Table 1.
Major classes of short and long regulatory non-coding RNAs.
| ncRNA | Length (nt) | Function | |
|---|---|---|---|
| SHORT | |||
| miRNAs | Micro RNAs | 21–23 | In animals, associate with the miRNA-induced silencing complex (RISC) and silence the expression of target genes mostly post-transcriptionally (5–7) |
| snoRNAs | Small nucleolar RNAs | 60–300 | Help the chemical modification of mRNAs, thereby influencing stability, folding, and protein-interaction properties (8, 9) |
| snRNAs | Small nuclear RNAs | 150 | Assist splicing of introns from primary genomic transcripts (10, 11) |
| piRNAs | Piwi-interacting RNAs | 25–33 | Associate with the highly conserved Piwi family of argonaute proteins and are essential for retrotransposon silencing in germline, epigenetic modifications, DNA rearrangements, mRNA turnover, and translational control also in soma (12–14) |
| PASRs | Promoter-associated short RNAs | 22–200 | Enriched at the 5′end of genes, within 0.5 kb of TSS. Can be transcribed both sense and antisense. Their function and biogenesis is not fully understood (15, 16) |
| TASRs | Termini-associated short RNAs | 22–200 | Can be transcribed both sense and antisense near termination sites of protein-coding genes. Their function and biogenesis is not fully understood (15, 16) |
| siRNAs | Short interfering RNAs | 21–23 | Processed from a plethora of genomic sources, both foreign (viruses) and endogenous (repetitive sequences). Canonically induce the degradation of perfectly complementary target RNAs (17, 18) |
| tiRNAs | Transcription initiation RNAs | 15–30 | Enriched immediately downstream transcriptional start sites (TSSs) of highly expressed genes. Their function and biogenesis is not fully understood (16, 19, 20) |
| LONG | |||
| NATs | Natural antisense transcripts | >200 | Transcribed from the same locus but opposite strand of the overlapping protein-coding sequence. Involved in gene expression regulation, RNA editing, stability, and translation (21, 22) |
| PALRs | Promoter-associated long RNAs | 200–1000 | Enriched at promoters, found to regulate gene expression (23, 24) |
| PROMPTs | Promoter upstream transcripts | 200–600 | Enriched at TATA-less, CpG-rich promoters with broad TSSs. Affect promoter methylation and regulate transcription (25–27) |
| T-UCRs | Transcribed ultraconserved regions | >200 | Perfectly conserved between human, rat, and mouse. Frequently located at fragile sites and at genomic regions involved in cancer (28) |
| Intronic RNAs | >200 | Transcribed from introns of overlapping protein-coding sequences. Involved in the control of gene expression, alternative splicing, and source for generation of shorter regulatory RNAs (29) | |
| eRNAs | Enhancer-derived RNAs | >200 | Function still not completely understood. May functionally contribute to the enhancer function (30–32) |
| LincRNAs | Long intervening (intergenic) RNAs | >200 | Gene expression regulation, regulation of cellular processes (33, 34) |
| uaRNAs | 3′UTR-derived RNAs | <1000 | Derive within 3′untranslated region (3′UTR) sequences. Function still not clearly understood (35) |
| circRNA | Circular RNA | 100 to >4000 | Diverse, from templates for viral replication to transcriptional regulators (36) |