Gene knockdown is an experimental technique by which the expression of one or more of an organism's genes is reduced. The reduction can occur either through genetic modification or by treatment with a reagent such as a short DNA or RNA oligonucleotide that has a sequence complementary to either gene or an mRNA transcript.
CRISPR is a family of DNA sequences found in the genomes of prokaryotic organisms such as bacteria and archaea. These sequences are derived from DNA fragments of bacteriophages that had previously infected the prokaryote. They are used to detect and destroy DNA from similar bacteriophages during subsequent infections. Hence these sequences play a key role in the antiviral defense system of prokaryotes and provide a form of acquired immunity. CRISPR is found in approximately 50% of sequenced bacterial genomes and nearly 90% of sequenced archaea.
Guide RNA (gRNA) or single guide RNA (sgRNA) is a short sequence of RNA that functions as a guide for the Cas9-endonuclease or other Cas-proteins that cut the double-stranded DNA and thereby can be used for gene editing. In bacteria and archaea, gRNAs are a part of the CRISPR-Cas system that serves as an adaptive immune defense that protects the organism from viruses. Here the short gRNAs serve as detectors of foreign DNA and direct the Cas-enzymes that degrades the foreign nucleic acid.
In Molecular biology, an insert is a piece of DNA that is inserted into a larger DNA vector by a recombinant DNA technique, such as ligation or recombination. This allows it to be multiplied, selected, further manipulated or expressed in a host organism.
Shredding refers to the process in bioinformatics of taking assembled gene sequences and disassembling them into short sequences of usually 500 to 750 base pairs (bp). This is generally done for the purpose of taking the short shredded sequences and reapplying various analysis and bioinformatic techniques. Being able to cut DNA samples and then run them through gel electrophoresis to study each strand in order to help find cures for diseases or illnesses is also another purpose.
Genome editing, or genome engineering, or gene editing, is a type of genetic engineering in which DNA is inserted, deleted, modified or replaced in the genome of a living organism. Unlike early genetic engineering techniques that randomly inserts genetic material into a host genome, genome editing targets the insertions to site-specific locations. The basic mechanism involved in genetic manipulations through programmable nucleases is the recognition of target genomic loci and binding of effector DNA-binding domain (DBD), double-strand breaks (DSBs) in target DNA by the restriction endonucleases, and the repair of DSBs through homology-directed recombination (HDR) or non-homologous end joining (NHEJ).
Cas9 is a 160 kilodalton protein which plays a vital role in the immunological defense of certain bacteria against DNA viruses and plasmids, and is heavily utilized in genetic engineering applications. Its main function is to cut DNA and thereby alter a cell's genome. The CRISPR-Cas9 genome editing technique was a significant contributor to the Nobel Prize in Chemistry in 2020 being awarded to Emmanuelle Charpentier and Jennifer Doudna.
CRISPR-Cas design tools are computer software platforms and bioinformatics tools used to facilitate the design of guide RNAs (gRNAs) for use with the CRISPR/Cas gene editing system.
CRISPR-associated protein 1 (cas1) is one of the two universally conserved proteins found in the CRISPR prokaryotic immune defense system. Cas1 is a metal-dependent DNA-specific endonuclease that produces double-stranded DNA fragments. Cas1 forms a stable complex with the other universally conserved CRISPR-associated protein, cas2, which is essential to spacer acquisition for CRISPR systems.
Yoshizumi Ishino is a Japanese molecular biologist, known for discovering the DNA sequence of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR).
Philippe Horvath is a French scientist working for DuPont Nutrition and Health. His work was integral to the development of CRISPR-Cas, a versatile biochemical method for targeted genetic engineering. For this work, he was awarded the 2015 Massry Prize along with Emmanuelle Charpentier and Jennifer Doudna, as well as the 2016 Canada Gairdner International Award, with his Massry co-laureates in addition to Feng Zhang, Rodolphe Barrangou, Anthony Fauci, and Frank Plummer.
Rodolphe Barrangou is the Todd R. Klaenhammer Distinguished Professor in Probiotics Research in the Department of Food, Bioprocessing and Nutrition Sciences at North Carolina State University; Co-Founder and Chief Executive Officer of CRISPR Biotechnologies; Co-Founder and Chief Scientific Officer of Ancilia Biosciences; Co-Founder, President and Chief Scientific Officer of TreeCo; and Co-Founder and member of the Scientific Advisory Board of Intellia Therapeutics. His research focuses on CRISPR-Cas9 in bacteria.
Francisco Juan Martínez Mojica is a Spanish molecular biologist and microbiologist at the University of Alicante in Spain. He is known for his discovery of repetitive, functional DNA sequences in bacteria which he named CRISPR. These were later developed into the first widespread genome editing tool, CRISPR-Cas9.
Samira Kiani is an Associate Professor in the department of Pathology of University of Pittsburgh School of Medicine and Pittsburgh Liver Research Center. Formerly, she was a Health Systems Engineer at Arizona State University. Her work combines Clustered Regularly Interspaced Short Palindromic Repeat (CRISPR) with synthetic biology. She is a 2019 AAAS Leshner Fellow.
Human Nature is a 2019 documentary film directed by Adam Bolt and written by Adam Bolt and Regina Sobel. Producers of the film include Greg Boustead, Elliot Kirschner and Dan Rather.
Genome-wide CRISPR-Cas9 knockout screens aim to elucidate the relationship between genotype and phenotype by ablating gene expression on a genome-wide scale and studying the resulting phenotypic alterations. The approach utilises the CRISPR-Cas9 gene editing system, coupled with libraries of single guide RNAs (sgRNAs), which are designed to target every gene in the genome. Over recent years, the genome-wide CRISPR screen has emerged as a powerful tool for performing large-scale loss-of-function screens, with low noise, high knockout efficiency and minimal off-target effects.
Joyce Van Eck is a plant biologist and faculty member at the Boyce Thompson Institute in Ithaca, NY. She is an Adjunct Professor in the Section of Plant Breeding and Genetics at Cornell University.
Cas2 is a protein associated with CRISPR that is involved with spacer acquisition. Representative cas2 proteins have been characterized as endonucleases that cleave single-stranded RNAs preferentially within U-rich regions, or as metal-dependent endonucleases targeting double-stranded (ds)DNA
CRISPR RNA or crRNA is a RNA transcript from the CRISPR locus. CRISPR-Cas is an adaptive immune system found in bacteria and archaea to protect against mobile genetic elements, like viruses, plasmids, and transposons. The CRISPR locus contains a series of repeats interspaced with unique spacers. These unique spacers can be acquired from MGEs.
