{"database":"EGA","file_versions":[],"scores":null,"additional":{"omics_type":["Genomics"],"contact_person":["Dr. Matthias Schlesner"],"full_dataset_link":["https://ega-archive.org/dacs/EGAC00001000346"],"host":["EGA"],"description":["EGA DAC EGAC00001000346"],"repository":["EGA"],"email":["m.schlesner@Dkfz-Heidelberg.de"],"pubmed_abstract":["Successful RNAi applications depend on strategies allowing robust and persistent expression of minimal gene silencing triggers without perturbing endogenous gene expression. Here, we propose a novel avenue which is integration of a promoterless shmiRNA, i.e. a shRNA embedded in a micro-RNA (miRNA) scaffold, into an engineered genomic miRNA locus. For proof-of-concept, we used TALE or CRISPR/Cas9 nucleases to site-specifically integrate an anti-hepatitis C virus (HCV) shmiRNA into the liver-specific miR-122/hcr locus in hepatoma cells, with the aim to obtain cellular clones that are genetically protected against HCV infection. Using reporter assays, Northern blotting and qRT-PCR, we confirmed anti-HCV shmiRNA expression as well as miR-122 integrity and functionality in selected cellular progeny. Moreover, we employed a comprehensive battery of PCR, cDNA/miRNA profiling and whole genome sequencing analyses to validate targeted integration of a single shmiRNA molecule at the expected position, and to rule out deleterious effects on the genomes or transcriptomes of the engineered cells. Importantly, a subgenomic HCV replicon and a full-length reporter virus, but not a Dengue virus control, were significantly impaired in the modified cells. Our original combination of DNA engineering and RNAi expression technologies benefits numerous applications, from miRNA, genome and transgenesis research, to human gene therapy."],"pubmed_title":["TALEN/CRISPR-mediated engineering of a promoterless anti-viral RNAi hairpin into an endogenous miRNA locus."],"pubmed_authors":["Senís Elena E, Mockenhaupt Stefan S, Rupp Daniel D, Bauer Tobias T, Paramasivam Nagarajan N, Knapp Bettina B, Gronych Jan J, Grosse Stefanie S, Windisch Marc P MP, Schmidt Florian F, Theis Fabian J FJ, Eils Roland R, Lichter Peter P, Schlesner Matthias M, Bartenschlager Ralf R, Grimm Dirk D"],"name_synonyms":["data analysis, Data Analyses., Analysis, data processing, Data, Analyses"],"pubmed_title_synonyms":["Post-Transcriptional Gene Silencings, pri miRNA, post-transcriptional gene silencing by RNA, RNA, miRNAs, Small Temporal, Micro, Engineerings, Posttranscriptional, Temporal RNA, Posttranscriptional Gene Silencing, stRNA, posttranscriptional gene silencing by siRNA, Small Temporal RNA, Primary MicroRNA, Primary, miRNA, Primary miRNA, cosuppression, quelling, Co Suppression, Cosuppression, pri-miRNA, INSDC_feature:ncRNA, Post Transcriptional Gene Silencing, RNAi, Gene Silencings, Small, Post-Transcriptional, Gene Silencing, Interference, Micro RNA, Post Transcriptional, MicroRNA, Primary., Co-Suppression, Post-Transcriptional Gene Silencing, RNA Silencing, pre-miRNA, pre miRNA, Silencing, Post-Transcriptional Gene"],"pubmed_abstract_synonyms":["Ribonucleic, Activity, HSN1E, Laboratory, bar, Hepatitis C-Like Viruses, Infestations and Infections, adult hepatoma, IDOL, Hepatomas, Liver Cell Carcinoma, Probes, prevention, Small, anon-WO0134654.19, qRT-PCR, cDNA library construction, DmelCG4637, Heme-regulated eukaryotic initiation factor eIF-2-alpha kinase, Post Transcriptional, Virus, Polymerase Chain, Mir, MIR, Research Activity, CG18546, prevention and control, Laboratory Research, Non Polyadenylated, RNA Gene Products, Miranda, Priorities, thymus nucleic acid, Small Temporal, Gene Expressions, Man (Taxonomy), reference sample, Genomes, Somatic Genetic Therapies, complementary DNA, iecur, adult primary hepatocellular carcinoma, Inverse Polymerase Chain Reaction, inhibition of gene expression, Replicons, mir, miRNA, Primary miRNA, Hepaciviruses, Adult, quelling, pri-miRNA, INSDC_feature:ncRNA, Hepatitis C Like Viruses, Hepatocellular Carcinoma, Fever Viruses, preventive measures, Gene Silencings, hepatitis C virus HCV, Reaction, hepatoblastoma, Therapies, cDNA Probes, Double-Stranded DNA, Infections and Infestations, deoxyribonucleic acids, Research Priority, DNAn, Idol, CXXC finger protein 9, Breakbone, Hepatitis C virus, HRI, Hri, 9430057C20Rik, Therapy, Genetic Therapy, Carcinoma, human hepatitis C virus, Liver, Anchored Polymerase Chain Reaction, preventive therapy, ribose nucleic acid, 6.3.2.-, RT-rt PCR, Modern, ribonucleic acids, Small Temporal RNA, Genome Sequencing, Research Priorities, Liver Cell, Double-Stranded, anon-WO03070958.3, Somatic Genetic Therapy, CG4637, CG12249, (Deoxyribonucleotide)n+m, Somatic Genetic, Genetic Therapies, Complete Genome, gene silencing, HCC, Gametic, Ribonukleinsaeure, bar3, pentosenucleic acids, Ribonucleic acids, Adult Liver, HCR, RNA Silencing, pre-miRNA, desoxyribose nucleic acid, HCV, region, Post-Transcriptional Gene, PCR, pri miRNA, Carcinomas, Research and Development, Acid, ADCADN, miRNAs, l(3)neo56, liver and intrahepatic bile duct carcinoma, Gametic Genetic, l(3)neo57, UNQ203/PRO229, Micro, Nested Polymerase Chain Reaction, Hepatoma, Somatic Gene Therapy, Engineerings, Breakbone Fever Viruses, DNA (cytosine-5-)-methyltransferase 1, Mira, Fever Virus, Infection and Infestation, Breakbone Fever, Inducible degrader of the LDL-receptor, whole genome, Somatic Gene, Replication Units, Co Suppression, Hepatitis C viruses, human, Post Transcriptional Gene Silencing, polymerase chain reaction, Activities, Gene Silencing, ds DNA, MIRA, Heme-controlled repressor, MicroRNA, Animal Viruses, Complementary DNA, DNA, Hepatocellular Carcinomas, Co-Suppression, Dengue Viruses, hg, HH, post-transcriptional gene silencing by RNA, epigenetic, human being, DNS, (Deoxyribonucleotide)n, stRNA, post-transfusion hepatitis non A non B virus, Gene, Cell Carcinoma, Replication Unit, Polymerase Chain Reactions, hepatoblastoma caused by somatic mutation, Inverse, Deoxyribonucleic acids, jecur, Hh, Human, Cell Carcinomas, Aim, AIM, Inverse PCR, Deoxyribonucleic Acid, Homo sapiens, Liver Cell Carcinomas, Core Genome, Gene Products, Adult Liver Cancer, Animal, Man, Hepatitis C-Like Virus, human hepatitis C virus HCV, DNMT1, Somatic, Animal Virus, Complete, Whole Genome, MONDOA, Genetic, Viruses, Liver Cancer, DNMT1_HUMAN, Research, Gametic Genetic Therapies, DNA Therapy, Mrt, Gene Inactivation, Heme-regulated inhibitor, Accessory Genome, Complete Genome Sequencing, Liver Cancers, Double Stranded, Deoxyribonucleic acid, Cosuppression, Expressions, clinical infection, Sequencing, Non-Polyadenylated RNA, API6, Infestation and Infection, Myosin regulatory light chain-interacting protein, 10^[-6], bar-3, Whole, C6orf18, site, Expression, Anchored PCR, (Deoxyribonucleotide)m, Development and Research, bHLHe36, human hepatitis virus C HCV, pre miRNA, Controlled, Cancer, DNA MTase HsaI, DNA (cytosine-5)-methyltransferase 1, RNA, l(3)hh, Controlling, Myosin regulatory light chain interacting protein, Inactivation, Unit, DNAn+1, posttranscriptional gene silencing by siRNA, DNMT, DmelCG31211, RNS, Primary, MCMT, cosuppression, cDNA, Pangenome, Cell, RNAi, AW228700, 2.7.11.1, Gene Therapy, Priority, Interference, Micro RNA, yeast nucleic acid, DNA methyltransferase HsaI, Gametic Genetic Therapy., Units, Research Activities, Infection, DmelCG12249, ds-DNA, Zoophaginae, Replication, Breakbone Fever Virus, Silencing, Post-Transcriptional Gene Silencings, CXXC9, Hepacivirus C, ribonucleic acid, Anchored, Reactions, Nested, Adult Liver Cancers, Hepatocellular carcinoma, CT-2, Hemin-sensitive initiation factor 2-alpha kinase, Posttranscriptional, Temporal RNA, Posttranscriptional Gene Silencing, prophylaxis, Non Polyadenylated RNA, Non-Polyadenylated, Primary MicroRNA, Ribonucleic Acid, Cancers, CG14732, CXXC-type zinc finger protein 9, SBP, Livers, Post-Transcriptional, Pan-genome, Dengue, RRT-PCR, anon-WO0182946.19, control, Modern Man, Hepatocellular, Desoxyribonukleinsaeure, Nested PCR, Post-Transcriptional Gene Silencing, liver cancer, Hepatitis C, CLEC2C, m.HsaI"],"additional_accession":[]},"is_claimable":false,"name":"Bioinformatics of Data Analysis (B240)","description":"Data Access Committee EGAC00001000346","dates":{"output":"2025-1-9"},"accession":"EGAC00001000346","cross_references":{"TAXONOMY":["9606"],"pubmed":["27614072"],"EGA":["EGAS00001001252","EGAD00001001386"]}}