CRISPR." Science-Business eXchange 6, no. 35 (2013): 950. http://dx.doi.org/10.1038/scibx.2013.950.

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16

Yang, Jiayi. "Applications of the CRISPR-Cas9 system in cancer models." Theoretical and Natural Science 21, no. 1 (2023): 28–33. http://dx.doi.org/10.54254/2753-8818/21/20230804.

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Cancer has a high mortality and prevalence rate in the world. CRISPR-Cas9 is one of the novel and most common gene-editing techniques. Compared with the first two generations of gene-editing technologies, CRISPR-Cas9 system has the advantages of easy design, low cost, high efficiency and so on. sgRNA guides Cas9 to the site of the targeted gene, and Cas9 cuts the DNA strand at that site, triggering the NHEJ or HDR mechanism so as to achieve the purpose of deletion or insertion. CRISPR-Cas9 can be combined with other factors for other purposes, such as CRISPRa, CRISPRi, and base editing. The CR

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Barrangou, Rodolphe, Anne-Claire Coûté-Monvoisin, Buffy Stahl, et al. "Genomic impact of CRISPR immunization against bacteriophages." Biochemical Society Transactions 41, no. 6 (2013): 1383–91. http://dx.doi.org/10.1042/bst20130160.

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CRISPR (clustered regularly interspaced short palindromic repeats) together with cas (CRISPR-associated) genes form the CRISPR–Cas immune system, which provides sequence-specific adaptive immunity against foreign genetic elements in bacteria and archaea. Immunity is acquired by the integration of short stretches of invasive DNA as novel ‘spacers’ into CRISPR loci. Subsequently, these immune markers are transcribed and generate small non-coding interfering RNAs that specifically guide nucleases for sequence-specific cleavage of complementary sequences. Among the four CRISPR–Cas systems present

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Yu, Jiaying, Xi Xiang, Jinrong Huang, et al. "Haplotyping by CRISPR-mediated DNA circularization (CRISPR-hapC) broadens allele-specific gene editing." Nucleic Acids Research 48, no. 5 (2020): e25-e25. http://dx.doi.org/10.1093/nar/gkz1233.

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Abstract Allele-specific protospacer adjacent motif (asPAM)-positioning SNPs and CRISPRs are valuable resources for gene therapy of dominant disorders. However, one technical hurdle is to identify the haplotype comprising the disease-causing allele and the distal asPAM SNPs. Here, we describe a novel CRISPR-based method (CRISPR-hapC) for haplotyping. Based on the generation (with a pair of CRISPRs) of extrachromosomal circular DNA in cells, the CRISPR-hapC can map haplotypes from a few hundred bases to over 200 Mb. To streamline and demonstrate the applicability of the CRISPR-hapC and asPAM CR

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Eitzinger, Simon, Amina Asif, Kyle E. Watters, et al. "Machine learning predicts new anti-CRISPR proteins." Nucleic Acids Research 48, no. 9 (2020): 4698–708. http://dx.doi.org/10.1093/nar/gkaa219.

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Abstract The increasing use of CRISPR–Cas9 in medicine, agriculture, and synthetic biology has accelerated the drive to discover new CRISPR–Cas inhibitors as potential mechanisms of control for gene editing applications. Many anti-CRISPRs have been found that inhibit the CRISPR–Cas adaptive immune system. However, comparing all currently known anti-CRISPRs does not reveal a shared set of properties for facile bioinformatic identification of new anti-CRISPR families. Here, we describe AcRanker, a machine learning based method to aid direct identification of new potential anti-CRISPRs using only

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20

Van Orden, Mason J., Peter Klein, Kesavan Babu, Fares Z. Najar, and Rakhi Rajan. "Conserved DNA motifs in the type II-A CRISPR leader region." PeerJ 5 (April 4, 2017): e3161. http://dx.doi.org/10.7717/peerj.3161.

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The Clustered Regularly Interspaced Short Palindromic Repeats associated (CRISPR-Cas) systems consist of RNA-protein complexes that provide bacteria and archaea with sequence-specific immunity against bacteriophages, plasmids, and other mobile genetic elements. Bacteria and archaea become immune to phage or plasmid infections by inserting short pieces of the intruder DNA (spacer) site-specifically into the leader-repeat junction in a process called adaptation. Previous studies have shown that parts of the leader region, especially the 3′ end of the leader, are indispensable for adaptation. How

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Stanley, Sabrina Y., and Karen L. Maxwell. "Phage-Encoded Anti-CRISPR Defenses." Annual Review of Genetics 52, no. 1 (2018): 445–64. http://dx.doi.org/10.1146/annurev-genet-120417-031321.

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The battle for survival between bacteria and bacteriophages (phages) is an arms race where bacteria develop defenses to protect themselves from phages and phages evolve counterstrategies to bypass these defenses. CRISPR-Cas adaptive immune systems represent a widespread mechanism by which bacteria protect themselves from phage infection. In response to CRISPR-Cas, phages have evolved protein inhibitors known as anti-CRISPRs. Here, we describe the discovery and mechanisms of action of anti-CRISPR proteins. We discuss the potential impact of anti-CRISPRs on bacterial evolution, speculate on thei

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Rousseau, C., M. Gonnet, M. Le Romancer, and J. Nicolas. "CRISPI: a CRISPR interactive database." Bioinformatics 25, no. 24 (2009): 3317–18. http://dx.doi.org/10.1093/bioinformatics/btp586.

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23

Mai, Guoqin, Ruiquan Ge, Guoquan Sun, Qinghan Meng, and Fengfeng Zhou. "A Comprehensive Curation Shows the Dynamic Evolutionary Patterns of Prokaryotic CRISPRs." BioMed Research International 2016 (2016): 1–7. http://dx.doi.org/10.1155/2016/7237053.

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Motivation.Clustered regularly interspaced short palindromic repeat (CRISPR) is a genetic element with active regulation roles for foreign invasive genes in the prokaryotic genomes and has been engineered to work with the CRISPR-associated sequence (Cas) gene Cas9 as one of the modern genome editing technologies. Due to inconsistent definitions, the existing CRISPR detection programs seem to have missed some weak CRISPR signals.Results.This study manually curates all the currently annotated CRISPR elements in the prokaryotic genomes and proposes 95 updates to the annotations. A new definition

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24

Cai, Ruijie, Runyu Lv, Xin’e Shi, Gongshe Yang, and Jianjun Jin. "CRISPR/dCas9 Tools: Epigenetic Mechanism and Application in Gene Transcriptional Regulation." International Journal of Molecular Sciences 24, no. 19 (2023): 14865. http://dx.doi.org/10.3390/ijms241914865.

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CRISPR/Cas9-mediated cleavage of DNA, which depends on the endonuclease activity of Cas9, has been widely used for gene editing due to its excellent programmability and specificity. However, the changes to the DNA sequence that are mediated by CRISPR/Cas9 affect the structures and stability of the genome, which may affect the accuracy of results. Mutations in the RuvC and HNH regions of the Cas9 protein lead to the inactivation of Cas9 into dCas9 with no endonuclease activity. Despite the loss of endonuclease activity, dCas9 can still bind the DNA strand using guide RNA. Recently, proteins wit

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Zhang, Yunxi. "Application and Prospect of CRISPR System in Alzheimer's Disease Treatment Research." Theoretical and Natural Science 90, no. 1 (2025): 146–51. https://doi.org/10.54254/2753-8818/2025.gu20970.

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Alzheimer's disease (abbreviated as AD), commonly known as senile dementia. As its name implies, it is the most common degenerative disease of the central nervous system that occurs in the elderly population. At present, there is still no effective treatment method. At present, CRISPR system-based research continues to advance in the field of AD therapy, such as CRISPR Cas9 for the construction of cell and animal models and gene knockout therapy, CRISPR Cas13 for the development of new detection technologies, CRISPRi has made progress in exploring related gene regulatory mechanisms, and CRISPR

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Tong, Yaojun, Christopher M. Whitford, Kai Blin, Tue S. Jørgensen, Tilmann Weber, and Sang Yup Lee. "CRISPR–Cas9, CRISPRi and CRISPR-BEST-mediated genetic manipulation in streptomycetes." Nature Protocols 15, no. 8 (2020): 2470–502. http://dx.doi.org/10.1038/s41596-020-0339-z.

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Shehreen, Saadlee, Te-yuan Chyou, Peter C. Fineran, and Chris M. Brown. "Genome-wide correlation analysis suggests different roles of CRISPR-Cas systems in the acquisition of antibiotic resistance genes in diverse species." Philosophical Transactions of the Royal Society B: Biological Sciences 374, no. 1772 (2019): 20180384. http://dx.doi.org/10.1098/rstb.2018.0384.

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CRISPR-Cas systems are widespread in bacterial and archaeal genomes, and in their canonical role in phage defence they confer a fitness advantage. However, CRISPR-Cas may also hinder the uptake of potentially beneficial genes. This is particularly true under antibiotic selection, where preventing the uptake of antibiotic resistance genes could be detrimental. Newly discovered features within these evolutionary dynamics are anti-CRISPR genes, which inhibit specific CRISPR-Cas systems. We hypothesized that selection for antibiotic resistance might have resulted in an accumulation of anti-CRISPR

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Wang, Jiawei, Wei Dai, Jiahui Li, et al. "PaCRISPR: a server for predicting and visualizing anti-CRISPR proteins." Nucleic Acids Research 48, W1 (2020): W348—W357. http://dx.doi.org/10.1093/nar/gkaa432.

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Abstract Anti-CRISPRs are widespread amongst bacteriophage and promote bacteriophage infection by inactivating the bacterial host's CRISPR–Cas defence system. Identifying and characterizing anti-CRISPR proteins opens an avenue to explore and control CRISPR–Cas machineries for the development of new CRISPR–Cas based biotechnological and therapeutic tools. Past studies have identified anti-CRISPRs in several model phage genomes, but a challenge exists to comprehensively screen for anti-CRISPRs accurately and efficiently from genome and metagenome sequence data. Here, we have developed an ensembl

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Weiss, Simone, Allegra Lord, Bernhard Schmierer, et al. "Abstract 3778: Genome-Scale CRISPRa and CRISPRi screening for lncRNA drivers of prostate cancer progression." Cancer Research 83, no. 7_Supplement (2023): 3778. http://dx.doi.org/10.1158/1538-7445.am2023-3778.

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Abstract Background: Overtreatment of indolent prostate cancer (PC) and delayed treatment of aggressive PC is common due to suboptimal risk stratification tools, thus warranting identification of novel prognostic biomarkers. Although a few long non-coding RNAs (lncRNAs) with biomarker potential in PC are known, the majority of lncRNAs remain uncharacterized. Here, we aimed to identify novel lncRNA biomarker candidates. We hypothesized that strong candidates would have a functional role in driving PC progression in addition to their expression being linked to PC prognosis, and we therefore comb

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Watters, Kyle E., Christof Fellmann, Hua B. Bai, Shawn M. Ren, and Jennifer A. Doudna. "Systematic discovery of natural CRISPR-Cas12a inhibitors." Science 362, no. 6411 (2018): 236–39. http://dx.doi.org/10.1126/science.aau5138.

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Cas12a (Cpf1) is a CRISPR-associated nuclease with broad utility for synthetic genome engineering, agricultural genomics, and biomedical applications. Although bacteria harboring CRISPR-Cas9 or CRISPR-Cas3 adaptive immune systems sometimes acquire mobile genetic elements encoding anti-CRISPR proteins that inhibit Cas9, Cas3, or the DNA-binding Cascade complex, no such inhibitors have been found for CRISPR-Cas12a. Here we use a comprehensive bioinformatic and experimental screening approach to identify three different inhibitors that block or diminish CRISPR-Cas12a–mediated genome editing in hu

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Hayes, Victoria M., Jun-Tao Zhang, Mark A. Katz, et al. "RNA-mediated CRISPR-Cas13 inhibition through crRNA structural mimicry." Science 388, no. 6745 (2025): 387–91. https://doi.org/10.1126/science.adr3656.

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To circumvent CRISPR-Cas immunity, phages express anti-CRISPR factors that inhibit the expression or activities of Cas proteins. Whereas most anti-CRISPRs described to date are proteins, recently described small RNAs called RNA anti-CRISPRs (rAcrs) have sequence homology to CRISPR RNAs (crRNAs) and displace them from cognate Cas nucleases. In this work, we report the discovery of rAcrVIA1—a plasmid-encoded small RNA that inhibits the RNA-targeting CRISPR-Cas13 system in its natural host, Listeria seeligeri . We solved the cryo–electron microscopy structure of the Cas13-rAcr complex, which reve

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Wang, Kai, and Chun Liang. "CRF: detection of CRISPR arrays using random forest." PeerJ 5 (April 25, 2017): e3219. http://dx.doi.org/10.7717/peerj.3219.

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CRISPRs (clustered regularly interspaced short palindromic repeats) are particular repeat sequences found in wide range of bacteria and archaea genomes. Several tools are available for detecting CRISPR arrays in the genomes of both domains. Here we developed a new web-based CRISPR detection tool named CRF (CRISPR Finder by Random Forest). Different from other CRISPR detection tools, a random forest classifier was used in CRF to filter out invalid CRISPR arrays from all putative candidates and accordingly enhanced detection accuracy. In CRF, particularly, triplet elements that combine both sequ

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Lin, Joseph, and Jun Yang. "CRISPR-Cas systems: A revolution in genome editing and its diverse applications." Journal of Biomed Research 5, no. 1 (2024): 108–14. http://dx.doi.org/10.46439/biomedres.5.050.

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The clustered regularly interspaced short palindromic repeats (CRISPR) Cas (CRISPR6 associated protein) system is an advanced adaptive immune system found in prokaryotes. First discovered in1987, CRISPR Cas has revolutionized genetic research in the past two decades. CRISPR-Cas9 the most widespread system enables precise gene editing by creating double strand breaks. Its ease of use and cost-effectiveness has lowered the barrier to entry for genetic research. CRISPR holds immense potential in many fields from agriculture to medicine. In agriculture, CRISPR has accelerated crop improvement by e

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Davidson, Alan R., Wang-Ting Lu, Sabrina Y. Stanley, et al. "Anti-CRISPRs: Protein Inhibitors of CRISPR-Cas Systems." Annual Review of Biochemistry 89, no. 1 (2020): 309–32. http://dx.doi.org/10.1146/annurev-biochem-011420-111224.

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Clustered regularly interspaced short palindromic repeats (CRISPR) together with their accompanying cas (CRISPR-associated) genes are found frequently in bacteria and archaea, serving to defend against invading foreign DNA, such as viral genomes. CRISPR-Cas systems provide a uniquely powerful defense because they can adapt to newly encountered genomes. The adaptive ability of these systems has been exploited, leading to their development as highly effective tools for genome editing. The widespread use of CRISPR-Cas systems has driven a need for methods to control their activity. This review fo

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Belato, Helen B., and George P. Lisi. "The Many (Inter)faces of Anti-CRISPRs: Modulation of CRISPR-Cas Structure and Dynamics by Mechanistically Diverse Inhibitors." Biomolecules 13, no. 2 (2023): 264. http://dx.doi.org/10.3390/biom13020264.

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The discovery of protein inhibitors of CRISPR-Cas systems, called anti-CRISPRs (Acrs), has enabled the development of highly controllable and precise CRISPR-Cas tools. Anti-CRISPRs share very little structural or sequential resemblance to each other or to other proteins, which raises intriguing questions regarding their modes of action. Many structure–function studies have shed light on the mechanism(s) of Acrs, which can act as orthosteric or allosteric inhibitors of CRISPR–Cas machinery, as well as enzymes that irreversibly modify CRISPR–Cas components. Only recently has the breadth of diver

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Kiro, Ruth, Moran G. Goren, Ido Yosef, and Udi Qimron. "CRISPR adaptation in Escherichia coli subtypeI-E system." Biochemical Society Transactions 41, no. 6 (2013): 1412–15. http://dx.doi.org/10.1042/bst20130109.

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The CRISPRs (clustered regularly interspaced short palindromic repeats) and their associated Cas (CRISPR-associated) proteins are a prokaryotic adaptive defence system against foreign nucleic acids. The CRISPR array comprises short repeats flanking short segments, called ‘spacers’, which are derived from foreign nucleic acids. The process of spacer insertion into the CRISPR array is termed ‘adaptation’. Adaptation allows the system to rapidly evolve against emerging threats. In the present article, we review the most recent studies on the adaptation process, and focus primarily on the subtype

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Syding, Linn Amanda, Petr Nickl, Petr Kasparek, and Radislav Sedlacek. "CRISPR/Cas9 Epigenome Editing Potential for Rare Imprinting Diseases: A Review." Cells 9, no. 4 (2020): 993. http://dx.doi.org/10.3390/cells9040993.

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Imprinting diseases (IDs) are rare congenital disorders caused by aberrant dosages of imprinted genes. Rare IDs are comprised by a group of several distinct disorders that share a great deal of homology in terms of genetic etiologies and symptoms. Disruption of genetic or epigenetic mechanisms can cause issues with regulating the expression of imprinted genes, thus leading to disease. Genetic mutations affect the imprinted genes, duplications, deletions, and uniparental disomy (UPD) are reoccurring phenomena causing imprinting diseases. Epigenetic alterations on methylation marks in imprinting

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Chaturvedi, Sarika, and Jinny Tomar. "CRISPR/CAS 9 Mediated Treatment for UTIs." International Journal for Modern Trends in Science and Technology 6, no. 5 (2020): 82–94. http://dx.doi.org/10.46501/ijmtst060515.

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“CRISPR" is short and used for "CRISPR-Cas9. CRISPR stands for clustered regularly interspaced short palindromic repeats. CRISPRs are specialized stretches of DNA. The protein Cas9 (or "CRISPR-associated") is an enzyme that acts like a pair of molecular scissors, capable of cutting strands of DNA and can be used in conjunction with engineered CRISPR sequences to hunt down codes and slice into them like a molecular scalpel, allowing geneticists to cut out a target gene, either to remove it or replace it with a new sequence. Therefore it is a simple and powerful tool for editing genomes to easil

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Zegans, Michael E., Jeffrey C. Wagner, Kyle C. Cady, Daniel M. Murphy, John H. Hammond, and George A. O'Toole. "Interaction between Bacteriophage DMS3 and Host CRISPR Region Inhibits Group Behaviors of Pseudomonas aeruginosa." Journal of Bacteriology 191, no. 1 (2008): 210–19. http://dx.doi.org/10.1128/jb.00797-08.

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ABSTRACT Bacteriophage infection has profound effects on bacterial biology. Clustered regular interspaced short palindromic repeats (CRISPRs) and cas (CRISPR-associated) genes are found in most archaea and many bacteria and have been reported to play a role in resistance to bacteriophage infection. We observed that lysogenic infection of Pseudomonas aeruginosa PA14 with bacteriophage DMS3 inhibits biofilm formation and swarming motility, both important bacterial group behaviors. This inhibition requires the CRISPR region in the host. Mutation or deletion of five of the six cas genes and one of

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Brown, Rachel Anne, Andrew W. Dangel, Ankita Saini, and Eugene M. Oltz. "Regulators of Type III Cytokines in Type III Innate lymphoid Cells Identified by CRISPR Activation and Inhibition Screens." Journal of Immunology 206, no. 1_Supplement (2021): 106.04. http://dx.doi.org/10.4049/jimmunol.206.supp.106.04.

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Abstract Type III cytokines interleukin (IL)-22 and IL-17 are expressed by both innate and adaptive immune cells to defend against extracellular pathogens, yet their dysregulation contributes to autoimmunity and malignancy. A deeper knowledge of IL-22/17 regulation is warranted to understand physiologic processes as well as disease pathogenesis, thereby elucidating druggable targets. Toward this goal, we applied genome-wide CRISPR activation (CRISPRa) and CRISPR inhibition (CRISPRi) screens to identify the collection of factors that positively or negatively regulate IL-17/22 expression in a mu

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Hegde, Shivanand, Hallie E. Rauch, Grant L. Hughes, and Nikki Shariat. "Identification and characterization of two CRISPR/Cas systems associated with the mosquito microbiome." Access Microbiology 5, no. 8 (2023). http://dx.doi.org/10.1099/acmi.0.000599.v4.

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The microbiome profoundly influences many traits in medically relevant vectors such as mosquitoes, and a greater functional understanding of host–microbe interactions may be exploited for novel microbial-based approaches to control mosquito-borne disease. Here, we characterized two novel clustered regularly interspaced short palindromic repeats (CRISPR)/Cas systems in Serratia sp. Ag1, which was isolated from the gut of an Anopheles gambiae mosquito. Two distinct CRISPR/Cas systems were identified in Serratia Ag1, CRISPR1 and CRISPR2. Based on cas gene composition, CRISPR1 is classified as a t

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Hoberecht, Luke, Pirunthan Perampalam, Aaron Lun, and Jean-Philippe Fortin. "A comprehensive Bioconductor ecosystem for the design of CRISPR guide RNAs across nucleases and technologies." Nature Communications 13, no. 1 (2022). http://dx.doi.org/10.1038/s41467-022-34320-7.

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AbstractThe success of CRISPR-mediated gene perturbation studies is highly dependent on the quality of gRNAs, and several tools have been developed to enable optimal gRNA design. However, these tools are not all adaptable to the latest CRISPR modalities or nucleases, nor do they offer comprehensive annotation methods for advanced CRISPR applications. Here, we present a new ecosystem of R packages, called crisprVerse, that enables efficient gRNA design and annotation for a multitude of CRISPR technologies. This includes CRISPR knockout (CRISPRko), CRISPR activation (CRISPRa), CRISPR interferenc

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Hu, Shijie, Mailin Gan, Ziang Wei, et al. "Identification of host factors for livestock and poultry viruses: genome-wide screening technology based on the CRISPR system." Frontiers in Microbiology 15 (November 21, 2024). http://dx.doi.org/10.3389/fmicb.2024.1498641.

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Genome-wide CRISPR library screening technology is a gene function research tool developed based on the CRISPR/Cas9 gene-editing system. The clustered regularly interspaced short palindromic repeats/CRISPR-associated genes (CRISPR/Cas) system, considered the third generation of gene editing after zinc finger nucleases (ZFN) and transcription activator-like effector nucleases (TALEN), is widely used for screening various viral host factors. CRISPR libraries are classified into three main categories based on the different functions of Cas9 enzymes: CRISPR knockout (CRISPR KO) library screening,

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Drobna-Śledzińska, Monika, Natalia Maćkowska-Maślak, Roman Jaksik, Paulina Dąbek, Michał Witt, and Małgorzata Dawidowska. "CRISPRi for specific inhibition of miRNA clusters and miRNAs with high sequence homology." Scientific Reports 12, no. 1 (2022). http://dx.doi.org/10.1038/s41598-022-10336-3.

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AbstractmiRNAs form a class of noncoding RNAs, involved in post-transcriptional regulation of gene expression, broadly studied for their involvement in physiological and pathological context. Inhibition of mature miRNA transcripts, commonly used in miRNA loss-of-function experiments, may not be specific in case of miRNAs with high sequence homology, e.g. miRNAs from the same seed family. Phenotypic effects of miRNA repression might be biased by the repression of highly similar miRNAs. Another challenge is simultaneous inhibition of multiple miRNAs encoded within policistronic clusters, potenti

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Horlbeck, Max A., Luke A. Gilbert, Jacqueline E. Villalta, et al. "Compact and highly active next-generation libraries for CRISPR-mediated gene repression and activation." eLife 5 (September 23, 2016). http://dx.doi.org/10.7554/elife.19760.

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We recently found that nucleosomes directly block access of CRISPR/Cas9 to DNA (<xref ref-type="bibr" rid="bib25">Horlbeck et al., 2016</xref>). Here, we build on this observation with a comprehensive algorithm that incorporates chromatin, position, and sequence features to accurately predict highly effective single guide RNAs (sgRNAs) for targeting nuclease-dead Cas9-mediated transcriptional repression (CRISPRi) and activation (CRISPRa). We use this algorithm to design next-generation genome-scale CRISPRi and CRISPRa libraries targeting human and mouse genomes. A CRISPRi screen fo

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Matsutani, Minenosuke, Takura Wakinaka, Jun Watanabe, Masafumi Tokuoka, and Akihiro Ohnishi. "Comparative Genomics of Closely Related Tetragenococcus halophilus Strains Elucidate the Diversity and Microevolution of CRISPR Elements." Frontiers in Microbiology 12 (June 18, 2021). http://dx.doi.org/10.3389/fmicb.2021.687985.

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Tetragenococcus halophilus – a halophilic lactic acid bacterium – is frequently used as a starter culture for manufacturing fermented foods. Tetragenococcus is sometimes infected with bacteriophages during fermentation for soy sauce production; however, bacteriophage infection in starter bacteria is one of the major causes of fermentation failure. Here, we obtained whole-genome sequences of the four T. halophilus strains YA5, YA163, YG2, and WJ7 and compared them with 18 previously reported genomes. We elucidated five types of clustered regularly interspaced short palindromic repeat (CRISPR) l

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Shen, Qiqing, Haihua Ruan, Hongyang Zhang, et al. "Utilization of CRISPR-Cas genome editing technology in filamentous fungi: function and advancement potentiality." Frontiers in Microbiology 15 (March 28, 2024). http://dx.doi.org/10.3389/fmicb.2024.1375120.

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Filamentous fungi play a crucial role in environmental pollution control, protein secretion, and the production of active secondary metabolites. The evolution of gene editing technology has significantly improved the study of filamentous fungi, which in the past was laborious and time-consuming. But recently, CRISPR-Cas systems, which utilize small guide RNA (sgRNA) to mediate clustered regularly interspaced short palindromic repeats (CRISPR) and CRISPR-associated proteins (Cas), have demonstrated considerable promise in research and application for filamentous fungi. The principle, function,

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Ma, Shuai, Feiyu Wang, Zhang Xuejing, et al. "Repurposing endogenous type II CRISPR‐Cas9 system for genome editing in Streptococcus thermophilus." Biotechnology and Bioengineering, November 23, 2023. http://dx.doi.org/10.1002/bit.28608.

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AbstractStreptococcus thermophilus has been extensively used in industrial milk fermentation. However, lack of efficient genetic manipulation approaches greatly hampered the industrial application of this species. Here, we repurposed the endogenous CRISPR1 and CRISPR3 systems, both belong to type II‐A CRISPR‐Cas9, by delivering a self‐targeting CRISPR array with DNA repair template into S. thermophilus LMD‐9. We achieved 785‐bp deletion in lacZ gene by repurposing CRISPR1 and CRISPR3 systems with efficiencies of 35% and 59%, respectively, when 1‐kb DNA repair template was provided. While provi

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Das, Ankita, Kamali Doss, and Jharna Mandal. "CRISPR-cas heterogeneity and plasmid incompatibility types in relation to virulence determinants of Shigella." Journal of Medical Microbiology 71, no. 10 (2022). http://dx.doi.org/10.1099/jmm.0.001607.

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Introduction. Virulence factors (VFs) are the most potent weapon in the molecular armoury of Shigella . In bacteria, the mobile genetic elements (MGEs) are contributors to the evolution of different types of clustered regularly interspaced short palindromic repeats-CRISPR associated genes (CRISPR-cas) variants and plasmid incompatibility types. The present study explored the virulence potential of Shigella in relation to the CRISPR-cas pattern and incompatibility types among the isolates. Hypothesis/Gap Statement. The profile of the CRISPR-cas systems among clinical isolates of Shigella in Ind

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Feng, Qing, Xiaoyu Ning, Lei Qin, Jun Li, and Chun Li. "Quantitative and modularized CRISPR/dCas9-dCpf1 dual function system in Saccharomyces cerevisiae." Frontiers in Bioengineering and Biotechnology 11 (October 18, 2023). http://dx.doi.org/10.3389/fbioe.2023.1218832.

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Introduction: Both CRISPR/dCas9 and CRISPR/dCpf1 genome editing systems have shown exciting promises in modulating yeast cell metabolic pathways. However, each system has its deficiencies to overcome. In this study, to achieve a compensatory effect, we successfully constructed a dual functional CRISPR activation/inhibition (CRISPRa/i) system based on Sp-dCas9 and Fn-dCpf1 proteins, along with their corresponding complementary RNAs.Methods: We validated the high orthogonality and precise quantity targeting of selected yeast promoters. Various activating effector proteins (VP64, p65, Rta, and VP

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