Abstract
The mammalian genome is composed of thousands of long non-coding RNAs (lncRNAs). Accumulating evidence suggests that lncRNAs play diverse biological roles through a variety of molecular mechanisms including epigenetic, transcriptional, and post-transcriptional regulation. This chapter reviews the molecular mechanisms of lncRNAs in gene regulation and the context of various human diseases associated with dysregulation of lncRNAs.
Access this chapter
Tax calculation will be finalised at checkout
Purchases are for personal use only
References
Albert, M. S. (1996). Cognitive and neurobiologic markers of early Alzheimer disease. Proceedings of the National Academy of Sciences of the United States of America, 93(24), 13547–13551.
Albrecht, S., et al. (1996). Variable imprinting of H19 and IGF2 in fetal cerebellum and medulloblastoma. Journal of Neuropathology and Experimental Neurology, 55(12), 1270–1276.
Arron, J. R., et al. (2006). NFAT dysregulation by increased dosage of DSCR and DYRK1A on chromosome 21. Nature, 441(7093), 595–600.
Banfai, B., et al. (2012). Long noncoding RNAs are rarely translated in two human cell lines. Genome Research, 22(9), 1646–1657.
Barsyte-Lovejoy, D., et al. (2006). The c-Myc oncogene directly induces the H19 noncoding RNA by allele-specific binding to potentiate tumorigenesis. Cancer Research, 66(10), 5330–5337.
Bei, J. X., et al. (2010). A genome-wide association study of nasopharyngeal carcinoma identifies three new susceptibility loci. Nature Genetics, 42(7), 599–603.
Beier, D., et al. (2007). CD133(+) and CD133(−) glioblastoma-derived cancer stem cells show differential growth characteristics and molecular profiles. Cancer Research, 67(9), 4010–4015.
Benetatos, L., Vartholomatos, G., & Hatzimichael, E. (2011). MEG3 imprinted gene contribution in tumorigenesis. International Journal of Cancer, 129(4), 773–779.
Bernard, D., et al. (2010). A long nuclear-retained non-coding RNA regulates synaptogenesis by modulating gene expression. EMBO Journal, 29(18), 3082–3093.
Bernstein, B. E., et al. (2012). An integrated encyclopedia of DNA elements in the human genome. Nature, 489(7414), 57–74.
Bertani, S., et al. (2011). The noncoding RNA Mistral activates Hoxa6 and Hoxa7 expression and stem cell differentiation by recruiting MLL1 to chromatin. Molecular Cell, 43(6), 1040–1046.
Berteaux, N., et al. (2005). H19 mRNA-like noncoding RNA promotes breast cancer cell proliferation through positive control by E2F1. Journal of Biological Chemistry, 280(33), 29625–29636.
Bilguvar, K., et al. (2008). Susceptibility loci for intracranial aneurysm in European and Japanese populations. Nature Genetics, 40(12), 1472–1477.
Brandon, N. J., et al. (2009). Understanding the role of DISC in psychiatric disease and during normal development. Journal of Neuroscience, 29(41), 12768–12775.
Brannan, C. I., et al. (1990). The product of the H19 gene may function as an RNA. Molecular and Cellular Biology, 10(1), 28–36.
Broadbent, H. M., et al. (2008). Susceptibility to coronary artery disease and diabetes is encoded by distinct, tightly linked SNPs in the ANRIL locus on chromosome 9p. Human Molecular Genetics, 17(6), 806–814.
Brown, C. J., et al. (1991). A gene from the region of the human X inactivation centre is expressed exclusively from the inactive X chromosome. Nature, 349(6304), 38–44.
Cabianca, D. S., & Gabellini, D. (2010). The cell biology of disease: FSHD: Copy number variations on the theme of muscular dystrophy. Journal of Cell Biology, 191(6), 1049–1060.
Cabianca, D. S., et al. (2012). A long ncRNA links copy number variation to a polycomb/trithorax epigenetic switch in FSHD muscular dystrophy. Cell, 149(4), 819–831.
Cabili, M. N., et al. (2011). Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes & Development, 25(18), 1915–1927.
Cesana, M., et al. (2011). A long noncoding RNA controls muscle differentiation by functioning as a competing endogenous RNA. Cell, 147(2), 358–369.
Chamberlain, S. J., & Brannan, C. I. (2001). The Prader-Willi syndrome imprinting center activates the paternally expressed murine Ube3a antisense transcript but represses paternal Ube3a. Genomics, 73(3), 316–322.
Chrousos, G. P., & Kino, T. (2005). Intracellular glucocorticoid signaling: A formerly simple system turns stochastic. Science STKE, 2005(304), pe48.
Chu, C., et al. (2011). Genomic maps of long noncoding RNA occupancy reveal principles of RNA-chromatin interactions. Molecular Cell, 44(4), 667–678.
Chubb, J. E., et al. (2008). The DISC locus in psychiatric illness. Molecular Psychiatry, 13(1), 36–64.
Daughters, R. S., et al. (2009). RNA gain-of-function in spinocerebellar ataxia type. PLoS Genet, 5(8), e1000600.
De Santa, F., et al. (2010). A large fraction of extragenic RNA pol II transcription sites overlap enhancers. PLoS Biology, 8(5), e1000384.
Derrien, T., et al. (2012). The GENCODE v7 catalog of human long noncoding RNAs: Analysis of their gene structure, evolution, and expression. Genome Research, 22(9), 1775–1789.
Devon, R. S., et al. (2001). Identification of polymorphisms within Disrupted in Schizophrenia 1 and Disrupted in Schizophrenia 2, and an investigation of their association with schizophrenia and bipolar affective disorder. Psychiatric Genetics, 11(2), 71–78.
Dinger, M. E., et al. (2008). Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation. Genome Research, 18(9), 1433–1445.
Djebali, S., et al. (2012). Landscape of transcription in human cells. Nature, 489(7414), 101–108.
Dugimont, T., et al. (1998). The HTATA-less promoter is efficiently repressed by wild-type tumor suppressor gene product p53. Oncogene, 16(18), 2395–2401.
Ebisuya, M., et al. (2008). Ripples from neighbouring transcription. Nature Cell Biology, 10(9), 1106–1113.
Ekelund, J., et al. (2004). Replication of 1q42 linkage in Finnish schizophrenia pedigrees. Molecular Psychiatry, 9(11), 1037–1041.
Faghihi, M. A., et al. (2008). Expression of a noncoding RNA is elevated in Alzheimer’s disease and drives rapid feed-forward regulation of beta-secretase. Nature Medicine, 14(7), 723–730.
Gibb, E. A., et al. (2011). Human cancer long non-coding RNA transcriptomes. PLoS ONE, 6(10), e25915.
Gong, C., & Maquat, L. E. (2011). lncRNAs transactivate STAU1-mediated mRNA decay by duplexing with 3′ UTRs via Alu elements. Nature, 470(7333), 284–288.
Gupta, R. A., et al. (2010). Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis. Nature, 464(7291), 1071–1076.
Guttman, M., & Rinn, J. L. (2012). Modular regulatory principles of large non-coding RNAs. Nature, 482(7385), 339–346.
Guttman, M., et al. (2009). Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature, 458(7235), 223–227.
Guttman, M., et al. (2010). Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs. Nature Biotechnology, 28(5), 503–510.
Guttman, M., et al. (2011). LincRNAs act in the circuitry controlling pluripotency and differentiation. Nature, 477(7364), 295–300.
Haywood, M. E., et al. (2006). Overlapping BXSB congenic intervals, in combination with microarray gene expression, reveal novel lupus candidate genes. Genes and Immunity, 7(3), 250–263.
Helgadottir, A., et al. (2008). The same sequence variant on 9p21 associates with myocardial infarction, abdominal aortic aneurysm and intracranial aneurysm. Nature Genetics, 40(2), 217–224.
Hogan, P. G., et al. (2003). Transcriptional regulation by calcium, calcineurin, and NFAT. Genes & Development, 17(18), 2205–2232.
Huarte, M., et al. (2010). A large intergenic noncoding RNA induced by p53 mediates global gene repression in the p53 response. Cell, 142(3), 409–419.
Hung, T., et al. (2011). Extensive and coordinated transcription of noncoding RNAs within cell-cycle promoters. Nature Genetics, 43(7), 621–629.
Ji, P., et al. (2003). MALAT-1, a novel noncoding RNA, and thymosin beta4 predict metastasis and survival in early-stage non-small cell lung cancer. Oncogene, 22(39), 8031–8041.
Johnson, R. (2012). Long non-coding RNAs in Huntington’s disease neurodegeneration. Neurobiology of Diseases, 46(2), 245–254.
Johnson, R., et al. (2009). Regulation of neural macroRNAs by the transcriptional repressor REST. RNA, 15(1), 85–96.
Johnstone, K. A., et al. (2006). A human imprinting centre demonstrates conserved acquisition but diverged maintenance of imprinting in a mouse model for Angelman syndrome imprinting defects. Human Molecular Genetics, 15(3), 393–404.
Khalil, A. M., et al. (2009). Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proceedings of the National Academy of Sciences of the United States of America, 106(28), 11667–11672.
Kim, T. K., et al. (2010). Widespread transcription at neuronal activity-regulated enhancers. Nature, 465(7295), 182–187.
Kino, T., et al. (2010). Noncoding RNA gas5 is a growth arrest- and starvation-associated repressor of the glucocorticoid receptor. Science Signal, 3(107), ra8.
Kobayashi, D., et al. (2008). BACE gene deletion: Impact on behavioral function in a model of Alzheimer’s disease. Neurobiology of Aging, 29(6), 861–873.
Koerner, M. V., et al. (2009). The function of non-coding RNAs in genomic imprinting. Development, 136(11), 1771–1783.
Kondrashov, A. V., et al. (2005). Inhibitory effect of naked neural BC1 RNA or BC200 RNA on eukaryotic in vitro translation systems is reversed by poly(A)-binding protein (PABP). Journal of Molecular Biology, 353(1), 88–103.
Lee, J. T., Davidow, L. S., & Warshawsky, D. (1999). Tsix, a gene antisense to Xist at the X-inactivation centre. Nature Genetics, 21(4), 400–404.
Leeb, M., et al. (2010). Polycomb complexes act redundantly to repress genomic repeats and genes. Genes & Development, 24(3), 265–276.
Loewer, S., et al. (2010). Large intergenic non-coding RNA-RoR modulates reprogramming of human induced pluripotent stem cells. Nature Genetics, 42(12), 1113–1117.
Mao, Y. S., et al. (2011). Direct visualization of the co-transcriptional assembly of a nuclear body by noncoding RNAs. Nature Cell Biology, 13(1), 95–101.
Mattick, J. S. (2003). Challenging the dogma: The hidden layer of non-protein-coding RNAs in complex organisms. Bioessays, 25(10), 930–939.
McConlogue, L., et al. (2007). Partial reduction of BACE has dramatic effects on Alzheimer plaque and synaptic pathology in APP Transgenic Mice. Journal of Biological Chemistry, 282(36), 26326–26334.
McPherson, R., et al. (2007). A common allele on chromosome associated with coronary heart disease. Science, 316(5830), 1488–1491.
Mercer, T. R., et al. (2008). Specific expression of long noncoding RNAs in the mouse brain. Proceedings of the National Academy of Sciences of the United States of America, 105(2), 716–721.
Mercer, T. R., Dinger, M. E., & Mattick, J. S. (2009). Long non-coding RNAs: Insights into functions. Nature Reviews Genetics, 10(3), 155–159.
Mikkelsen, T. S., et al. (2007). Genome-wide maps of chromatin state in pluripotent and lineage-committed cells. Nature, 448(7153), 553–560.
Millar, J. K., et al. (2000). Disruption of two novel genes by a translocation co-segregating with schizophrenia. Human Molecular Genetics, 9(9), 1415–1423.
Miyoshi, N., et al. (2000). Identification of an imprinted gene, Meg3/Gtl2 and its human homologue MEG3, first mapped on mouse distal chromosome 12 and human chromosome 14q. Genes to Cells, 5(3), 211–220.
Morrison, L. E., et al. (2007). Effects of ERBB2 amplicon size and genomic alterations of chromosomes 1, 3, and 10 on patient response to trastuzumab in metastatic breast cancer. Genes, Chromosomes and Cancer, 46(4), 397–405.
Moseley, M. L., et al. (2006). Bidirectional expression of CUG and CAG expansion transcripts and intranuclear polyglutamine inclusions in spinocerebellar ataxia type 8. Nature Genetics, 38(7), 758–769.
Mourtada-Maarabouni, M., et al. (2009). GAS5, a non-protein-coding RNA, controls apoptosis and is downregulated in breast cancer. Oncogene, 28(2), 195–208.
Muller, S., et al. (2000). Genomic imprinting of IGF and H19 in human meningiomas. European Journal of Cancer, 36(5), 651–655.
Mus, E., Hof, P. R., & Tiedge, H. (2007). Dendritic BC200 RNA in aging and in Alzheimer’s disease. Proceedings of the National Academy of Sciences of the United States of America, 104(25), 10679–10684.
Mutsuddi, M., & Rebay, I. (2005). Molecular genetics of spinocerebellar ataxia type 8 (SCA8). RNA Biology, 2(2), 49–52.
Nakamura, Y., et al. (2008). The GAS5 (growth arrest-specific transcript 5) gene fuses to BCL6 as a result of t(1;3)(q25;q27) in a patient with B-cell lymphoma. Cancer Genetics and Cytogenetics, 182(2), 144–149.
Nupponen, N. N., & Carpten, J. D. (2001). Prostate cancer susceptibility genes: Many studies, many results, no answers. Cancer and Metastasis Reviews, 20(3–4), 155–164.
Orom, U. A., et al. (2010). Long noncoding RNAs with enhancer-like function in human cells. Cell, 143(1), 46–58.
O’Rourke, J. R., & Swanson, M. S. (2009). Mechanisms of RNA-mediated disease. Journal of Biological Chemistry, 284(12), 7419–7423.
Pandey, R. R., et al. (2008). Kcnq1ot1 antisense noncoding RNA mediates lineage-specific transcriptional silencing through chromatin-level regulation. Molecular Cell, 32(2), 232–246.
Pasmant, E., et al. (2007). Characterization of a germ-line deletion, including the entire INK4/ARF locus, in a melanoma-neural system tumor family: Identification of ANRIL, an antisense noncoding RNA whose expression coclusters with ARF. Cancer Research, 67(8), 3963–3969.
Ponjavic, J., et al. (2009). Genomic and transcriptional co-localization of protein-coding and long non-coding RNA pairs in the developing brain. PLoS Genetics, 5(8), e1000617.
Ponting, C. P., Oliver, P. L., & Reik, W. (2009). Evolution and functions of long noncoding RNAs. Cell, 136(4), 629–641.
Qureshi, I. A., Mattick, J. S., & Mehler, M. F. (2010). Long non-coding RNAs in nervous system function and disease. Brain Research, 1338, 20–35.
Ranum, L. P., & Cooper, T. A. (2006). RNA-mediated neuromuscular disorders. Annual Review of Neuroscience, 29, 259–277.
Ravache, M., et al. (2010). Transcriptional activation of REST by Spin Huntington’s disease models. PLoS ONE, 5(12), e14311.
Ravasi, T., et al. (2006). Experimental validation of the regulated expression of large numbers of non-coding RNAs from the mouse genome. Genome Research, 16(1), 11–19.
Rinn, J. L., et al. (2007). Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. Cell, 129(7), 1311–1323.
Samani, N. J., et al. (2008). Coronary artery disease-associated locus on chromosome 9p and early markers of atherosclerosis. Arteriosclerosis, Thrombosis, and Vascular Biology, 28(9), 1679–1683.
Schneider, C., King, R. M., & Philipson, L. (1988). Genes specifically expressed at growth arrest of mammalian cells. Cell, 54(6), 787–793.
Sheik Mohamed, J., et al. (2010). Conserved long noncoding RNAs transcriptionally regulated by Octand Nanog modulate pluripotency in mouse embryonic stem cells. RNA, 16(2), 324–337.
Shete, S., et al. (2009). Genome-wide association study identifies five susceptibility loci for glioma. Nature Genetics, 41(8), 899–904.
Smedley, D., et al. (2000). Characterization of chromosome abnormalities in malignant melanomas. Genes, Chromosomes and Cancer, 28(1), 121–125.
Smith, C. M., & Steitz, J. A. (1998). Classification of gas5 as a multi-small-nucleolar-RNA (snoRNA) host gene and a member of the 5′-terminal oligopyrimidine gene family reveals common features of snoRNA host genes. Molecular and Cellular Biology, 18(12), 6897–6909.
Sone, M., et al. (2007). The mRNA-like noncoding RNA Gomafu constitutes a novel nuclear domain in a subset of neurons. Journal of Cell Science, 120(Pt 15), 2498–2506.
Sotomaru, Y., et al. (2002). Unregulated expression of the imprinted genes H19 and Igf2r in mouse uniparental fetuses. Journal of Biological Chemistry, 277(14), 12474–12478.
Stacey, S. N., et al. (2009). New common variants affecting susceptibility to basal cell carcinoma. Nature Genetics, 41(8), 909–914.
Stange, D. E., et al. (2006). High-resolution genomic profiling reveals association of chromosomal aberrations on 1q and 16p with histologic and genetic subgroups of invasive breast cancer. Clinical Cancer Research, 12(2), 345–352.
Struhl, K. (2007). Transcriptional noise and the fidelity of initiation by RNA polymerase II. Nature Structural & Molecular Biology, 14(2), 103–105.
Tian, D., Sun, S., & Lee, J. T. (2010). The long noncoding RNA, Jpx, is a molecular switch for X chromosome inactivation. Cell, 143(3), 390–403.
Tiedge, H., Chen, W., & Brosius, J. (1993). Primary structure, neural-specific expression, and dendritic location of human BC200 RNA. Journal of Neuroscience, 13(6), 2382–2390.
Tremblay, D. C., et al. (2010). Expression, tandem repeat copy number variation and stability of four macrosatellite arrays in the human genome. BMC Genomics, 11, 632.
Tripathi, V., et al. (2010). The nuclear-retained noncoding RNA MALAT1 regulates alternative splicing by modulating SR splicing factor phosphorylation. Molecular Cell, 39(6), 925–938.
Tsai, M. C., et al. (2010). Long noncoding RNA as modular scaffold of histone modification complexes. Science, 329(5992), 689–693.
Vitali, P., et al. (2010). Long nuclear-retained non-coding RNAs and allele-specific higher-order chromatin organization at imprinted snoRNA gene arrays. Journal of Cell Science, 123(Pt 1), 70–83.
Wang, K. C., & Chang, H. Y. (2011). Molecular mechanisms of long noncoding RNAs. Molecular Cell, 43(6), 904–914.
Wang, H., & Tiedge, H. (2004). Translational control at the synapse. Neuroscientist, 10(5), 456–466.
Wang, X., et al. (2008). Induced ncRNAs allosterically modify RNA-binding proteins in cis to inhibit transcription. Nature, 454(7200), 126–130.
Wang, K. C., et al. (2011). A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression. Nature, 472(7341), 120–124.
Wapinski, O., & Chang, H. Y. (2011). Long noncoding RNAs and human disease. Trends in Cell Biology, 21(6), 354–361.
Warburton, P. E., et al. (2008). Analysis of the largest tandemly repeated DNA families in the human genome. BMC Genomics, 9, 533.
Williams, J. M., et al. (2009). A 1q42 deletion involving DISC1, DISC2, and TSNAX in an autism spectrum disorder. American Journal of Medical Genetics Part A, 149A(8), 1758–1762.
Willingham, A. T., et al. (2005). A strategy for probing the function of noncoding RNAs finds a repressor of NFAT. Science, 309(5740), 1570–1573.
Yap, K. L., et al. (2010). Molecular interplay of the noncoding RNA ANRIL and methylated histone H3 lysine 27 by polycomb CBX7 in transcriptional silencing of INK4a. Molecular Cell, 38(5), 662–674.
Yasuno, K., et al. (2010). Genome-wide association study of intracranial aneurysm identifies three new risk loci. Nature Genetics, 42(5), 420–425.
Yoon, J. W., et al. (2002). Gene expression profiling leads to identification of GLI1-binding elements in target genes and a role for multiple downstream pathways in GLI1-induced cell transformation. Journal of Biological Chemistry, 277(7), 5548–5555.
Yoon, J. H., et al. (2012). LincRNA-p21 suppresses target mRNA translation. Molecular Cell, 47(4), 648–655.
Zeggini, E., et al. (2007). Replication of genome-wide association signals in UK samples reveals risk loci for type diabetes. Science, 316(5829), 1336–1341.
Zhang, X., et al. (2003). A pituitary-derived MEG3 isoform functions as a growth suppressor in tumor cells. Journal of Clinical Endocrinology and Metabolism, 88(11), 5119–5126.
Zhao, J., et al. (2008). Polycomb proteins targeted by a short repeat RNA to the mouse X chromosome. Science, 322(5902), 750–756.
Zhao, J., et al. (2010). Genome-wide identification of polycomb-associated RNAs by RIP-seq. Molecular Cell, 40(6), 939–953.
Zhong, Z., et al. (2007). Levels of beta-secretase (BACE1) in cerebrospinal fluid as a predictor of risk in mild cognitive impairment. Archives of General Psychiatry, 64(6), 718–726.
Zuccato, C., et al. (2003). Huntingtin interacts with REST/NRSF to modulate the transcription of NRSE-controlled neuronal genes. Nature Genetics, 35(1), 76–83.
Author information
Authors and Affiliations
Corresponding author
Editor information
Editors and Affiliations
Rights and permissions
Copyright information
© 2013 Springer Science+Business Media New York
About this chapter
Cite this chapter
Lin, N., Rana, T.M. (2013). Dysregulation of Long Non-coding RNAs in Human Disease. In: Khalil, A., Coller, J. (eds) Molecular Biology of Long Non-coding RNAs. Springer, New York, NY. https://doi.org/10.1007/978-1-4614-8621-3_5
Download citation
DOI: https://doi.org/10.1007/978-1-4614-8621-3_5
Published:
Publisher Name: Springer, New York, NY
Print ISBN: 978-1-4614-8620-6
Online ISBN: 978-1-4614-8621-3
eBook Packages: Biomedical and Life SciencesBiomedical and Life Sciences (R0)