{"title":"Bioinformatic tools for CRISPR-mediated genome editing","authors":"Fatemeh Gila , Shayan Shakeri , Somayeh Khoddam , Zahra Jamali , Ali Saber Sichani , Zeinab Dehghan , Jafar Fallahi","doi":"10.1016/j.genrep.2025.102204","DOIUrl":null,"url":null,"abstract":"<div><div>The groundbreaking gene-editing tool CRISPR-Cas9 has revolutionized molecular biology. It is a method that enables scientists to precisely alter the DNA of living cells, which holds great promise for treating genetic illnesses. The Cas9 protein and a guide RNA (gRNA) are the two critical parts of the CRISPR-Cas9 system. While the gRNA guides the Cas9 protein to the appropriate region in the genome, the Cas9 protein functions as a pair of molecular scissors, cutting the DNA at a specific location. In recent years, several databases have been created to assist researchers in designing efficient gRNAs. These databases provide information on the specificity and efficiency of various gRNAs and tools for designing custom gRNAs. This review article will go over the most beneficial and recent databases for gRNA design that are now accessible. These databases are crucial for attaining effective and precise gene editing and therapy using the CRISPR-Cas9 system.</div></div>","PeriodicalId":12673,"journal":{"name":"Gene Reports","volume":"39 ","pages":"Article 102204"},"PeriodicalIF":1.0000,"publicationDate":"2025-03-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":"0","resultStr":null,"platform":"Semanticscholar","paperid":null,"PeriodicalName":"Gene Reports","FirstCategoryId":"1085","ListUrlMain":"https://www.sciencedirect.com/science/article/pii/S2452014425000779","RegionNum":0,"RegionCategory":null,"ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":null,"EPubDate":"","PubModel":"","JCR":"Q4","JCRName":"GENETICS & HEREDITY","Score":null,"Total":0}
引用次数: 0
Abstract
The groundbreaking gene-editing tool CRISPR-Cas9 has revolutionized molecular biology. It is a method that enables scientists to precisely alter the DNA of living cells, which holds great promise for treating genetic illnesses. The Cas9 protein and a guide RNA (gRNA) are the two critical parts of the CRISPR-Cas9 system. While the gRNA guides the Cas9 protein to the appropriate region in the genome, the Cas9 protein functions as a pair of molecular scissors, cutting the DNA at a specific location. In recent years, several databases have been created to assist researchers in designing efficient gRNAs. These databases provide information on the specificity and efficiency of various gRNAs and tools for designing custom gRNAs. This review article will go over the most beneficial and recent databases for gRNA design that are now accessible. These databases are crucial for attaining effective and precise gene editing and therapy using the CRISPR-Cas9 system.
Gene ReportsBiochemistry, Genetics and Molecular Biology-Genetics
CiteScore
3.30
自引率
7.70%
发文量
246
审稿时长
49 days
期刊介绍:
Gene Reports publishes papers that focus on the regulation, expression, function and evolution of genes in all biological contexts, including all prokaryotic and eukaryotic organisms, as well as viruses. Gene Reports strives to be a very diverse journal and topics in all fields will be considered for publication. Although not limited to the following, some general topics include: DNA Organization, Replication & Evolution -Focus on genomic DNA (chromosomal organization, comparative genomics, DNA replication, DNA repair, mobile DNA, mitochondrial DNA, chloroplast DNA). Expression & Function - Focus on functional RNAs (microRNAs, tRNAs, rRNAs, mRNA splicing, alternative polyadenylation) Regulation - Focus on processes that mediate gene-read out (epigenetics, chromatin, histone code, transcription, translation, protein degradation). Cell Signaling - Focus on mechanisms that control information flow into the nucleus to control gene expression (kinase and phosphatase pathways controlled by extra-cellular ligands, Wnt, Notch, TGFbeta/BMPs, FGFs, IGFs etc.) Profiling of gene expression and genetic variation - Focus on high throughput approaches (e.g., DeepSeq, ChIP-Seq, Affymetrix microarrays, proteomics) that define gene regulatory circuitry, molecular pathways and protein/protein networks. Genetics - Focus on development in model organisms (e.g., mouse, frog, fruit fly, worm), human genetic variation, population genetics, as well as agricultural and veterinary genetics. Molecular Pathology & Regenerative Medicine - Focus on the deregulation of molecular processes in human diseases and mechanisms supporting regeneration of tissues through pluripotent or multipotent stem cells.