Table 1.
lncRNA-mediated gene expression control
| lncRNA | Function | Mechanism | Refs |
|---|---|---|---|
| Regulation of mRNA transcription | |||
| XIST | X inactivation | Chromatin-mediated repression | 23,121 |
| HOTA1R | Repression at the HOXD locus |
Chromatin-mediated repression | 24,122 |
| HOTT1P | Activation at the HOXA locus | Chromatin-mediated activation | 123 |
| KCNQIOT1 | Imprinting at the KCNQ1 cluster |
Chromatin-mediated repression | 27 |
| ANR1L | Repression at the lNK4b ARF-INK4a locus |
Chromatin-mediated repression | 26,28 |
| AIRN | Imprinting at the IGF2R cluster |
Chromatin-mediated repression, transcription interference |
30 |
| ME4 antisense | Repression of ME4 mRNA | Transcription interference | 31 |
| IRT1 | Repression of IME1 mRNA | Chromatin-mediated repression | 32 |
| GAL10 lncRNA | Repression of GAL1 and CAL10 mRNAs |
Chromatin-mediated repression | 35 |
| PH084 antisense | Repression of PH084 mRNA | Chromatin-mediated repression | 33 |
| ICR1 | Repression of FLO11 mRNA | Modulation of transcription factor recruitment |
37,41 |
| PWR1 | Activation of FLO11 mRNA | Modulation of transcription factor recruitment |
37,41 |
| SRG1 | Repression of SER3 mRNA | Nucleosome remodelling | 38 |
| fbp1 ncRNA | Activation of fbp1 | Chromatin remodelling | 39 |
| UNOCR | Activation of lysozyme mRNA |
Nucleosome remodelling | 40 |
| Alu repeat-containing RNA | Transcriptional repression during heat shock |
Inhibition of Pol II | 47 |
| HSR1 | Activation of the HSF1 transcription factor |
Allosteric activation together with eEFIA | 49 |
| Non-coding DHFR | Transcriptional repression of DHFR |
Inhibition of pre-initiation complex formation |
48 |
| CAS5 | Repression of glucocorticoid receptor-mediated transcription |
DNA mimicry | 50 |
| EVF2 | Transcriptional activation of DLX2 targets, transcriptional repression of MeCP2 targets |
Recruitment of DLX2 or MeCP2 | 51,52 |
| CCND1 promoter RNA | Repression of CCND1 transcription |
Allosteric activation of TLS | 53 |
| NRON | Repression of NFAT-mediated transcription |
Inhibition of transcription factor nucleocytoplasmic shuttling |
54 |
| Regulation of mRNA processing | |||
| Neuroblastoma MYC (NAT) | Inhibition of neuroblastoma MYC intron 1 splicing |
Unknown mechanism involving the inhibition of splicing via RNA-RNA duplex formation |
61 |
| Rev-ErbAalpha | Inhibition of the c-ErbAalpha 2 splice isoform |
Unknown mechanism involving the inhibition of splicing via RNA-RNA duplex formation |
62 |
| ZEB2 (NAT) | Activation of ZEB2 translation |
Unknown mechanism involving regulated splicing of an IRES-containing intron |
59 |
| MALAT1 | Ser/Arg splicing factor regulation |
Scaffolding of subnuclear domains | 64 |
| Sas10 mRNA 3′UTR | Repression of Rnp4F mRNA | Unknown mechanism involving RNA editing |
66 |
| Modulation of mRNA post-transcriptional regulatory pathways | |||
| Antisense UCHL1 | Upregulation of UCHL1 protein production |
SINE2B element-mediated translational upregulation |
68 |
| KCS1 antisense | Production of truncated KCS1 protein |
Unknown mechanism involving base pairing | 69 |
| 1/2-sbsRNA1 | Down-regulation of SERPINE1 and FLJ21870 mRNAs |
Staufen-mediated decaythrough Alu element base pairing | 70 |
| BACE1AS | Up-regulation of BACE1 | Stabilization of BACE1 mRNA by blocking miRNA-induced repression |
71,72 |
| UNCMD1 | Control of muscle differentiation through upregulation of MAML1 and MEF2C transcript ion factors |
Sequestration of miRNAs | 74 |
| HULC | Downregulation of miRNA-mediated repression |
Sequestration of miRNAs | 75 |
| PTENP1 pseudogene | Upregulation of PTEN | Sequestration of miRNAs | 79 |
| IPS1 | Downregulation of miRNA-mediated repression |
Sequestration of miRNAs | 76 |
| CDR1as | Downregulation of miRNA-mediated repression |
Sequestration of miRNAs | 77,78 |
1/2-sbsRNA1, half-STAU1-binding site RNA1;AIRN, antisense of IGFR2 non-coding RNA; BACE1AS, beta-site APP-cleaving enzyme 1 antisense; CCND1, cyclin D1; CDR1as, CDR1 antisense; DHFR, dihydrofolate reductase; fbp1, fructose-l,6-bisphosphatase 1; eEF1A, eukaryotic elongation factor 1A; FLO11; GAS5, growth arrest specific 5; HOTAIR, HOX transcript antisense RNA; HOTTIP, HOXA transcript at the distal tip; HOX, homeobox cluster; HSF1, heat shock factor 1; HSR1, heat shock RNA1; HULC, highly upregulated in liver cancer; IGF2R, insulin-like growth factor 2 receptor; IME, inducer of meiosis; IPS1, INDUCED BY PHOSPHATE STARVATION 1; IRES, internal ribosome entry site; IRT1, IME1 regulatory transcript 1; KCNQ1, potassium voltage-gated channel, KQT-like subfamily, member 1; KCNQ1OT1, KCNQ1 opposite strand or antisense transcript 1; LINOCR, LPS-inducible non-coding RNA; lncRNA, long non-coding RNA; MALAT1, metastasis associated lung adenocarcinoma transcript 1; MAML1, mastermind-like 1; MeCP2, methyl CpG binding-protein 2; MEF2C, myocyte enhancer factor 2C; miRNA, microRNA; NAT, natural antisense transcript; ncRNA, non-coding RNA; NFAT, nuclear factor of activated T cells; NRON, non-coding repressor of N FAT; Pol II, RNA polymerase II; PTENP1, phosphatase and tensin homologue; Rnp4F, RNA-binding protein 4F; TLS, translocated in liposarcoma; UCHL1, ubiquitin carboxyl-terminal esterase LI; UTR, untranslated region; XIST, X inactivation-specific transcript; ZEB2, zinc-finger E-box binding homeobox 2.