Table 1.
Examples of Mammalian lncRNA Sequences and Their Binding Partners
| shorthand | name | size (kb)a,b | binding partner(s) | known biological pathways | ref |
|---|---|---|---|---|---|
| Xist | Xi-specific transcripts | 17 | PRC2 | inactivates one X chromosome to ensure genetic equality between sexes | 25 |
| HOTAIR | HOX transcript antisense intergenic RNA | 2.2 | LSD1; PRC2 | suppression of transcription through modification of histone 3 on the HOXD locus | 26 |
| MEG3 (GTL2) | maternally expressed gene 3 (gene trap locus 2) | 1.5–1.8 | PRC2 | potentially forms RNA-DNA triplex structures to regulate TGF-β genes | 27, |
| ANRIL | antisense noncoding RNA in the INK4 locus | 2.2 | PRC1; PRC2 | regulates histone modification in the CDKN2A/B locus | 29 |
| FENDRR | fetal-lethal noncoding developmental regulatory RNA | 2.6; 3.1 | PRC2; TrxG/MLL | binds Foxf1 gene promoter to regulate pathways controlling fate of ES cell differentiation | 30 |
| MALAT1 (NEAT2) | metastasis associated lung adenocarcinoma transcript 1 (nuclear-enriched abundant transcript 2) | 8.8 | SR proteins | recruits SR proteins, a family of splicing proteins, to nuclear speckles to control alternative splicing of pre-mRNA | 31 |
| NEAT1 (VINC) | nuclear paraspeckle assembly transcript 1 (virus inducible noncoding RNA) | 3.2; 22.7 | P54nrb; PSP1a | forms and maintains paraspeckle structure | 32 |
| PCAT1 | prostate cancer associated transcript 1 | 2 | PRC2 | post-transcriptionally silences BRCA2 | 33, 34 |
| SChLAP1 | second chromosome locus associated with prostate-1 | 1.3–1.7 | SWI/SNF | binds SWI/SNF complex, leading to aberrant gene expression | 35 |
| DANCR (ANCR) | differentiation antagonizing nonprotein coding RNA (antidifferentiation ncRNA) | 0.9 | PRC2 | promotes expression of IL6 and TNF-α at mRNA and protein levels in post-menopausal osteoporosis | 36, 37 |
| Lnc_bc060912 | 1.2 | PARP1; NPM | binds PARP1 and NPM1, DNA damage repair proteins, to suppress cell apoptosis | 38 | |
| Kcnq1ot1 | KCNQ1 overlapping transcript 1 | 91.5 | DNMT1 | imprints on multiple genes, leading to gene silencing | 39 |
| SRA | steroid receptor RNA activator | 0.87–0.92 | ER-α; SRC-1; Sharp; SLIRP; RNA helicases p68 and p72 | breast cancer tumorigenesis | 40 |
| PARTICLE | promoter of MAT2A-antisense radiation- induced circulating lncRNA | 1.4 | G9a; SUZ12 | implication in transcription regulation via triple-helix formation | 41 |
a
For lncRNA with <3 transcript isoforms, the transcripts are separated as such: ##; ##.
b
For lncRNA with ≥3 transcript isoforms, a range of transcript lengths are shown: ##-##.