scholarly journals CRISPR Cas9 Tip of an Iceberg: It’s Potential in Genome Editing and Many More

2021 ◽  
Author(s):  
Jalal Ahmad ◽  
Nayyer Siddique
Keyword(s):  
Genome Editing ◽  
Genetic Diseases ◽  
Adaptive Immune System ◽  
Biological Research ◽  
Adaptive Immune ◽  
Scientific World ◽  
A Genome ◽  
Foreign Dna ◽  
Immense Potential ◽  
Potential Use

Clustered regularly interspaced short palindromic repeats or CRISPR, one of the major technological tools from nature's toolbox, has revolutionized the scientific world with its potential use in humans and plants. CRISPR Cas9 was first known as an adaptive immune system of bacteria. It is a system that cleaves foreign DNA. It has been exploited to be used as a genome editing tool for correcting genetic diseases in humans, for plants to create stress-resistant plants, and for a variety of different purposes. This review provides a basic overview of its applications in different areas of biological research. It has immense potential for a variety of researches, but it's still a mystery for science. It feels like scientists just know a tip of an iceberg.

scholarly journals Use of CRISPR systems in plant genome editing: toward new opportunities in agriculture

2017 ◽  
Vol 1 (2) ◽  
pp. 169-182 ◽  
Author(s):  
Agnès Ricroch ◽  
Pauline Clairand ◽  
Wendy Harwood
Keyword(s):  
Oryza Sativa ◽  
Genome Editing ◽  
Abiotic Stress Tolerance ◽  
Adaptive Immune System ◽  
Plant Genome ◽  
Biotic And Abiotic Stress ◽  
Yield Performance ◽  
Adaptive Immune ◽  
A Genome ◽  
Agricultural Applications

Initially discovered in bacteria and archaea, CRISPR–Cas9 is an adaptive immune system found in prokaryotes. In 2012, scientists found a way to use it as a genome editing tool. In 2013, its application in plants was successfully achieved. This breakthrough has opened up many new opportunities for researchers, including the opportunity to gain a better understanding of plant biological systems more quickly. The present study reviews agricultural applications related to the use of CRISPR systems in plants from 52 peer-reviewed articles published since 2014. Based on this literature review, the main use of CRISPR systems is to achieve improved yield performance, biofortification, biotic and abiotic stress tolerance, with rice (Oryza sativa) being the most studied crop.

scholarly journals Programming Native CRISPR Arrays for the Generation of Targeted Immunity

mBio ◽  
2016 ◽  
Vol 7 (3) ◽  
Author(s):  
Alexander P. Hynes ◽  
Simon J. Labrie ◽  
Sylvain Moineau
Keyword(s):  
Immune System ◽  
Nucleic Acid ◽  
Genome Editing ◽  
Dna Sequence ◽  
Adaptive Immune System ◽  
Natural Process ◽  
The Public ◽  
Adaptive Immune ◽  
Public Consciousness ◽  
Industrial Settings

ABSTRACT The adaptive immune system of prokaryotes, called CRISPR-Cas (clustered regularly interspaced short palindromic repeats and CRISPR-associated genes), results in specific cleavage of invading nucleic acid sequences recognized by the cell’s “memory” of past encounters. Here, we exploited the properties of native CRISPR-Cas systems to program the natural “memorization” process, efficiently generating immunity not only to a bacteriophage or plasmid but to any specifically chosen DNA sequence. IMPORTANCE CRISPR-Cas systems have entered the public consciousness as genome editing tools due to their readily programmable nature. In industrial settings, natural CRISPR-Cas immunity is already exploited to generate strains resistant to potentially disruptive viruses. However, the natural process by which bacteria acquire new target specificities (adaptation) is difficult to study and manipulate. The target against which immunity is conferred is selected stochastically. By biasing the immunization process, we offer a means to generate customized immunity, as well as provide a new tool to study adaptation.

scholarly journals Mechanism of Foreign DNA Selection in a Bacterial Adaptive Immune System

2012 ◽  
Vol 46 (5) ◽  
pp. 606-615 ◽  
Author(s):  
Dipali G. Sashital ◽  
Blake Wiedenheft ◽  
Jennifer A. Doudna
Keyword(s):  
Immune System ◽  
Adaptive Immune System ◽  
Adaptive Immune ◽  
Foreign Dna

scholarly journals Snippets of virus integrated into human genome suggests possibility of CRISPR-like adaptive immune system in human cells

2019 ◽  
Author(s):  
Wenfa Ng
Keyword(s):  
Immune Response ◽  
Immune System ◽  
Human Genome ◽  
Adaptive Immune Response ◽  
Adaptive Immune System ◽  
Human Cells ◽  
Rna Seq ◽  
Viral Dna ◽  
Adaptive Immune ◽  
Foreign Dna

Snippets of virus that infect humans have been shown to be incorporated into the human genome. Could such virus snippets provide a form of adaptive immunity similar to that offered by CRISPR to bacterial cells? To answer the question, RNA-seq could be used to provide a broad view of the RNA transcribed from DNA in the genome. Using known genome sequence of viruses that infect humans as template, reads obtained from RNA-seq would be profiled for virus snippets integrated into human genome and subsequently transcribed as part of an adaptive immune system. Subsequently, viruses corresponding to the virus snippets in human genome would be used to infect human cell lines to obtain direct evidence of how virus snippets mediate an adaptive immune response at the cellular level. Specifically, successful defence of the cell by virus snippets triggering an adaptive immune response would manifest as viable cells compared to lysed cells unable to mount an immune response. Following demonstration of cell viability under viral challenge, in vitro biochemical assays using cell lysate would interrogate the specific proteins and enzymes that mediate possible cutting of the foreign DNA or RNA. To this end, beads immobilized with virus snippets would serve as bait for binding to complementary viral DNA or RNA as well as potential endogenous endonuclease protein. Following precipitation and recovery of beads, possible endonuclease that bind to both viral DNA or RNA and virus snippets immobilized on beads would be isolated through gel electrophoresis and subsequently purified. Purified endonuclease would be assayed for activity against a variety of nucleic acids (both DNA and RNA) from various sources with and without added virus snippets. This provides important information on substrate range and specificity of the potential endonuclease. Amino acid sequencing of the purified endonuclease would help downstream bioinformatic search for candidate protein in the human genome. Finally, cryo-electron microscopy could help determine the structure of the endonuclease in complex with viral nucleic acids and virus snippets. Such structural information would provide more insights into mechanistic details describing the binding and cleavage of viral DNA or RNA in a CRISPR-like adaptive immune response in human cells. Overall, tantalizing clues have emerged that a CRISPR-like adaptive immune response may exist in human cells for defending against viral attack. Combination of cell biological, biochemical and structural tools could lend insights into the potential endonuclease that mediate double strand break of foreign DNA or RNA using virus snippets transcribed from the human genome as guide RNA. If demonstrated to be true for a variety of human viruses across different cell lines, the newly discovered viral defence mechanism in human cells hold important implications for understanding the adoption and evolution of CRISPR in eukaryotic cells.

scholarly journals CASPredict: a web service for identifying Cas proteins

PeerJ ◽  
2021 ◽  
Vol 9 ◽  
pp. e11887
Author(s):  
Shanshan Yang ◽  
Jian Huang ◽  
Bifang He
Keyword(s):  
Web Service ◽  
Genome Editing ◽  
Search Algorithm ◽  
Adaptive Immune System ◽  
Support Vector ◽  
Adaptive Immune ◽  
Complementary Role ◽  
Fold Cross Validation ◽  
Eukaryotic Genomes ◽  
Cas Proteins

Clustered regularly interspaced short palindromic repeats (CRISPR) and their associated (Cas) proteins constitute the CRISPR-Cas systems, which play a key role in prokaryote adaptive immune system against invasive foreign elements. In recent years, the CRISPR-Cas systems have also been designed to facilitate target gene editing in eukaryotic genomes. As one of the important components of the CRISPR-Cas system, Cas protein plays an irreplaceable role. The effector module composed of Cas proteins is used to distinguish the type of CRISPR-Cas systems. Effective prediction and identification of Cas proteins can help biologists further infer the type of CRISPR-Cas systems. Moreover, the class 2 CRISPR-Cas systems are gradually applied in the field of genome editing. The discovery of Cas protein will help provide more candidates for genome editing. In this paper, we described a web service named CASPredict (http://i.uestc.edu.cn/caspredict/cgi-bin/CASPredict.pl) for identifying Cas proteins. CASPredict first predicts Cas proteins based on support vector machine (SVM) by using the optimal dipeptide composition and then annotates the function of Cas proteins based on the hmmscan search algorithm. The ten-fold cross-validation results showed that the 84.84% of Cas proteins were correctly classified. CASPredict will be a useful tool for the identification of Cas proteins, or at least can play a complementary role to the existing methods in this area.

scholarly journals Allele specific repair of splicing mutations in cystic fibrosis through AsCas12a genome editing

2019 ◽  
Vol 10 (1) ◽  
Author(s):  
Giulia Maule ◽  
Antonio Casini ◽  
Claudia Montagna ◽  
Anabela S. Ramalho ◽  
Kris De Boeck ◽  
...  
Keyword(s):  
Cystic Fibrosis ◽  
Genome Editing ◽  
Genetic Diseases ◽  
Airway Epithelial Cells ◽  
Airway Epithelial ◽  
Gene Correction ◽  
Splicing Mutations ◽  
Mutant Sequence ◽  
A Genome ◽  
Allele Specific

Abstract Cystic fibrosis (CF) is an autosomal recessive disease caused by mutations in the CFTR gene. The 3272–26A>G and 3849+10kbC>T CFTR mutations alter the correct splicing of the CFTR gene, generating new acceptor and donor splice sites respectively. Here we develop a genome editing approach to permanently correct these genetic defects, using a single crRNA and the Acidaminococcus sp. BV3L6, AsCas12a. This genetic repair strategy is highly precise, showing very strong discrimination between the wild-type and mutant sequence and a complete absence of detectable off-targets. The efficacy of this gene correction strategy is verified in intestinal organoids and airway epithelial cells derived from CF patients carrying the 3272–26A>G or 3849+10kbC>T mutations, showing efficient repair and complete functional recovery of the CFTR channel. These results demonstrate that allele-specific genome editing with AsCas12a can correct aberrant CFTR splicing mutations, paving the way for a permanent splicing correction in genetic diseases.

CRISPR/Cas-Systems: characteristics and possibilities of use for editing bacterial genomes

Bacteriology ◽  
2020 ◽  
Vol 5 (2) ◽  
pp. 38-48
Author(s):  
I.A. Blatov ◽  
◽  
A.S. Shchurova ◽  
D.Yu. Guschin ◽  
S.D. Zvereva ◽  
...  
Keyword(s):  
Immune System ◽  
Genome Editing ◽  
Bacterial Species ◽  
Adaptive Immune System ◽  
Bacterial Genomes ◽  
Modern Biology ◽  
Adaptive Immune ◽  
History Of ◽  
Genomic Editing ◽  
Classification Structure

CRISPR-Cas is the adaptive immune system of bacteria and archaea. Since 2012, when the first opportunity to use the CRISPR/Cas system for genome editing was realized, the number of studies in this area has been growing rapidly. Today, genomic editing to modify specific regions of the genomes of various organisms is considered one of the key methodologies of modern biology. This review is devoted to the history of discovery, classification, structure, operational mechanisms of CRISPRCas systems and strategies for editing the genomes of various bacterial species using this technology. Key words: genome editing, genome, CRISPR-Cas system, bacteria

scholarly journals The Fascinating & Controversial New Science of CRISPR

2020 ◽  
Vol 82 (5) ◽  
pp. 279-288
Author(s):  
David Wollert
Keyword(s):  
Adaptive Immune System ◽  
Word Processor ◽  
Biological Research ◽  
Human Embryos ◽  
New Era ◽  
New Science ◽  
Adaptive Immune ◽  
Cultured Human Cells ◽  
Living Organisms ◽  
Science Educators

CRISPR (also known as CRISPR-Cas9) is a powerful biotechnology tool that gives scientists unprecedented access to the genetic makeup of all living organisms, including humans. It originally evolved as an adaptive immune system in bacteria to defend against viruses. When artificially harnessed in the laboratory it allows scientists to accurately and precisely edit genes, almost as if using a word processor. In mice, CRISPR has already been used to treat diabetes, muscular dystrophy, cancer, and blindness. CRISPR has made cultured human cells immune to HIV, and a variety of CRISPR experiments involving human embryos are well under way. But CRISPR is not limited to biomedical applications. It is also revolutionizing the food industry and many areas of biological research. This article provides science educators a broad and up-to-date overview of CRISPR, including its discovery, application, and bioethical challenges. It is imperative that science educators help prepare students, both majors and nonmajors, for this compelling new era of biology.

scholarly journals Editor's cut: DNA cleavage by CRISPR RNA-guided nucleases Cas9 and Cas12a

2019 ◽  
Vol 48 (1) ◽  
pp. 207-219 ◽  
Author(s):  
Thomas Swartjes ◽  
Raymond H.J. Staals ◽  
John van der Oost
Keyword(s):  
Immune System ◽  
Genome Editing ◽  
Dna Cleavage ◽  
Adaptive Immune System ◽  
New Developments ◽  
Biochemical Characteristics ◽  
Base Editing ◽  
Dna Cleaving ◽  
Adaptive Immune ◽  
General Method

Discovered as an adaptive immune system of prokaryotes, CRISPR–Cas provides many promising applications. DNA-cleaving Cas enzymes like Cas9 and Cas12a, are of great interest for genome editing. The specificity of these DNA nucleases is determined by RNA guides, providing great targeting adaptability. Besides this general method of programmable DNA cleavage, these nucleases have different biochemical characteristics, that can be exploited for different applications. Although Cas nucleases are highly promising, some room for improvement remains. New developments and discoveries like base editing, prime editing, and CRISPR-associated transposons might address some of these challenges.

In utero gene transfer to the mouse nervous system

2010 ◽  
Vol 38 (6) ◽  
pp. 1489-1493 ◽  
Author(s):  
Ahad A. Rahim ◽  
Andrew M.S. Wong ◽  
Suzanne M.K. Buckley ◽  
Jerry K.Y. Chan ◽  
Anna L. David ◽  
...  
Keyword(s):  
Nervous System ◽  
Gene Transfer ◽  
Progenitor Cell ◽  
Muscular Atrophy ◽  
Genetic Diseases ◽  
Adaptive Immune System ◽  
Early Gene ◽  
Fetal Mouse ◽  
Adaptive Immune ◽  
Technological Perspective

The cellular and molecular environment present in the fetus and early newborn provides an excellent opportunity for effective gene transfer. Innate and pre-existing anti-vector immunity may be attenuated or absent and the adaptive immune system predisposed to tolerance towards xenoproteins. Stem cell and progenitor cell populations are abundant, active and accessible. In addition, for treatment of early lethal genetic diseases of the nervous system, the overarching advantage may be that early gene supplementation prevents the onset of irreversible pathological changes. Gene transfer to the fetal mouse nervous system was achieved, albeit inefficiently, as far back as the mid-1980s. Recently, improvements in vector design and production have culminated in near-complete correction of a mouse model of spinal muscular atrophy. In the present article, we review perinatal gene transfer from both a therapeutic and technological perspective.

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