Table 1.
Summary of identified IncRNAs involved in skeletal biology and disease.
| Gene name | Gene symbol | ENSEMBL Gene ID | Expression pattern | Proposed function | Reference |
|---|---|---|---|---|---|
| Chondrogenesis associated transcript |
DA125942 Synonym: CISTR |
ENSG00000260492 | Genetic mutation results in brachydactyly type E (BDE) | Interacts with PTHLH in trans and with SOX9 in cis | (93) |
| Differentiation antagonizing non-protein coding RNA |
DANCR Synonym: ANCR |
ENSG00000226950 | Upregulated during chondrocyte differentiation | May promote cell proliferation and differentiation toward the chondrocyte lineage |
(90) |
| Downregulated during osteogenesis | Recruits EZH2 to the RUNX2 promoter and suppresses RUNX2 expression |
(165) | |||
| Inhibits osteogenesis via suppression of Wnt/ βcatenin pathway. |
(166) | ||||
| Upregulated in osteosarcoma | (193) | ||||
| F0XC2 antisense RNA 1 Synonym: Osteosarcoma doxorubicin-resistance upregulated IncRNA |
FOXC2-AS1 Synonym: ODRUL |
ENSG00000260944 | Expression correlates with poor response to doxorubicin chemotherapy |
(200) | |
| Growth arrest-specific 5 | GAS5 | ENSG00000234741 | Primarily expressed in the nucleus of healthy chondrocytes, and in the cytoplasm of OA chondrocytes |
Induces catabolic effect by regulating miR-21 | (142) |
| Elevated in OA chondrocytes | (138, 139) | ||||
| H19, imprinted maternally expressed transcript (Mus musculus) |
H19 | ENSMUSG00000000031 |
H19 is upregulated by overexpression of Hh and Yap1, Overexpression of Yap1 and H19 is responsible for the pathogenesis of osteoblastic osteosarcoma |
(173) | |
| H19, imprinted maternally expressed transcript (Homo sapiens) |
H19 | ENSG00000130600 | Highly expressed in mature chondrocytes | Functions downstream of SOX9. H19 is processed into miR-675 that subsequently upregulates COL2A1. |
(133) |
| Elevated in OA chondrocytes | (134, 138, 139) |
||||
| Upregulated in osteogenesis |
H19 is processed into miR-675, which targets TGFB1 for degradation. |
(136) | |||
|
H19 acts as a ceRNA, binding to miR-141 and miR- 22, thus preventing their binding to target mRNAs. |
(135) | ||||
| HIF1A antisense RNA | HIF1A-AS1 | ENSG00000258777 | Knockdown of HIF1a-AS1 decreases HOXD10 expression |
(168) | |
| Highly upregulated in liver cancer conserved region |
HULC | ENSG00000276019 | Upregulated in osteosarcoma | (189) | |
| HOX transcript antisense RNA (Mus musculus) | Hotair | ENSMUSG00000086903 | Hotair knockout mice exhibit patterning malformations in the limbs and lumbosacral junction |
Recruits EZH2 and SUZ12 to the HoxD cluster and silences the locus. |
(101) |
| HOX transcript antisense RNA (Homo sapiens) | HOTAIR | ENSG00000228630 | Elevated in OA chondrocytes | Recruits EZH2 and SUZ12 to the HoxD cluster and silences the locus. |
(138, 139) |
| Upregulated in osteosarcoma | (195) | ||||
| Decreased in AVICs by cyclic stretch, leading to calcification | β-catenin is a stretch responsive signaling pathway that represses HOTAIR |
(102) | |||
| HOXA transcript at the distal tip | HOTTIP | ENSG00000243766 | Elevated in OA chondrocytes | (139) | |
| Upregulated in osteosarcoma | (194) | ||||
| HOXA transcript induced by TGFβ |
IncRNA-HIT Synonym: 9530018H14RIK |
ENSMUSG00000102373 | Expressed in the developing mouse limb | Binds to p100/CBP complexes to maintain active chromatin mark H3K27ac at the HoxA locus |
(104) |
| KCNK15 antisense RNA 1 |
KCNK15-AS1 Synonym: RP11- 445H22.4 |
ENSG00000244558 | Elevated in OA chondrocytes | (138) | |
| Long intergenic non-protein coding RNA 707 |
LINC00707 | ENSG00000238266 | Downregulated during chondrogenesis | (87) | |
| Long intergenic non-protein coding RNA 1589 |
UNC01589 Synonym: CTA- 941F9.9 |
ENSG00000238120 | Upregulated during chondrogenesis | (87) | |
| Maternally expressed gene 3 | MEG3 | ENSG00000214548 | Downregulated in osteoarthritis chondrocytes | (144) | |
| Increased during osteogenic differentiation | Upregulates BMP4 by disrupting the interaction between the SOX2 and BMP4 promoter. |
(170) | |||
| Decreased expression of MEG3 is correlated with poor prognosis in osteosarcoma |
(198) | ||||
| Metastasis-associated lung adenocarcinoma transcript 1 |
MALAT1 | ENSG00000278217 | Upregulated in osteosarcoma | (183, 184) | |
| Downregulated in MG63 osteosarcoma cell line by high- dose estrogen |
Sequesters SFPQ and disrupts the SFPQ/PTBP2 complex, resulting in PTBP2-mediated increases in cellular proliferation and migration. |
(180, 185) | |||
| Not assigned | CTD2574D22.4 | ENSG00000260114 | Elevated in OA chondrocytes | (138) | |
| Not assigned | RP11–815M8.1 | ENSG00000238042 | Upregulated during chondrogenesis | (87) | |
| PMS1 homolog 2, mismatch repair system component pseudogene 2 |
PMS2L2 | ENSG00000278416 | Elevated in OA chondrocytes | (138) | |
| PTGS2 antisense NFKB1 complex-mediated expression regulator RNA Synonym: PS- associated COX2 extragenic RNA |
PACERR Synonym: |
ENSG00000273129 | Increased following 1L1-β treatment of primary OA chondrocytes |
(260) | |
|
PACER, PTGS2- AS1 |
Upregulated in osteosarcoma | Upregulates oncogene COX2 in an NF-kB dependent manner |
(196) | ||
| Small nucleolar RNA host gene 12 | SNHG12 | ENSG00000197989 | Upregulated in osteosarcoma | (187, 188) | |
| Taurine upregulated 1 | TUG1 | ENSG00000253352 | Increased expression is correlated with poor prognosis in osteosarcoma |
(199) | |
| Tumor-suppressor candidate 7 |
TUSC7 Synonym: LSAMP-AS3 LOC285194 |
ENSG00000243197 | Downregulated in osteosarcoma | (190, 191) | |
| Vimentin 2, pseudogene Synonym: Cartilage injury-related IncRNA |
VIM2P Synonym: IncRNA-CIR RP11- 162L10.1 |
ENSG00000220548 | Downregulated in OA chondrocytes | (141) | |
| ZBED3 antisense RNA 1 | ZBED3-AS1 | ENSG00000250802 | Upregulated during chondrogenesis | (87) |