Table 1.
Characteristics of major noncoding RNAs (ncRNAs)
| piRNA | miRNA | siRNA | |
|---|---|---|---|
| Structure | 5′ terminal uridine or tenth adenosine and 2′ O-methyl group on the 3′ ribose | phosphorylated 5ʹ ends and hydroxylated 3ʹ ends | phosphorylated 5ʹ ends and hydroxylated 3ʹ ends with two overhanging nucleotides |
| Size | 24–32 nt | 20–24 nt | 21–23 nt |
| Processing | Dicer-independent | Dicer-dependent | Dicer-dependent |
| Precursor | single-stranded RNA | double-stranded RNA | double-stranded RNA |
| Associated protein | PIWI subfamily proteins (mainly enriched in germline) | AGO subfamily proteins (ubiquitously expressed) | AGO subfamily proteins (ubiquitously expressed) |
| Organism | Eukaryotes | Eukaryotes | Eukaryotes |
| Source | Genomic loci (transposons, repeats, piRNA loci) | Genomic loci (miRNA loci, introns) | Exogenous siRNA: Viral or other exogenous RNAs Endogenous siRNA: Genomic loci (mRNAs, Transposons, repeats), miRNA-cleaved RNAs, bidirectional transcripts |
| number of loci in the human genome | >30,000 | 2,000 | Endogenous siRNA: More than 200 |
| Expression | Highly enriched in the germline | Broad expression in most cell and tissue types | Broad expression in most cell and tissue types |
| Major target genes | Transposons and other genes | Coding genes | Transposons and exogenous genes |
| Primary functional mechanism | Transcriptional repression, heterochromatin formation (DNA methylation), RNA cleavage | Translational repression of mRNA, mRNA cleavage | Exogenous siRNA: Cleavage of exogenous RNA endogenous siRNA:RNA cleavage |