Table 2.
Broad overview of PIWI-associating RNA classes, from the perspective of small RNA genome source.
| small RNA genome source | general small RNA “class”1 | phyletic spread2 | functional role(s)3 |
|---|---|---|---|
| genomically-encoded, independently-transcribed hairpins | imperfectly-complementary hairpins | Giardia, Trichomonas | at least one example is linked to PTGS [79] |
| genomically-encoded, independently-transcribed hairpins | miRNA | plants, animals, T. gondii*, D. discoideum* | PTGS |
| genomically-encoded, non- independently-transcribed double-stranded sequences | miRtrons | animals | PTGS |
| genomically-encoded, non- independently-transcribed double-stranded sequences | Endo-siRNA (including esiRNAs and social RNA∧) | animals, plants, fungi/yeast, T. brucei∧ | PTGS, viral resistance |
| double-stranded sequences derived from s-as transcription | Endo-siRNAs, proximal promoter/transcriptional unit-derived small RNA3, and small RNA toxins/effectors∧ | animals, plants, fungi/yeast, slime mold, T. thermophila, E. histolytica, T. gondii∧, T. brucei, Giardia | PTGS, retrotransposon silencing, co-transcriptional regulation, polII positioning |
| double-stranded sequences derived from single-stranded transcription4 | endo-siRNAs (including qiRNAs, priRNAs, meiotic silencing RNAs, nat-siRNAs, plant heterochromatic siRNAs, ta-siRNAs, 22G-RNAs) | C. elegans, plants, some fungi | regulation of chromatin dynamics, germline surveillance |
| double-stranded sequences derived from s-as transcription | splice site-associated RNA | animals, E. histolytica∧ | regulation of splicing |
| double-stranded sequences derived from s-as transcription | scan RNAs (scnRNAs) | ciliates | DNA elimination |
| double-stranded sequences derived from s-as transcription | DNA damage-induced small RNA | animals, plants | recruitment of DSB repair proteins, clearance of DSB- proximal transcribed byproducts |
| single-stranded sequences | piRNAs | animals | germline surveillance, regulation of chromatin dynamics |
| ncRNA precursor | sdRNAs (snoRNA-derived) | animals, plants, fungi, Giardia | PTGS |
| ncRNA precursor | tRF (includes 3′ tRF-CCA, 3′ tRF-U, and 5′ tRF classes) (tRNA-derived) | animals, plants, Magnaporthe oryzae*, amoebozoans*, ciliates, T. gondii* | PTGS, rRNA processing |
| ncRNA precursor | svRNAs (vault RNA-derived) | animals | PTGS |
| ncRNA precursor | other (including potential snRNA, RMRP, and rRNA- derived small RNAs) | animals | RMRP fragments likely involved in PTGS [105], otherwise unknown |
small RNA classes have often been labeled according to functional roles. Rendering the functional role secondary to the source potentially enables better delineation of the evolutionary descent of small RNA classes.
symbol meanings: *, association with PIWI inferred from small RNA-seq; ∧, inclusion pending further investigation.
abbreviation: PTGS, post-transcriptional gene silencing
further research is needed to resolve differences or overlap between s-as gene body-derived small RNAs involved in regulating gene expression (as “endo-siRNAs”) and those involved in regulation of chromatin dynamics/polII positioning.
classes of small RNA derived from gene bodies or repeat regions which form a duplex by adding the complementary strand after transcription via RdRP activity instead of independently transcribing the opposite strand.