Table of Contents Author Guidelines Submit a Manuscript
Table of Contents Alerts

To receive news and publication updates for Journal of Immunology Research, enter your email address in the box below.

Journal of Immunology Research
Volume 2015, Article ID 848790, 9 pages
http://dx.doi.org/10.1155/2015/848790
Review Article

The Emerging Functions of Long Noncoding RNA in Immune Cells: Autoimmune Diseases

Keshav Raj Sigdel,1,2 Ao Cheng,1,2 Yin Wang,1,2 Lihua Duan,3 and YanLin Zhang1,2

1Department of Nephrology, The First Affiliated Hospital of Xiamen University, Xiamen University, Xiamen 361003, China
2Department of Nephrology, The First Hospital of Xiamen, Fujian Medical University, Xiamen 361003, China
3Department of Rheumatology and Clinical Immunology, The First Affiliated Hospital of Xiamen University, Xiamen 361003, China

Received 10 September 2014; Accepted 19 February 2015

Academic Editor: Jianying Zhang

Copyright © 2015 Keshav Raj Sigdel et al. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Linked References

  1. P. Carninci, T. Kasukawa, S. Katayama et al., “The transcriptional landscape of the mammalian genome,” Science (New York, N.Y.), vol. 309, no. 5740, pp. 1559–1563, 2005. View at Publisher · View at Google Scholar · View at Scopus
  2. E. Birney, J. A. Stamatoyannopoulos, A. Dutta et al., “Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project,” Nature, vol. 447, no. 7146, pp. 799–816, 2007. View at Google Scholar
  3. C. Liu, B. Bai, G. Skogerbø et al., “NONCODE: an integrated knowledge database of non-coding RNAs,” Nucleic Acids Research, vol. 33, supplement 1, pp. D112–D115, 2005. View at Publisher · View at Google Scholar · View at Scopus
  4. J. E. Wilusz, H. Sunwoo, and D. L. Spector, “Long noncoding RNAs: functional surprises from the RNA world,” Genes & Development, vol. 23, no. 13, pp. 1494–1504, 2009. View at Publisher · View at Google Scholar · View at Scopus
  5. D. Bhartiya, K. Pal, S. Ghosh et al., “LncRNome: a comprehensive knowledgebase of human long noncoding RNAs,” Database, vol. 2013, Article ID bat034, 2013. View at Publisher · View at Google Scholar · View at Scopus
  6. J. Zhao, B. K. Sun, J. A. Erwin, J.-J. Song, and J. T. Lee, “Polycomb proteins targeted by a short repeat RNA to the mouse X chromosome,” Science, vol. 322, no. 5902, pp. 750–756, 2008. View at Publisher · View at Google Scholar · View at Scopus
  7. T. R. Mercer, M. E. Dinger, and J. S. Mattick, “Long non-coding RNAs: insights into functions,” Nature Reviews Genetics, vol. 10, no. 3, pp. 155–159, 2009. View at Publisher · View at Google Scholar · View at Scopus
  8. K. C. Wang and H. Y. Chang, “Molecular mechanisms of long noncoding RNAs,” Molecular Cell, vol. 43, no. 6, pp. 904–914, 2011. View at Publisher · View at Google Scholar · View at Scopus
  9. E. A. Gibb, E. A. Vucic, K. S. S. Enfield et al., “Human cancer long non-coding RNA transcriptomes,” PLoS ONE, vol. 6, no. 10, Article ID e25915, 2011. View at Publisher · View at Google Scholar · View at Scopus
  10. M. A. Faghihi, F. Modarresi, A. M. Khalil et al., “Expression of a noncoding RNA is elevated in Alzheimer's disease and drives rapid feed-forward regulation of β-secretase,” Nature Medicine, vol. 14, no. 7, pp. 723–730, 2008. View at Publisher · View at Google Scholar · View at Scopus
  11. R. McPherson, A. Pertsemlidis, N. Kavaslar et al., “A common allele on chromosome 9 associated with coronary heart disease,” Science, vol. 316, no. 5830, pp. 1488–1491, 2007. View at Publisher · View at Google Scholar · View at Scopus
  12. J. Li, Z. Xuan, and C. Liu, “Long non-coding RNAs and complex human diseases,” International Journal of Molecular Sciences, vol. 14, no. 9, pp. 18790–18808, 2013. View at Publisher · View at Google Scholar · View at Scopus
  13. S. Carpenter, D. Aiello, M. K. Atianand et al., “A long noncoding RNA mediates both activation and repression of immune response genes,” Science, vol. 341, no. 6147, pp. 789–792, 2013. View at Publisher · View at Google Scholar · View at Scopus
  14. S. P. Collier, P. L. Collins, C. L. Williams, M. R. Boothby, and T. M. Aune, “Cutting edge: influence of Tmevpg1, a long intergenic noncoding RNA, on the expression of Ifng by Th1 cells,” The Journal of Immunology, vol. 189, no. 5, pp. 2084–2088, 2012. View at Publisher · View at Google Scholar · View at Scopus
  15. J. A. Gomez, O. L. Wapinski, Y. W. Yang et al., “The NeST long ncRNA controls microbial susceptibility and epigenetic activation of the interferon-γ locus,” Cell, vol. 152, no. 4, pp. 743–754, 2013. View at Publisher · View at Google Scholar · View at Scopus
  16. K. C. Pang, M. E. Dinger, T. R. Mercer et al., “Genome-wide identification of long noncoding RNAs in CD8+ T cells,” The Journal of Immunology, vol. 182, no. 12, pp. 7738–7748, 2009. View at Publisher · View at Google Scholar · View at Scopus
  17. G. Hu, Q. Tang, S. Sharma et al., “Expression and regulation of intergenic long noncoding RNAs during T cell development and differentiation,” Nature Immunology, vol. 14, no. 11, pp. 1190–1198, 2013. View at Publisher · View at Google Scholar · View at Scopus
  18. P. Wang, Y. Xue, Y. Han et al., “The STAT3-binding long noncoding RNA Inc-DC controls human dendritic cell differentiation,” Science, vol. 344, no. 6181, pp. 310–313, 2014. View at Publisher · View at Google Scholar · View at Scopus
  19. S. Shirasawa, H. Harada, K. Furugaki et al., “SNPs in the promoter of a B cell-specific antisense transcript, SAS-ZFAT, determine susceptibility to autoimmune thyroid disease,” Human Molecular Genetics, vol. 13, no. 19, pp. 2221–2231, 2004. View at Publisher · View at Google Scholar · View at Scopus
  20. C. S. Lee, A. Ungewickell, A. Bhaduri et al., “Transcriptome sequencing in Sézary syndrome identifies Sézary cell and mycosis fungoides-associated IncRNAs and novel transcripts,” Blood, vol. 120, no. 16, pp. 3288–3297, 2012. View at Publisher · View at Google Scholar · View at Scopus
  21. J. Verma-Gaur, A. Torkamani, L. Schaffer, S. R. Head, N. J. Schork, and A. J. Feeney, “Noncoding transcription within the Igh distal VH region at PAIR elements affects the 3D structure of the Igh locus in pro-B cells,” Proceedings of the National Academy of Sciences of the United States of America, vol. 109, no. 42, pp. 17004–17009, 2012. View at Publisher · View at Google Scholar · View at Scopus
  22. R. K. Dave, M. E. Dinger, M. Andrew, M. Askarian-Amiri, D. A. Hume, and S. Kellie, “Regulated expression of PTPRJ/CD148 and an antisense long noncoding RNA in macrophages by proinflammatory stimuli,” PLoS ONE, vol. 8, no. 6, Article ID e68306, 2013. View at Publisher · View at Google Scholar · View at Scopus
  23. M. Guttman, I. Amit, M. Garber et al., “Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals,” Nature, vol. 458, no. 7235, pp. 223–227, 2009. View at Publisher · View at Google Scholar · View at Scopus
  24. Z. Li, T. C. Chao, K. Y. Chang et al., “The long noncoding RNA THRIL regulates TNFalpha expression through its interaction with hnRNPL,” Proceedings of the National Academy of Sciences of the United States of America, vol. 111, no. 3, pp. 1002–1007, 2014. View at Publisher · View at Google Scholar · View at Scopus
  25. M. Krawczyk and B. M. Emerson, “p50-associated COX-2 extragenic RNA (PACER) activates COX-2 gene expression by occluding repressive NF-kappaB complexes,” eLife, vol. 3, Article ID e01776, 2014. View at Publisher · View at Google Scholar
  26. P. W. Wright, A. Huehn, F. Cichocki et al., “Identification of a KIR antisense lncRNA expressed by progenitor cells,” Genes and Immunity, vol. 14, no. 7, pp. 427–433, 2013. View at Publisher · View at Google Scholar · View at Scopus
  27. L. Shi, Z. Zhang, A. M. Yu et al., “The SLE transcriptome exhibits evidence of chronic endotoxin exposure and has widespread dysregulation of non-coding and coding RNAs,” PLoS ONE, vol. 9, no. 5, Article ID e93846, 2014. View at Publisher · View at Google Scholar · View at Scopus
  28. N. Müller, F. Döring, M. Klapper et al., “Interleukin-6 and Tumour Necrosis Factor-α differentially regulate lincRNA transcripts in cells of the innate immune system in vivo in human subjects with rheumatoid arthritis,” Cytokine, vol. 68, no. 1, pp. 65–68, 2014. View at Publisher · View at Google Scholar · View at Scopus
  29. E. Sonkoly, Z. Bata-Csorgo, A. Pivarcsi et al., “Identification and characterization of a novel, psoriasis susceptibility-related noncoding RNA gene, PRINS,” The Journal of Biological Chemistry, vol. 280, no. 25, pp. 24159–24167, 2005. View at Publisher · View at Google Scholar · View at Scopus
  30. O. Wapinski and H. Y. Chang, “Long noncoding RNAs and human disease,” Trends in Cell Biology, vol. 21, no. 6, pp. 354–361, 2011. View at Publisher · View at Google Scholar · View at Scopus
  31. C. P. Ponting, P. L. Oliver, and W. Reik, “Evolution and functions of long noncoding RNAs,” Cell, vol. 136, no. 4, pp. 629–641, 2009. View at Publisher · View at Google Scholar · View at Scopus
  32. V. A. Moran, R. J. Perera, and A. M. Khalil, “Emerging functional and mechanistic paradigms of mammalian long non-coding RNAs,” Nucleic Acids Research, vol. 40, no. 14, pp. 6391–6400, 2012. View at Publisher · View at Google Scholar · View at Scopus
  33. P. Kapranov, J. Cheng, S. Dike et al., “RNA maps reveal new RNA classes and a possible function for pervasive transcription,” Science, vol. 316, no. 5830, pp. 1484–1488, 2007. View at Publisher · View at Google Scholar · View at Scopus
  34. T. Kino, D. E. Hurt, T. Ichijo, N. Nader, and G. P. Chrousos, “Noncoding RNA Gas5 is a growth arrest- and starvation-associated repressor of the glucocorticoid receptor,” Science Signaling, vol. 3, no. 107, p. ra8, 2010. View at Publisher · View at Google Scholar · View at Scopus
  35. M. Guttman and J. L. Rinn, “Modular regulatory principles of large non-coding RNAs,” Nature, vol. 482, no. 7385, pp. 339–346, 2012. View at Publisher · View at Google Scholar · View at Scopus
  36. M. Cabili, C. Trapnell, L. Goff et al., “Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses,” Genes and Development, vol. 25, no. 18, pp. 1915–1927, 2011. View at Publisher · View at Google Scholar · View at Scopus
  37. I. Ulitsky and D. P. Bartel, “XLincRNAs: genomics, evolution, and mechanisms,” Cell, vol. 154, no. 1, pp. 26–46, 2013. View at Publisher · View at Google Scholar · View at Scopus
  38. J. T. Y. Kung, D. Colognori, and J. T. Lee, “Long noncoding RNAs: past, present, and future,” Genetics, vol. 193, no. 3, pp. 651–669, 2013. View at Publisher · View at Google Scholar · View at Scopus
  39. A. C. Marques and C. P. Ponting, “Intergenic lncRNAs and the evolution of gene expression,” Current Opinion in Genetics & Development, vol. 27, no. 48, pp. 48–53, 2014. View at Publisher · View at Google Scholar · View at Scopus
  40. Y. Ogawa, B. K. Sun, and J. T. Lee, “Intersection of the RNA interference and X-inactivation pathways,” Science, vol. 320, no. 5881, pp. 1336–1341, 2008. View at Publisher · View at Google Scholar · View at Scopus
  41. F. Sleutels, R. Zwart, and D. P. Barlow, “The non-coding Air RNA is required for silencing autosomal imprinted genes,” Nature, vol. 415, no. 6873, pp. 810–813, 2002. View at Publisher · View at Google Scholar · View at Scopus
  42. J. L. Rinn, M. Kertesz, J. K. Wang et al., “Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs,” Cell, vol. 129, no. 7, pp. 1311–1323, 2007. View at Publisher · View at Google Scholar · View at Scopus
  43. H. T. Zheng, D. B. Shi, Y. W. Wang et al., “High expression of lncRNA MALAT1 suggests a biomarker of poor prognosis in colorectal cancer,” International Journal of Clinical and Experimental Pathology, vol. 7, no. 6, pp. 3174–3181, 2014. View at Google Scholar
  44. M. Huarte, M. Guttman, D. Feldser et al., “A large intergenic noncoding RNA induced by p53 mediates global gene repression in the p53 response,” Cell, vol. 142, no. 3, pp. 409–419, 2010. View at Publisher · View at Google Scholar · View at Scopus
  45. N. Ishii, K. Ozaki, H. Sato et al., “Identification of a novel non-coding RNA, MIAT, that confers risk of myocardial infarction,” Journal of Human Genetics, vol. 51, no. 12, pp. 1087–1099, 2006. View at Publisher · View at Google Scholar · View at Scopus
  46. Y.-S. Huang, H.-Y. Hsieh, H.-M. Shih, H.-K. Sytwu, and C.-C. Wu, “Urinary Xist is a potential biomarker for membranous nephropathy,” Biochemical and Biophysical Research Communications, vol. 452, no. 3, pp. 415–421, 2014. View at Publisher · View at Google Scholar
  47. K. A. Fitzgerald and D. R. Caffrey, “Long noncoding RNAs in innate and adaptive immunity,” Current Opinion in Immunology, vol. 26, no. 1, pp. 140–146, 2014. View at Publisher · View at Google Scholar · View at Scopus
  48. G. C. Tsokos, “Systemic lupus erythematosus,” The New England Journal of Medicine, vol. 365, no. 22, pp. 2110–2121, 2011. View at Publisher · View at Google Scholar · View at Scopus
  49. S. L. Foster, D. C. Hargreaves, and R. Medzhitov, “Gene-specific control of inflammation by TLR-induced chromatin modifications,” Nature, vol. 447, no. 7147, pp. 972–978, 2007. View at Publisher · View at Google Scholar · View at Scopus
  50. S. L. Doyle and L. A. J. O'Neill, “Toll-like receptors: from the discovery of NFκB to new insights into transcriptional regulations in innate immunity,” Biochemical Pharmacology, vol. 72, no. 9, pp. 1102–1113, 2006. View at Publisher · View at Google Scholar · View at Scopus
  51. R. Dai and S. A. Ahmed, “MicroRNA, a new paradigm for understanding immunoregulation, inflammation, and autoimmune diseases,” Translational Research, vol. 157, no. 4, pp. 163–179, 2011. View at Publisher · View at Google Scholar · View at Scopus
  52. R. P. Singh, I. Massachi, S. Manickavel et al., “The role of miRNA in inflammation and autoimmunity,” Autoimmunity Reviews, vol. 12, no. 12, pp. 1160–1165, 2013. View at Publisher · View at Google Scholar · View at Scopus
  53. M. Pagani, G. Rossetti, I. Panzeri et al., “Role of microRNAs and long-non-coding RNAs in CD4+ T-cell differentiation,” Immunological Reviews, vol. 253, no. 1, pp. 82–96, 2013. View at Publisher · View at Google Scholar · View at Scopus
  54. S. Vigneau, P.-S. Rohrlich, M. Brahic, and J.-F. Bureau, “Tmevpg1, a candidate gene for the control of Theiler's virus persistence, could be implicated in the regulation of gamma interferon,” Journal of Virology, vol. 77, no. 10, pp. 5632–5638, 2003. View at Publisher · View at Google Scholar · View at Scopus
  55. C. Mauri and A. Bosma, “Immune regulatory function of B cells,” Annual Review of Immunology, vol. 30, pp. 221–241, 2012. View at Publisher · View at Google Scholar · View at Scopus
  56. D. J. Bolland, A. L. Wood, C. M. Johnston et al., “Antisense intergenic transcription in V(D)J recombination,” Nature Immunology, vol. 5, no. 6, pp. 630–637, 2004. View at Publisher · View at Google Scholar · View at Scopus
  57. N. Stoy, “Macrophage biology and pathobiology in the evolution of immune responses: a functional analysis,” Pathobiology, vol. 69, no. 4, pp. 179–211, 2001. View at Publisher · View at Google Scholar · View at Scopus
  58. E. Vivier, D. H. Raulet, A. Moretta et al., “Innate or adaptive immunity? The example of natural killer cells,” Science (New York, N.Y.), vol. 331, no. 6013, pp. 44–49, 2011. View at Publisher · View at Google Scholar · View at Scopus
  59. C.-C. Liu, A. H. Kao, S. Manzi, and J. M. Ahearn, “Biomarkers in systemic lupus erythematosus: challenges and prospects for the future,” Therapeutic Advances in Musculoskeletal Disease, vol. 5, no. 4, pp. 210–233, 2013. View at Publisher · View at Google Scholar · View at Scopus
  60. B. Rhodes and T. J. Vyse, “The genetics of SLE: an update in the light of genome-wide association studies,” Rheumatology, vol. 47, no. 11, pp. 1603–1611, 2008. View at Publisher · View at Google Scholar · View at Scopus
  61. M. H. Biermann, S. Veissi, C. Maueröder et al., “The role of dead cell clearance in the etiology and pathogenesis of systemic lupus erythematosus: dendritic cells as potential targets,” Expert Review of Clinical Immunology, vol. 10, no. 9, pp. 1151–1164, 2014. View at Publisher · View at Google Scholar
  62. L. E. Muñoz, C. Janko, C. Schulze et al., “Autoimmunity and chronic inflammation—two clearance-related steps in the etiopathogenesis of SLE,” Autoimmunity Reviews, vol. 10, no. 1, pp. 38–42, 2010. View at Publisher · View at Google Scholar · View at Scopus
  63. J. S. Smolen, D. Aletaha, M. Koeller, M. H. Weisman, and P. Emery, “New therapies for treatment of rheumatoid arthritis,” The Lancet, vol. 370, no. 9602, pp. 1861–1874, 2007. View at Publisher · View at Google Scholar · View at Scopus
  64. I. Duroux-Richard, C. Jorgensen, and F. Apparailly, “miRNAs and rheumatoid arthritis—promising novel biomarkers,” Swiss Medical Weekly, vol. 141, Article ID w13175, 2011. View at Publisher · View at Google Scholar · View at Scopus
  65. G. Stassi and R. de Maria, “Autoimmune thyroid disease: new models of cell death in autoimmunity,” Nature Reviews Immunology, vol. 2, no. 3, pp. 195–204, 2002. View at Publisher · View at Google Scholar · View at Scopus
  66. R. I. Fox, “Sjögren's syndrome,” The Lancet, vol. 366, no. 9482, pp. 321–331, 2005. View at Publisher · View at Google Scholar · View at Scopus
  67. S. Gaidamakov, O. A. Maximova, H. Chon et al., “Targeted deletion of the gene encoding the La autoantigen (Sjögren's syndrome antigen b) in b cells or the frontal brain causes extensive tissue loss,” Molecular and Cellular Biology, vol. 34, no. 1, pp. 123–131, 2014. View at Publisher · View at Google Scholar · View at Scopus
  68. A. Triantafyllopoulou, N. Tapinos, and H. M. Moutsopoulos, “Evidence for coxsackievirus infection in primary Sjögren's syndrome,” Arthritis and Rheumatism, vol. 50, no. 9, pp. 2897–2902, 2004. View at Publisher · View at Google Scholar · View at Scopus