Question

Repeat-associated small-interfering RNAs (rasiRNAs) account for 90-95% of the global small RNA population in all plant species. As their name suggests, rasiRNAs are derived from the various classes of repetitive DNA that constitute more than 95% of the entire nuclear genome sequence of a plant. The rasiRNAs keep the majority of the repetitive DNA in an inactive state. State; (1) the DNA-dependent RNA polymerase(s) involved in rasiRNA precursor transcript transcription; (2) whether rasiRNA precursors are molecules of perfectly or imperfectly structured double-stranded RNA (dsRNA); (3) the DICER-LIKE (DCL) endonuclease(s) responsible for rasiRNA production; (4) the size of rasiRNAs, and; (5) the mechanism of RNA silencing directed by rasiRNAs in order to maintain repetitive DNA in an inactive state.

Answer 1

1. In plants, the biogenesis of rasiRNA starts with DNA-dependent RNA polymerase to produce single stranded RNA, this strand gets converted in to double stranded RNA by the RNA-dependent RNA polymerases RDR2 and SDE4, the plant homologs dicer-like DCL2 and DCL3 and AGO4
2. Precursor molecules are single stranded RNA molecules, with imperfect double stranded pseudo or imperfectly double stranded
3. Yes DICER-LIKE (DCL) endonuclease(s) responsible for rasiRNA production, They produce 2-nt 3’ overhangs
4. rasiRNAs are 24 nucleotides long with 2-nt 3’ overhangs
5. To keep repetitive DNA in an inactive state rasiRNAs are involved in RNA-directed DNA methylation (RdDM) and histone methylation particularly methylation of lysine at ninth position of histone H3 (H3K9), This prevents opening of DNA for transcription. Also, Ra-siRNA/AGO4 RISC directs DNA methyltransferases and H3K9 methyltransferases towards target sequence for the purpose of transcriptional gene silencing. Overall, methylation prevents transcription of repetitive DNA