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Concept
Antisense RNA
Summary
Antisense RNA (asRNA), also referred to as antisense transcript, natural antisense transcript (NAT) or antisense oligonucleotide, is a single stranded RNA that is complementary to a protein coding messenger RNA (mRNA) with which it hybridizes, and thereby blocks its translation into protein. The asRNAs (which occur naturally) have been found in both prokaryotes and eukaryotes, and can be classified into short (200 nucleotides) non-coding RNAs (ncRNAs). The primary function of asRNA is regulating gene expression. asRNAs may also be produced synthetically and have found wide spread use as research tools for gene knockdown. They may also have therapeutic applications.
Antisense therapy
Some of the earliest asRNAs were discovered while investigating functional proteins. An example was micF asRNA. While characterizing the outer membrane porin in E.coli, some of the promoter clones observed were capable of repressing the expression of other membrane porin such as . The region responsible for this repression function was found to be a 300 base-pair locus upstream of the promoter. This 300 base-pair region is 70% homologous in sequence with the 5' end of the mRNA and thus the transcript of this 300 base pair locus was complementary to the mRNA. Later on, this transcript, denoted micF, was found to be an asRNA of and capable of downregulating the expression of under stress by forming a duplex with the mRNA. This induces the degradation of the mRNA.
Unlike micF RNA being discovered by accident, the majority of asRNAs were discovered by genome wide searches for small regulatory RNAs and by transcriptome analysis. Conventionally, the first step involves computational predictions based on some known characteristics of asRNAs. During computational searches, the encoding regions are excluded. The regions that are predicted to have conserved RNA structures and act as orphan promoters and Rho independent terminators are preferenced during analysis.
Official source
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