Table 2.
Identified tumor and disease-associated LncRNAs
| Name | Function/Characterization | References |
|---|---|---|
| H19 | Imprinted at the lgf2 locus; controls igf2 expression in cis, implicated in both tumor suppressors and oncogenes | Maher, ER. et al., 2000 [94]; Gaston, V. et al., 2001 [95] |
| HOTAIR | Intergenic transcript of HoxC locus, gene silencing in trans through interacting with PCR2 and LSD1 complex, involved in breast cancer metastasis | Tsai, MC. et al., 2010 [15]; Gupta, RA. et al., 2010 [16]; Rinn, JL. et al., 2007 [28] |
| AIR | Imprinted, monoallelically expressed from the paternal allele, interacts with histone methyltransferase G9a | Wutz, A. et al., 1997 [24]; Nagano, T. et al., 2008 [25]; Sleutels, F et al, 2002 [27] |
| ANRIL | Antisense transcript of INK4n/ARF/INK4a and p15/CDKN2B, required for the PRC2 recruitment to and silencing p15INK4b tumor suppressor gene | Pasmant, E. et al., 2007 [29]; Yap, KL. et al., 2010 [31]; Kotake, Y. et al., 2011 [32] |
| HOTAIRM1 | Antisense intergenic RNA myeloid 1, transcribed antisense to the HOXA genes, plays a role in the myelopoiesis through modulation of gene expression in the HOXA cluster | Zhang X., et al., 2009 [140] |
| KCNQ1OT1 | Tissue-specific imprinted genes within the Kcnq1 domain, interacting with both PRC2 and G9a leading to gene silencing in a lineage-specific manner | Kanduri, C. et al., 2006 [37]; Pandey, RR. et al., 2008 [33]; Lee, MP. et al., 1999 [97]; Nakano, S. et al., 2006 [98] |
| Evf-1 | Activates transcriptional activity by directly influencing Dlx-2 activity | Kohtz JD & Fishekk G., 2004 [141] |
| Evf-2 | An alternatively spliced form of Evf-1 activates transcriptional activity by directly influencing Dlx-2 activity | Feng, J. et al., 2006 [49] |
| P15AS | Antisense transcript of p15, highly expressed in leukemia, epigenetically silences the tumor suppressor gene p15 | Yu, W. et al., 2008 [107] |
| Xist | Mosaic expression, spreads on Xi in cis, interacts with BRCA1, correlated with breast cancer, cervical, ovarian, and testis tumors | Zhao, J. et al., 2008 [19]; Weakley SM et al. 2011 [80] |
| Tsix | Antisense transcript to Xist , prevents Xist stabilization and inhibits the interaction between Rep A and PRC2, silencing Xist expression | Zhao,J. et al., 2008 [19]; Navarro, P. et al., 2005 [22] |
| Zeb2NAT | Antisense to Zeb2, regulates splicing of the IRES-containing intron of Zeb 2, involved in EMT | Beltran, M. et al., 2008 [60] |
| MALAT-1/NEAT2 | Expressed in many cancers, regulates alternative splicing of pre-mRNA and promotes cell motility through transcriptional and post-transcriptional regulation of motility related gene expression | Tripathi, V., 2010 [66] |
| MEG3 | Imprinted transcripts, highly expressed in human pituitary, stimulates p53-mediated transactivation and suppresses tumor growth in the absence of p53 | Gejman, R. et al., 2008 [108]; Benetatos, L. et al., 2011 [110]; Zhou, Y. et al., 2007 [111] |
| GAS5 | Growth arrest-specific transcripts, controls apoptosis and cell cycle, down-regulated in breast cancers | Mourtada-Maarabouni, M. et al., 2008 [114]; Mour-tada-Maarabouni, M. et al., 2009 [115] |
| PCGEM1 | Prostate tissue-specific and prostate-associated, overexpressed in prostate cancers, regulates cell proliferation and apoptosis, promotes colony formation | Srikantan, V. et al., 2000 [76] |
| UCA1 | Urothelial carcinoma-associated transcript, upregulated in bladder carcinoma and embryo, influences cell growth and promotes invasion | Wang, F. et al., 2008 [142]; Wang, XS et al., 2006 [143] |
| SRA-1 | Alternative splicing of SRA-1, loss of coding frame, an increased expression is associated with tumor metastasis | Yao, H et al., 2010 [144] |
| CUDR | Upregulated in drug-resistant human squamous carcinoma, regulates drug sensitivity, cellular transformation and apoptosis | Tsang, WP et al., 2007 [145] |
| VL30-1 | A mouse noncoding retroelement RNA, binds and releases PSF from a proto-oncogene, thus activating Rab23 proto-oncogene transcription | Li, L et al., 2009 [146]; Wang, G. et al., 2009 [147] |
| Myc | Antisense transcript to myc gene, may be targeting the sense transcripts for immediate degradation | Yu, W. et al., 2008 [107] |
| p21NAT | Antisense to cdkn1a/p21, requires Ago1 for epigenetic silencing of Cdkn1a/p21 | Yu, W. et al., 2008 [107] |
| CCND1/Cyclin D1 | Transcribed from 5’ end of Cyclin D1 gene, induced by DNA damage and binding to TLS protein, leading to allosteric changes and repression of Cyclin D1 and anti-sense transcripts of tie-1 related to vascular malformation | Wang, X. et al., 2008 [52] |
| PTENP1 | Transcript of PTEN tumor suppressor pseudogene, PTENP1 3’-UTR exerts a tumor suppressive function by acting as a decoy for PTEN-targeting miRNAs | Poliseno, L et al, 2010 [67]; He, L. 2010 [68] |
| KRAS1P | Transcript of KRAS pseudogene, overexpression of KRAS1P 3’-UTR, increases KRAS mRNA abundance and accelerates cell growth | Poliseno, L et al, 2010 [67] |
| DHFR | Transcribed from upstream of DHFR gene, regulates DHFR expression by forming triple helix with the promoter and disassociating pre-initiation complex | Martianov, I. et al., 2007 [53] |
| TERRA | Telomeric UUAGG repeat-containing RNA, inhibits telomerase activity, also regulates Xist and HOTAIR | Azzalin, CM. et al., 2007 [42]; Schoeftner, S. and Blasco, MA., 2008 [44]; Luke, B. and Lingner, J., 2009 [120] |
| AK023948 | Antisense transcribed from the intron of SIR-like adaptor gene (SLA), significantly downregulated in most of papillary thyroid carcinoma | He, H et al., 2009 [148] |
| TUG1 | Ubiquitously expressed in human and mouse cell types and tissues, involves eye development, upregulated by p53, repressed cell proliferation via bound to PRC2 | Zhou, Y. et al., 2007 [111]; Huarte, M. et al., 2010 [113] |
| LincRNA ROR | Expressed in the induced pluripotent stem cells (iPSCs), involved in the conversion of lineage-committed cells by interacting with reprogramming complexes | Loewer, S. et al., 2010 [149] |
| HAR1 | REST target gene, decreased in the neurons of Huntington's disease | Tsai, MC. et al, 2010 [15] |
| Tie-1AS | Expressed temporally and spatially in vivo with its native gene tie-1, binds tie-1 mRNA, regulating tie-1 transcripts; imbalance of sense | Li, K. et al., 2010 [61] |
| BACE1AS | Antisense transcript for beta-secretase-1, directly implicated in the increased abundance of Abeta 1-42 in Alzheimer's disease | Faghihi, MA. et al., 2008 [62]; Jiang, Y. et al., 2010 [63] |