Question

Compare and contrast small RNA (sRNA) regulators and cis-antisense RNAs (asRNA).

Answer 1

Small RNAs (sRNA) are a type of RNA transcripts that may or may not code for protein products but make potentially functional RNAs. sRNA can modify protein activity and regulate mRNA translation and stability. Small regulatory RNAs can modify the activity of proteins and the stability and translation of mRNAs. The bacterial small RNAs include two major classes.

cis-antisense RNAs (asRNA), also known as natural antisense transcript, found in both prokaryotes and eukaryotes, are primarily involved in the regulation of gene expression. These are single-stranded RNAs complementary to a target mRNA to hybridize with it and block its protein translation and are also used as an important tool for gene knockdown.

There are substantial similarities as well as differences between asRNAs and sRNAs. Both sRNA and asRNA are similar in mechanisms inhibiting translation or decrease target stability. Also both types of regulatory RNAs (i) form complementary base pair with their RNA target, (ii) interact stoichiometrically with their target, and (iii) can be codegraded or sequestered by interactions with their target.

However, both type of RNAs also has several important differences (i) asRNAs have complete or extended complementarity with their target and can form more stable RNA duplexes. This may have implications for binding kinetics where the interaction may be independent of proteins such as Hfq. (ii) asRNAs originate from the genomic region similar to their target. (iii) The cis position offers the additional effect of transcription of asRNA in close proximity of target resulting in an enhanced local concentration and interactions. (iv) Transcriptional interference relies on transcription from closely spaced promoters, and therefore, this kind of regulation is restricted to asRNAs. (v) The length of some asRNAs as high as 7,000 nt is another major difference in comparison to sRNAs that could be advantageous for the transcriptional interference collision mechanism or other unknown mechanisms.