Antisense RNA
The region responsible for this repression function was found to be a 300 base-pair locus upstream of the ompC promoter.
The regions that are predicted to have conserved RNA structures and act as orphan promoters and Rho independent terminators are preferenced during analysis.
Because computational searches focuses on the intergenic region, the asRNAs that are transcribed from the opposite strand of an encoding gene are likely to be missed using this method.
In addition to computational searches and microarrays, some asRNAs were discovered by sequencing cDNA clones as well as mapping promoter elements.
To minimize the number of false positive results, new approaches from recent years have been focusing on strand-specific transcription, chromatin binding noncoding RNAs and single cell studies.
Mipomersen was developed to manage the level of low-density lipoprotein cholesterol (LDL) in patients with homozygous familial hypercholesterolemia (HoFH), which is a rare autosomal dominant genetic condition.
Because the protein apo-B-100 has been found to be required to produce very low-density lipoprotein (VLDL) and LDL, mipomersen complements with the mRNA of apo-B-100 and target it for RNAse H dependent degradation.
Consequently, RNA II cannot hybridize with its DNA template which results in a low copy number of ColE1.
In bacteriophage P22, the asRNA sar helps regulate between lytic and lysogenic cycle by control the expression of Ant.
Instead of targeting individual mRNAs, these cis-acting epigenetic regulators can recruit chromatin modifying enzymes which can exert effects on both the transcription loci and the neighboring genes.
Because of these properties of trans-acting asRNAs, they form less stable complexes with their targeting transcripts and sometimes require aids from RNA chaperone protein such as Hfq to exert their functions.
Repression of functional proteins via asRNA induced DNA methylation has been found in several human disease.
In a class of alpha-thalassemia, a type of blood disorder that has reduced level of hemoglobin leading to insufficient oxygen in the tissues,[13] hemoglobin alpha1 gene (HBA1) is downregulated by an abnormal transcript of putative RNA-binding protein Luc7-like (LUC71) that serves as an asRNA to HBA1 and induces methylation of HBA1's promoter.
One classic example in human is zinc-finger E-box binding homeobox 2 gene (ZEB2) which encodes E-cadherin, a transcriptional repressor.
With the asRNA of ZEB2 being expressed, it can mask the splicing site and maintain the IRES in the mRNA which results in an efficient synthesis of E-cadherin.
Therefore, asRNA dependent regulation is not limited to on/off mechanism; rather, it presents a fine tone control system.
As described in the cis-acting asRNAs, the mRNA-asRNA pairing can result in blockage of ribosome entry and RNase H dependent degradation.
Overall, mRNA-targeting asRNAs can either activate or inhibit translation of the sense mRNAs with inhibitory effect being the most abundant.
First of all, asRNAs regulate gene expression at multiple levels including transcription, post-transcription and epigenetic modification.
In terms of drug targets, this represents a huge advantage because only a low dosage is required for effectiveness.
[4] Recent years the idea of targeting asRNAs to increase gene expression in a locus specific manner has been drawing much attention.
In addition, enzyme replacement therapies are life-long commitment and carry a large financial burden for the patient.
Adverse effects including fever, chills or nausea have been observed after local injection of phosphrothioate modified oligonucleotides.
Despite the locus-specific nature of the endogenous asRNAs, only 10–50% synthesized oligonucleotides showed expected targeting effect.
[5] Although neurons and glia have been shown to have the ability to freely uptake naked antisense oligonucleotides, a traceable carriers such as virus and lipid vesicles would still be ideal to control and monitor the intracellular concentration and metabolism.
