Table 1.
Explanation of nomenclature of short RNAs and other terms used in the gene silencing field.
| name | description |
|---|---|
| post-transcriptional gene silencing (PTGS) | an umbrella term for all gene-silencing phenomena (sequence-specific RNA degradation) in plants that act in the cytoplasm and do not affect transcription in the nucleus |
| virus-induced gene silencing (VIGS) | a specific case of PTGS where the trigger is a replicating viral RNA |
| co-suppression | a specific case of PTGS when a transgene-induced silencing mechanism suppresses the transgene and a homologous endogenous gene at the same time |
| RNA interference (RNAi) | the name of a sequence-specific RNA degradation mechanism in animal cells that is very similar to PTGS |
| microRNA (miRNA) | a single-stranded 20–22 nucleotide short RNA that is encoded by the host genome; produced from a longer precursor RNA molecule with a characteristic stem-loop structure where the miRNA is in one arm of the stem; only one double-stranded miRNA is produced from one stem-loop structure; one of the strands is called mature miRNA that is incorporated into RISC and regulates the expression of mRNAs |
| small interfering RNA (siRNA) | double-stranded 20–22 nucleotide short RNA molecules that are either produced from long double-stranded RNA by Dicer or synthesized in vitro; if generated from long dsRNA, many siRNA is produced from one dsRNA molecule; siRNAs are incorporated into RISC and mediate mRNA cleavage |
| trans-acting endogenous siRNA (ta-siRNA) | a specific type of 20–22 nucleotide siRNA molecules in plants; generated from non-coding transcripts encoded by the plant genome following miRNA-mediated cleavage of the primary transcript that is then turned into dsRNA and processed by DCL-4; several ta-siRNAs are produced from one locus and they are in the same phase (i.e. do not overlap with each other and there is no gap between them); also incorporated into RISC and target mRNAs |
| chromatin siRNA | a specific type of 24–26 nucleotide siRNA molecules in plants; generated from repeat or transposon sequences in the plant genome and act in the nucleus; they cause transcriptional gene silencing by heterochromatin formation through methylation of chromosomal DNA |
| natural antisense siRNA (nat-siRNA) | a specific type of 20–22 nucleotide siRNA molecules in plants; derived from naturally occurring overlapping complementary transcripts that can form dsRNA and are processed by Dicer; they are incorporated into RISC and target mRNAs |