Table 1.
Regulatory ncRNAs produced from eukaryotic genomes and their characteristics and functions
| Type | Long name | Length (nt) | Characteristics | Function |
|---|---|---|---|---|
| miRNA | Micro RNA | 20–24 | Pri-miRNA produced in the nucleus as capped and polyadenylated ssRNA with a imperfectly paired stem-loop structure | Perfect complementarity: Ago2-mediated cleavage of mRNA |
| Processing by Drosha and Dicer lead to a production of mature dsRNA with exact ends | Non-perfect complementarity: Suppression of translation or mRNA degradation (deadenylation, decapping, and exonucleocytic degradation) | |||
| Effector phase occurs primarily in the cytoplasm mediated by Ago proteins | Minor functions in transcriptional silencing and translational activation | |||
| piRNA | PIWI-interacting RNA | 24–31 | Precursor ssRNA, which is modified to contain 3′-terminal 2′-O-methyl | Silencing of transposable elements in the germline |
| Strong preference for uridine at the 5′ end | ||||
| siRNA | Small interfering RNA | 20–24 | Canonical form long, linear, perfectly base-paired dsRNA | Perfect match: endonucleocytic cleavage |
| Processed by Dicer into mature siRNA with heterogenous end composition | Non-perfect match or endonuclease-inactive RISC: translational repression or exonucleocytic degradation | |||
| Effector functions occur primarily in the cytoplasm supported by Ago proteins | Induction of heterochromatin formation | |||
| Silencing of the same locus from which they are derived | ||||
| PAR (aPASR, TSSa-RNA, tiRNA, PROMPT) | Promoter-associated RNA | 16–200 | Weakly expressed ssRNAs | Partly unknown but indications of transcriptional regulation (example interaction with Polycomb group of proteins) |
| Short half-life | ||||
| Bidirectional expression reflecting PolII distribution | ||||
| eRNA | Enhancer RNA | 100–9000 | ssRNA produced bidirectionally from enhancer regions enriched for H3K4me1, PolII and coactivators such as p300 | Mostly unknown but plays a role in transcriptional gene activation |
| Short half-life | ||||
| Evolutionarily conserved sequences | ||||
| Dynamically regulated upon signalling | ||||
| Expression correlates positively with nearby mRNA expression | ||||
| lncRNA | Long non-coding RNA | >200 | Precursor ssRNA | Chromatin remodelling |
| Many lncRNAs are subject to splicing, polyadenylation, and other post-transcriptional modifications | Transcriptional regulation | |||
| Mostly nuclear RNAs but a subset also located in the cytoplasm | Post-transcriptional regulation (splicing, TF localization) | |||
| Not evolutionary conserved with the exception of large intergenic ncRNAs, lincRNAs (H3K4me3-H3K36me3 signature) | Precursors for siRNAs | |||
| Component of nuclear organelles (paraspeckles, nuclear speckles) |
aPASR, promoter-associated small RNA; TSSa-RNA, transcription start site-associated RNA; tiRNA, transcription initiation RNA; PROMTs, promoter upstream transcript.