UCRs and T-UCRs
Ultraconserved regions (UCRs) are DNA segments greater than 200 nucleotides in length that are 100% identical among humans, rats, and mice. 481 UCRs have been described (Bejerano et al., 2004). As the original UCR annotations are based on an older (hg17) human genome assembly (Bejerano et al., 2004), we re-annotated all UCRs using the most recent genome build, hg19. Further, we re-organized the UCRs into three specific categories (exonic, intronic, and intergenic) by associating the locations of each with that of nearby human Refseq genes.
The strong degree of sequence conservation of the UCRs suggests that they play essential roles in the biology of mammals. However, the function(s) of the UCRs are not yet completely understood. Two groups demonstrated independently that some exonic UCRs regulate their own expression through unproductive alternative exon splicing leading to nonsense-mediated decay in humans and mice (Lareau et al., 2007; Ni et al., 2007). In addition, non-exonic UCRs (intronic and intergenic) can regulate the expression of other genes in cis, by acting as enhancers (Calin et al., 2007; Pennacchio et al., 2006).
Figure 1. Re-annotation of UCRs. Representation of the different UCR classes according to their genomic location with respect to protein-coding genes deﬁned by Refseq. An example of each class is shown.
Although only 255 (47%) of the UCRs were originally classified as transcribed (exonic) or possibly transcribed (possibly exonic) through their overlap with coding exons (Bejerano et al., 2004), Calin et al. (2007) subsequently demonstrated that the majority (68%) of the UCRs are expressed in one or more tissues. This latter class of UCRs has been termed ''Transcribed UCRs" (T-UCRs), and comprises a new category of noncoding RNA. The transcription units of T-UCRs are often up to 2 kb in length. (Calin et al., 2007). Some exonic T-UCRs, such as TUC338, can be transcribed independently of their host genes (Braconi et al., 2011), while others are transcribed antisense to their host genes (Calin et al., 2007). TUC338 is also an example of a subset of T-UCRs that do not undergo splicing, while some T-UCRs, such as Evf2, are spliced from intron-containing precursors (Feng et al., 2006).
T-UCRs and Cancer
T-UCRs have recently been shown to be abnormally expressed in a number of human cancers such as leukemia, colorectal carcinoma and hepatocellular carcinoma (Braconi et al., 2011; Calin et al., 2007; Lujambio et al., 2010). In addition, the expression profile of T-UCRs appears to be well-correlated with clinical prognosis in patients with neuroblastoma (Mestdagh et al., 2010). T-UCR expression patterns might therefore be useful as clinical indicators for diagnosis, prognosis and prediction of response to therapy.
At least two T-UCRs, uc.73A (Calin et al., 2007) and TUC338 (Braconi et al., 2011) contribute to neoplastic transformation of cells leading to cancer. Further, Calin, et al (2007) demonstrated that the overexpression of uc.73A in colon cancer cells inhibits apoptosis. On the other hand, some T-UCRs, such as uc283+, can act as tumor suppressors (Lujambio et al., 2010). Like miRNAs, T-UCRs that are differentially expressed in a specific cancer tend to be located in cancer-associated genomic regions (CAGRs) and, in fact, several of these T-UCRs are located at fragile sites, amplified regions and loss of heterozygosity loci (Calin et al., 2007). In addition, the aberrant regulation of T-UCR expression in cancer occurs in two primary ways: by altered interactions with miRNA (Calin et al., 2007) and by hypermethylation of CpG island promoters (Lujambio et al., 2010). Moreover, many T-UCRs show significant complementarity to specific miRNAs and could act as miRNA targets (Bejerano et al., 2004; Scaruffi et al., 2009), and in fact miRNAs can significantly reduce expression of some T-UCRs (Calin et al., 2007). Finally, T-UCR expression can be reduced as a result of hypermethylation of promoter CpG islands, as is the case for uc160+ (Lujambio et al., 2010).
Bejerano, G., Pheasant, M., Makunin, I., Stephen, S., Kent, W.J., Mattick, J.S., and Haussler, D. (2004). Ultraconserved elements in the human genome. Science 304, 1321-1325.
Braconi, C., Valeri, N., Kogure, T., Gasparini, P., Huang, N., Nuovo, G.J., Terracciano, L., Croce, C.M., and Patel, T. (2011). Expression and functional role of a transcribed noncoding RNA with an ultraconserved element in hepatocellular carcinoma. Proc Natl Acad Sci U S A 108, 786-791.
Calin, G.A., Liu, C.G., Ferracin, M., Hyslop, T., Spizzo, R., Sevignani, C., Fabbri, M., Cimmino, A., Lee, E.J., Wojcik, S.E., et al. (2007). Ultraconserved regions encoding ncRNAs are altered in human leukemias and carcinomas. Cancer Cell 12, 215-229.
Feng, J., Bi, C., Clark, B.S., Mady, R., Shah, P., and Kohtz, J.D. (2006). The Evf-2 noncoding RNA is transcribed from the Dlx-5/6 ultraconserved region and functions as a Dlx-2 transcriptional coactivator. Genes Dev 20, 1470-1484.
Lareau, L.F., Inada, M., Green, R.E., Wengrod, J.C., and Brenner, S.E. (2007). Unproductive splicing of SR genes associated with highly conserved and ultraconserved DNA elements. Nature 446, 926-929.
Lujambio, A., Portela, A., Liz, J., Melo, S.A., Rossi, S., Spizzo, R., Croce, C.M., Calin, G.A., and Esteller, M. (2010). CpG island hypermethylation-associated silencing of non-coding RNAs transcribed from ultraconserved regions in human cancer. Oncogene 29, 6390-6401.
Mestdagh, P., Fredlund, E., Pattyn, F., Rihani, A., Van Maerken, T., Vermeulen, J., Kumps, C., Menten, B., De Preter, K., Schramm, A., et al. (2010). An integrative genomics screen uncovers ncRNA T-UCR functions in neuroblastoma tumours. Oncogene 29, 3583-3592.
Ni, J.Z., Grate, L., Donohue, J.P., Preston, C., Nobida, N., O'Brien, G., Shiue, L., Clark, T.A., Blume, J.E., and Ares, M., Jr. (2007). Ultraconserved elements are associated with homeostatic control of splicing regulators by alternative splicing and nonsense-mediated decay. Genes Dev 21, 708-718.
Pennacchio, L.A., Ahituv, N., Moses, A.M., Prabhakar, S., Nobrega, M.A., Shoukry, M., Minovitsky, S., Dubchak, I., Holt, A., Lewis, K.D., et al. (2006). In vivo enhancer analysis of human conserved non-coding sequences. Nature 444, 499-502.
Scaruffi, P., Stigliani, S., Moretti, S., Coco, S., De Vecchi, C., Valdora, F., Garaventa, A., Bonassi, S., and Tonini, G.P. (2009). Transcribed-Ultra Conserved Region expression is associated with outcome in high-risk neuroblastoma. BMC Cancer 9, 441.