LEAPER (Leveraging endogenous ADAR for programmable editing of RNA) is a genetic engineering technique in molecular biology by which RNA can be edited. The technique relies on engineered strands of RNA to recruit native ADAR enzymes to swap out different compounds in RNA. Developed by researchers at Peking University in 2019, the technique, some have claimed, is more efficient than the CRISPR gene editing technique. [1] Initial studies have claimed that editing efficiencies of up to 80%.
As opposed to DNA gene editing techniques (e.g., using CRISPR-Cas proteins to make modifications directly to a defective gene), LEAPER targets editing messenger RNA (mRNA) for the same gene which is transcribed into a protein. [3] Post-transcriptional RNA modification typically involves the strategy of converting adenosine-to-inosine (A-to-I) since inosine (I) demonstrably mimics guanosine (G) during translation into a protein. A-to-I editing is catalyzed by adenosine deaminase acting on RNA (ADAR) enzymes, whose substrates are double-stranded RNAs. [4] Three human ADAR genes have been identified with ADAR1 (official symbol ADAR) and ADAR2 (ADARB1) proteins developed activity profiles. LEAPER achieves this targeted RNA editing through the use of short engineered ADAR-recruiting RNAs (arRNAs). arRNAs consist of endogenous ADAR1 proteins with several RNA binding domains (RBDs) fused with a peptide, CRISPR-Cas13b protein, and a guide RNA (gRNA) between 100 and 150 nt in length for high editing efficiency designed to recruit the chimeric ADAR protein to a target site. [2]
This results in a change in which protein is synthesized during translation.
The technique was discovered by a team of researchers at Peking University in Beijing, China. The discovery was announced in the journal Nature Biotechnology in July 2019. [5]
Chinese researchers have utilized LEAPER to restore functional enzyme activity in cells from patients with Hurler syndrome. They have claimed that LEAPER could have the potential to treat almost half of all known hereditary disorders. [5]
Highly specific editing efficiencies of up to 80% can be achieved when LEAPER editing using arRNA151 is delivered via a plasmid or viral vector or as a synthetic oligonucleotide, though this efficiency varied significantly across cell types. [4] Based on these preliminary results, LEAPER may have the most therapeutic promise with no production of functional protein but if a partial restoration of protein expression would provide therapeutic benefit. For example, in human cells with defective α-L-iduronidase (IDUA) expression in cells from patients with IDUA-defective Hurler syndrome, LEAPER resulted in a W53X truncation mutant of p53 being edited using arRNA151 to achieve a "normal" p53 translation and functional p53-mediated transcriptional responses. [4]
LEAPER is analogous to CRISPR Cas-13 in that it targets RNA before proteins are synthesized. However, LEAPER is simpler and more efficient as it only requires arRNA, rather than Cas and a guide RNA. [5] According to the developers of LEAPER, it has the potential to be easier and more precise than any CRISPR technique. [6]
LEAPER also eliminates health concerns and technical barriers arising from the introduction of exogenous proteins. [7]
It has also been called more ethical as it does not change DNA and thus does not result in heritable changes, unlike methods using CRISPR Cas-9. [8]
Z-DNA is one of the many possible double helical structures of DNA. It is a left-handed double helical structure in which the helix winds to the left in a zigzag pattern, instead of to the right, like the more common B-DNA form. Z-DNA is thought to be one of three biologically active double-helical structures along with A-DNA and B-DNA.
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.
RNA editing is a molecular process through which some cells can make discrete changes to specific nucleotide sequences within an RNA molecule after it has been generated by RNA polymerase. It occurs in all living organisms and is one of the most evolutionarily conserved properties of RNAs. RNA editing may include the insertion, deletion, and base substitution of nucleotides within the RNA molecule. RNA editing is relatively rare, with common forms of RNA processing not usually considered as editing. It can affect the activity, localization as well as stability of RNAs, and has been linked with human diseases.
Guide RNA (gRNA) or singel 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 therebye 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.
Potassium voltage-gated channel subfamily A member 1 also known as Kv1.1 is a shaker related voltage-gated potassium channel that in humans is encoded by the KCNA1 gene. Isaacs syndrome is a result of an autoimmune reaction against the Kv1.1 ion channel.
Filamin A, alpha (FLNA) is a protein that in humans is encoded by the FLNA gene.
The double-stranded RNA-specific adenosine deaminase enzyme family are encoded by the ADAR family genes. ADAR stands for adenosine deaminase acting on RNA. This article focuses on the ADAR proteins; This article details the evolutionary history, structure, function, mechanisms and importance of all proteins within this family.
Insulin-like growth factor-binding protein 7 is a protein that in humans is encoded by the IGFBP7 gene. The major function of the protein is the regulation of availability of insulin-like growth factors (IGFs) in tissue as well as in modulating IGF binding to its receptors. IGFBP7 binds to IGF with low affinity compared to IGFBPs 1-6. It also stimulates cell adhesion. The protein is implicated in some cancers.
Cytoplasmic FMR1-interacting protein 2 is a protein that in humans is encoded by the CYFIP2 gene. Cytoplasmic FMR1 interacting protein is a 1253 amino acid long protein and is highly conserved sharing 99% sequence identity to the mouse protein. It is expressed mainly in brain tissues, white blood cells and the kidney.
Bladder cancer-associated protein is a protein that in humans is encoded by the BLCAP gene.
Within the science of molecular biology and cell biology, for human genetics, the GRIA2 gene is located on chromosome 4q32-q33. The gene product is the ionotropic AMPA glutamate receptor 2. The protein belongs to a family of ligand-activated glutamate receptors that are sensitive to alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate (AMPA). Glutamate receptors function as the main excitatory neurotransmitter at many synapses in the central nervous system. L-glutamate, an excitatory neurotransmitter, binds to the Gria2 resulting in a conformational change. This leads to the opening of the channel converting the chemical signal to an electrical impulse. AMPA receptors (AMPAR) are composed of four subunits, designated as GluR1 (GRIA1), GluR2 (GRIA2), GluR3 (GRIA3), and GluR4(GRIA4) which combine to form tetramers. They are usually heterotrimeric but can be homodimeric. Each AMPAR has four sites to which an agonist can bind, one for each subunit.[5]
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).
In molecular biology, the protein domain Adenosine deaminase z-alpha domain refers to an evolutionary conserved protein domain. This family consists of the N-terminus and thus the z-alpha domain of double-stranded RNA-specific adenosine deaminase (ADAR), an RNA-editing enzyme. The z-alpha domain is a Z-DNA binding domain, and binding of this region to B-DNA has been shown to be disfavoured by steric hindrance.
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 interference (CRISPRi) is a genetic perturbation technique that allows for sequence-specific repression of gene expression in prokaryotic and eukaryotic cells. It was first developed by Stanley Qi and colleagues in the laboratories of Wendell Lim, Adam Arkin, Jonathan Weissman, and Jennifer Doudna. Sequence-specific activation of gene expression refers to CRISPR activation (CRISPRa).
Cas12a is a subtype of Cas12 proteins and an RNA-guided endonuclease that forms part of the CRISPR system in some bacteria and archaea. It originates as part of a bacterial immune mechanism, where it serves to destroy the genetic material of viruses and thus protect the cell and colony from viral infection. Cas12a and other CRISPR associated endonucleases use an RNA to target nucleic acid in a specific and programmable matter. In the organisms from which it originates, this guide RNA is a copy of a piece of foreign nucleic acid that previously infected the cell.
CRISPR-Display (CRISP-Disp) is a modification of the CRISPR/Cas9 system for genome editing. The CRISPR/Cas9 system uses a short guide RNA (sgRNA) sequence to direct a Streptococcus pyogenes Cas9 nuclease, acting as a programmable DNA binding protein, to cleave DNA at a site of interest.
Multiplexed Accurate Genome Editing with Short, Trackable, Integrated Cellular barcodes (MAGESTIC) is a platform that builds on the CRISPR/Cas technique. It further improves CRISPR/Cas by making the gene-editing process more precise. It also increases cell survival during the editing process up to sevenfold.
CRISPR gene editing is a genetic engineering technique in molecular biology by which the genomes of living organisms may be modified. It is based on a simplified version of the bacterial CRISPR-Cas9 antiviral defense system. By delivering the Cas9 nuclease complexed with a synthetic guide RNA (gRNA) into a cell, the cell's genome can be cut at a desired location, allowing existing genes to be removed and/or new ones added in vivo.
CRISPR-associated transposons or CASTs are mobile genetic elements (MGEs) that have evolved to make use of minimal CRISPR systems for RNA-guided transposition of their DNA. Unlike traditional CRISPR systems that contain interference mechanisms to degrade targeted DNA, CASTs lack proteins and/or protein domains responsible for DNA cleavage. Specialized transposon machinery, similar to that of the well characterized Tn7 transposon, complexes with the CRISPR RNA (crRNA) and associated Cas proteins for transposition. CAST systems have been characterized in a wide range of bacteria and make use of variable CRISPR configurations including Type I-F, Type I-B, Type I-C, Type I-D, Type I-E, Type IV, and Type V-K. MGEs remain an important part of genetic exchange by horizontal gene transfer and CASTs have been implicated in the exchange of antibiotic resistance and antiviral defense mechanisms, as well as genes involved in central carbon metabolism. These systems show promise for genetic engineering due to their programmability, PAM flexibility, and ability to insert directly into the host genome without double strand breaks requiring activation of host repair mechanisms. They also lack Cas1 and Cas2 proteins and so rely on other more complete CRISPR systems for spacer acquisition in trans.