Long non-coding RNA in health and disease

Journal of Molecular Medicine

Volumn 92, Issue 4, 2014, Pages 337-346

  Maass, Philipp G ^a   Luft, Friedrich C ^a   Bähring, Sylvia ^a  

^a MAX DELBRÜCK CENTER FOR MOLECULAR MEDICINE   (Germany)

Author keywords

Boveri; Chromatin loop; Chromosomal territories; CISTR ACT; Gene regulation; Histone code; In cis; In trans; lncRNA; Long non coding RNA; Transcriptional regulation; Waddington

Indexed keywords

LONG UNTRANSLATED RNA;

CARDIOVASCULAR DISEASE; CHROMATIN; GENE ACTIVATION; GENE CONTROL; GENOME IMPRINTING; HUMAN; NEOPLASM; NEUROLOGIC DISEASE; NONHUMAN; PHENOTYPE; REVIEW; ANIMAL; GENETIC EPIGENESIS; GENETICS; METABOLISM; NUCLEOTIDE SEQUENCE; PHYSIOLOGY;

ANIMALS; BASE SEQUENCE; CARDIOVASCULAR DISEASES; EPIGENESIS, GENETIC; HUMANS; NEOPLASMS; NERVOUS SYSTEM DISEASES; RNA, LONG NONCODING;

EID: 84898432405     PISSN: 09462716     EISSN: 14321440     Source Type: Journal    
DOI: 10.1007/s00109-014-1131-8     Document Type: Review

References (122)

1. Waddington CH (2012) The epigenotype. 1942. Int J Epidemiol 41:10-13
2. Mercer TR, Mattick JS (2013) Understanding the regulatory and transcriptional complexity of the genome through structure. Genome Res 23:1081-1088
3. Chen K, Rajewsky N (2007) The evolution of gene regulation by transcription factors and microRNAs. Nat Rev Genet 8:93-103
4. Poulos MG, Batra R, Charizanis K, Swanson MS (2011) Developments in RNA splicing and disease. Cold Spring Harb Perspect Biol 3:a000778
5. Phillips-Cremins JE, Corces VG (2013) Chromatin insulators: linking genome organization to cellular function. Mol Cell 50:461-474
6. Odom DT et al (2007) Tissue-specific transcriptional regulation has diverged significantly between human and mouse. Nat Genet 39:730-732
7. Vavouri T, Walter K, Gilks WR, Lehner B, Elgar G (2007) Parallel evolution of conserved non-coding elements that target a common set of developmental regulatory genes from worms to humans. Genome Biol 8:R15
8. Vavouri T, McEwen GK, Woolfe A, Gilks WR, Elgar G (2006) Defining a genomic radius for long-range enhancer action: duplicated conserved non-coding elements hold the key. Trends Genet 22:5-10
9. Schubeler D, Francastel C, Cimbora DM, Reik A, Martin DI, Groudine M (2000) Nuclear localization and histone acetylation: a pathway for chromatin opening and transcriptional activation of the human beta-globin locus. Genes Dev 14:940-950
10. Vignali M, Hassan AH, Neely KE, Workman JL (2000) ATP-dependent chromatin-remodeling complexes. Mol Cell Biol 20:1899-1910
11. Kouzarides T (2007) Chromatin modifications and their function. Cell 128:693-705
12. Blackwood EM, Kadonaga JT (1998) Going the distance: a current view of enhancer action. Science 281:60-63
13. Lee JT, Bartolomei MS (2013) X-inactivation, imprinting, and long noncoding RNAs in health and disease. Cell 152:1308-1323
14. Berger SL (2002) Histone modifications in transcriptional regulation. Curr Opin Genet Dev 12:142-148
15. Lee JS, Smith E, Shilatifard A (2010) The language of histone crosstalk. Cell 142:682-685
16. Kleinjan DA, van Heyningen V (2005) Long-range control of gene expression: emerging mechanisms and disruption in disease. Am J Hum Genet 76:8-32
17. Wijchers PJ, de Laat W (2011) Genome organization influences partner selection for chromosomal rearrangements. Trends Genet 27:63-71
18. Maher B (2012) ENCODE: the human encyclopaedia. Nature 489:46-48
19. Cabili MN, Trapnell C, Goff L, Koziol M, Tazon-Vega B, Regev A, Rinn JL (2011) Integrative annotation of human large intergenic noncoding RNAs reveals global properties and specific subclasses. Genes Dev 25:1915-1927
20. Guttman M et al (2009) Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals. Nature 458:223-227
21. Hansen TB, Jensen TI, Clausen BH, Bramsen JB, Finsen B, Damgaard CK, Kjems J (2013) Natural RNA circles function as efficient microRNA sponges. Nature 495:384-388
22. Memczak S et al (2013) Circular RNAs are a large class of animal RNAs with regulatory potency. Nature 495:333-338
23. Khalil AM et al (2009) Many human large intergenic noncoding RNAs associate with chromatin-modifying complexes and affect gene expression. Proc Natl Acad Sci U S A 106:11667-11672
24. Rinn JL, Chang HY (2012) Genome regulation by long noncoding RNAs. Annu Rev Biochem 81:145-166
25. Kogo R et al (2011) Long noncoding RNA HOTAIR regulates polycomb-dependent chromatin modification and is associated with poor prognosis in colorectal cancers. Cancer Res 71:6320-6326
26. Brown CJ, Ballabio A, Rupert JL, Lafreniere RG, Grompe M, Tonlorenzi R, Willard HF (1991) A gene from the region of the human X inactivation centre is expressed exclusively from the inactive X chromosome. Nature 349:38-44
27. Dinger ME et al (2008) Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation. Genome Res 18:1433-1445
28. Pauli A, Rinn JL, Schier AF (2011) Non-coding RNAs as regulators of embryogenesis. Nat Rev Genet 12:136-149
29. Engreitz JM et al (2013) The Xist lncRNA exploits three-dimensional genome architecture to spread across the X chromosome. Science 341:1237973
30. Simon MD et al (2013) High-resolution Xist binding maps reveal two-step spreading during X-chromosome inactivation. Nature 504:465-469
31. Lee JT, Davidow LS, Warshawsky D (1999) Tsix, a gene antisense to Xist at the X-inactivation centre. Nat Genet 21:400-404
32. Tian D, Sun S, Lee JT (2010) The long noncoding RNA, Jpx, is a molecular switch for X chromosome inactivation. Cell 143:390-403
33. Sun S, Del Rosario BC, Szanto A, Ogawa Y, Jeon Y, Lee JT (2013) Jpx RNA activates Xist by evicting CTCF. Cell 153:1537-1551
34. Rinn JL et al (2007) Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs. Cell 129:1311-1323
35. Nagano T, Mitchell JA, Sanz LA, Pauler FM, Ferguson-Smith AC, Feil R, Fraser P (2008) The Air noncoding RNA epigenetically silences transcription by targeting G9a to chromatin. Science 322:1717-1720
36. Pandey RR, Mondal T, Mohammad F, Enroth S, Redrup L, Komorowski J, Nagano T, Mancini-Dinardo D, Kanduri C (2008) Kcnq1ot1 antisense noncoding RNA mediates lineage-specific transcriptional silencing through chromatin-level regulation. Mol Cell 32:232-246
37. Orom UA et al (2010) Long noncoding RNAs with enhancer-like function in human cells. Cell 143:46-58
38. Wang KC et al (2011) A long noncoding RNA maintains active chromatin to coordinate homeotic gene expression. Nature 472:120-124
39. Maass PG et al (2012) A misplaced lncRNA causes brachydactyly in humans. J Clin Invest 122:3990-4002
40. Strickfaden H, Zunhammer A, van Koningsbruggen S, Kohler D, Cremer T (2010) 4D chromatin dynamics in cycling cells: Theodor Boveri's hypotheses revisited. Nucleus 1:284-297
41. Cremer T, Cremer M (2010) Chromosome territories. Cold Spring Harb Perspect Biol 2:a003889
42. Bickmore WA (2013) The spatial organization of the human genome. Annu Rev Genomics Hum Genet 14:67-84
43. Fullwood MJ et al (2009) An oestrogen-receptor-alpha-bound human chromatin interactome. Nature 462:58-64
44. Lieberman-Aiden E et al (2009) Comprehensive mapping of long-range interactions reveals folding principles of the human genome. Science 326:289-293
45. Batista PJ, Chang HY (2013) Long noncoding RNAs: cellular address codes in development and disease. Cell 152:1298-1307
46. Hung T et al (2011) Extensive and coordinated transcription of noncoding RNAs within cell-cycle promoters. Nat Genet 43:621-629
47. Zappulla DC, Cech TR (2006) RNA as a flexible scaffold for proteins: yeast telomerase and beyond. Cold Spring Harb Symp Quant Biol 71:217-224
48. Mayer C, Schmitz KM, Li J, Grummt I, Santoro R (2006) Intergenic transcripts regulate the epigenetic state of rRNA genes. Mol Cell 22:351-361
49. Schmitz KM, Mayer C, Postepska A, Grummt I (2010) Interaction of noncoding RNA with the rDNA promoter mediates recruitment of DNMT3b and silencing of rRNA genes. Genes Dev 24:2264-2269
50. Huarte M et al (2010) A large intergenic noncoding RNA induced by p53 mediates global gene repression in the p53 response. Cell 142:409-419
51. Yoon JH et al (2012) LincRNA-p21 suppresses target mRNA translation. Mol Cell 47:648-655
52. Jeon Y, Lee JT (2011) YY1 tethers Xist RNA to the inactive X nucleation center. Cell 146:119-133
53. Gong C, Maquat LE (2011) lncRNAs transactivate STAU1-mediated mRNA decay by duplexing with 3 UTRs via Alu elements. Nature 470:284-288
54. Kretz M et al (2013) Control of somatic tissue differentiation by the long non-coding RNA TINCR. Nature 493:231-235
55. Klattenhoff CA et al (2013) Braveheart, a long noncoding RNA required for cardiovascular lineage commitment. Cell 152:570-583
56. Wagner LA, Christensen CJ, Dunn DM, Spangrude GJ, Georgelas A, Kelley L, Esplin MS, Weiss RB, Gleich GJ (2007) EGO, a novel, noncoding RNA gene, regulates eosinophil granule protein transcript expression. Blood 109:5191-5198
57. Grote P et al (2013) The tissue-specific lncRNA Fendrr is an essential regulator of heart and body wall development in the mouse. Dev Cell 24:206-214
58. Barry G et al (2013) The long non-coding RNA Gomafu is acutely regulated in response to neuronal activation and involved in schizophrenia-associated alternative splicing. Mol Psychiatry. doi: 10.1038/mp.2013.45
59. Cesana M, Cacchiarelli D, Legnini I, Santini T, Sthandier O, Chinappi M, Tramontano A, Bozzoni I (2011) A long noncoding RNA controls muscle differentiation by functioning as a competing endogenous RNA. Cell 147:358-369
60. Khalil AM, Faghihi MA, Modarresi F, Brothers SP, Wahlestedt C (2008) A novel RNA transcript with antiapoptotic function is silenced in fragile X syndrome. PLoS ONE 3:e1486
61. Landers M, Calciano MA, Colosi D, Glatt-Deeley H, Wagstaff J, Lalande M (2005) Maternal disruption of Ube3a leads to increased expression of Ube3a-ATS in trans. Nucleic Acids Res 33:3976-3984
62. Meng L, Person RE, Beaudet AL (2012) Ube3a-ATS is an atypical RNA polymerase II transcript that represses the paternal expression of Ube3a. Hum Mol Genet 21:3001-3012
63. Yildirim E, Kirby JE, Brown DE, Mercier FE, Sadreyev RI, Scadden DT, Lee JT (2013) Xist RNA is a potent suppressor of hematologic cancer in mice. Cell 152:727-742
64. Tripathi V et al (2010) The nuclear-retained noncoding RNA MALAT1 regulates alternative splicing by modulating SR splicing factor phosphorylation. Mol Cell 39:925-938
65. Schmidt LH et al (2011) The long noncoding MALAT-1 RNA indicates a poor prognosis in non-small cell lung cancer and induces migration and tumor growth. J Thorac Oncol 6:1984-1992
66. Tripathi V et al (2013) Long noncoding RNA MALAT1 controls cell cycle progression by regulating the expression of oncogenic transcription factor B-MYB. PLoS Genet 9:e1003368
67. Wilusz JE, JnBaptiste CK, Lu LY, Kuhn CD, Joshua-Tor L, Sharp PA (2012) A triple helix stabilizes the 3 ends of long noncoding RNAs that lack poly(A) tails. Genes Dev 26:2392-2407
68. Gupta RA et al (2010) Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis. Nature 464:1071-1076
69. Quagliata L et al (2013) lncRNA HOTTIP/HOXA13 expression is associated with disease progression and predicts outcome in hepatocellular carcinoma patients. Hepatology. doi: 10.1002/hep.26740
70. Panzitt K et al (2007) Characterization of HULC, a novel gene with striking up-regulation in hepatocellular carcinoma, as noncoding RNA. Gastroenterology 132:330-342
71. Wang J, Liu X, Wu H, Ni P, Gu Z, Qiao Y, Chen N, Sun F, Fan Q (2010) CREB up-regulates long non-coding RNA, HULC expression through interaction with microRNA-372 in liver cancer. Nucleic Acids Res 38:5366-5383
72. Du Y, Kong G, You X, Zhang S, Zhang T, Gao Y, Ye L, Zhang X (2012) Elevation of highly up-regulated in liver cancer (HULC) by hepatitis B virus X protein promotes hepatoma cell proliferation via down-regulating p18. J Biol Chem 287:26302-26311
73. Faghihi MA et al (2008) Expression of a noncoding RNA is elevated in Alzheimer's disease and drives rapid feed-forward regulation of beta-secretase. Nat Med 14:723-730
74. Burd CE, Jeck WR, Liu Y, Sanoff HK, Wang Z, Sharpless NE (2010) Expression of linear and novel circular forms of an INK4/ARF-associated non-coding RNA correlates with atherosclerosis risk. PLoS Genet 6:e1001233
75. Pasmant E, Laurendeau I, Heron D, Vidaud M, Vidaud D, Bieche I (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 Res 67:3963-3969
76. Ge X, Chen Y, Liao X, Liu D, Li F, Ruan H, Jia W (2013) Overexpression of long noncoding RNA PCAT-1 is a novel biomarker of poor prognosis in patients with colorectal cancer. Med Oncol 30:588
77. Prensner JR et al (2011) Transcriptome sequencing across a prostate cancer cohort identifies PCAT-1, an unannotated lincRNA implicated in disease progression. Nat Biotechnol 29:742-749
78. Prensner JR et al (2013) The long noncoding RNA SChLAP1 promotes aggressive prostate cancer and antagonizes the SWI/SNF complex. Nat Genet 45:1392-1398
79. Takayama K et al (2013) Androgen-responsive long noncoding RNA CTBP1-AS promotes prostate cancer. Embo J 32:1665-1680
80. Lu P, Roberts CW (2013) The SWI/SNF tumor suppressor complex: regulation of promoter nucleosomes and beyond. Nucleus 4:374-378
81. Wahlestedt C (2013) Targeting long non-coding RNA to therapeutically upregulate gene expression. Nat Rev Drug Discov 12:433-446
82. Wheeler TM, Leger AJ, Pandey SK, MacLeod AR, Nakamori M, Cheng SH, Wentworth BM, Bennett CF, Thornton CA (2012) Targeting nuclear RNA for in vivo correction of myotonic dystrophy. Nature 488:111-115
83. Eissmann M et al (2012) Loss of the abundant nuclear non-coding RNA MALAT1 is compatible with life and development. RNA Biol 9:1076-1087
84. Zhang B et al (2012) The lncRNA Malat1 is dispensable for mouse development but its transcription plays a cis-regulatory role in the adult. Cell Rep 2:111-123
85. Nakagawa S, Naganuma T, Shioi G, Hirose T (2011) Paraspeckles are subpopulation-specific nuclear bodies that are not essential in mice. J Cell Biol 193:31-39
86. Nakagawa S, Ip JY, Shioi G, Tripathi V, Zong X, Hirose T, Prasanth KV (2012) Malat1 is not an essential component of nuclear speckles in mice. RNA 18:1487-1499
87. Li L et al (2013) Targeted disruption of Hotair leads to homeotic transformation and gene derepression. Cell Rep 5:3-12
88. Sauvageau M et al (2013) Multiple knockout mouse models reveal lincRNAs are required for life and brain development. Elife 2:e01749
89. Zhang X et al (2009) A myelopoiesis-associated regulatory intergenic noncoding RNA transcript within the human HOXA cluster. Blood 113:2526-2534
90. Hu W, Yuan B, Flygare J, Lodish HF (2011) Long noncoding RNA-mediated anti-apoptotic activity in murine erythroid terminal differentiation. Genes Dev 25:2573-2578
91. Onoguchi M, Hirabayashi Y, Koseki H, Gotoh Y (2012) A noncoding RNA regulates the neurogenin1 gene locus during mouse neocortical development. Proc Natl Acad Sci U S A 109:16939-16944
92. Navarro P et al (2010) Molecular coupling of Tsix regulation and pluripotency. Nature 468:457-460
93. Ogawa Y, Lee JT (2003) Xite, X-inactivation intergenic transcription elements that regulate the probability of choice. Mol Cell 11:731-743
94. van Dijk M et al (2012) HELLP babies link a novel lincRNA to the trophoblast cell cycle. J Clin Invest 122:4003-4011
95. Sonkoly E et al (2005) Identification and characterization of a novel, psoriasis susceptibility-related noncoding RNA gene, PRINS. J Biol Chem 280:24159-24167
96. Beckedorff FC, Ayupe AC, Crocci-Souza R, Amaral MS, Nakaya HI, Soltys DT, Menck CF, Reis EM, Verjovski-Almeida S (2013) The intronic long noncoding RNA ANRASSF1 recruits PRC2 to the RASSF1A promoter, reducing the expression of RASSF1A and increasing cell proliferation. PLoS Genet 9:e1003705
97. Cunnington MS, Santibanez Koref M, Mayosi BM, Burn J, Keavney B (2010) Chromosome 9p21 SNPs associated with multiple disease phenotypes correlate with anril expression. PLoS Genet 6:e1000899
98. Kotake Y, Nakagawa T, Kitagawa K, Suzuki S, Liu N, Kitagawa M, Xiong Y (2011) Long non-coding RNA ANRIL is required for the PRC2 recruitment to and silencing of p15(INK4B) tumor suppressor gene. Oncogene 30:1956-1962
99. Pasmant E, Sabbagh A, Vidaud M, Bieche I (2011) ANRIL, a long, noncoding RNA, is an unexpected major hotspot in GWAS. FASEB J 25:444-448
100. Yap KL, Li S, Munoz-Cabello AM, Raguz S, Zeng L, Mujtaba S, Gil J, Walsh MJ, Zhou MM (2010) Molecular interplay of the noncoding RNA ANRIL and methylated histone H3 lysine 27 by polycomb CBX7 in transcriptional silencing of INK4a. Mol Cell 38:662-674
101. Arita T et al (2013) Circulating long non-coding RNAs in plasma of patients with gastric cancer. Anticancer Res 33:3185-3193
102. Kallen AN et al (2013) The imprinted H19 lncRNA antagonizes let-7 microRNAs. Mol Cell 52:101-112
103. Matouk IJ, DeGroot N, Mezan S, Ayesh S, Abu-lail R, Hochberg A, Galun E (2007) The H19 non-coding RNA is essential for human tumor growth. PLoS ONE 2:e845
104. Thorvaldsen JL, Duran KL, Bartolomei MS (1998) Deletion of the H19 differentially methylated domain results in loss of imprinted expression of H19 and Igf2. Genes Dev 12:3693-3702
105. Yang Z, Zhou L, Wu LM, Lai MC, Xie HY, Zhang F, Zheng SS (2011) Overexpression of long non-coding RNA HOTAIR predicts tumor recurrence in hepatocellular carcinoma patients following liver transplantation. Ann Surg Oncol 18:1243-1250
106. Liu Y et al (2012) A genetic variant in long non-coding RNA HULC contributes to risk of HBV-related hepatocellular carcinoma in a Chinese population. PLoS ONE 7:e35145
107. Golding MC, Magri LS, Zhang L, Lalone SA, Higgins MJ, Mann MR (2011) Depletion of Kcnq1ot1 non-coding RNA does not affect imprinting maintenance in stem cells. Development 138:3667-3678
108. Nakano S et al (2006) Expression profile of LIT1/KCNQ1OT1 and epigenetic status at the KvDMR1 in colorectal cancers. Cancer Sci 97:1147-1154
109. Gutschner T et al (2013) The noncoding RNA MALAT1 is a critical regulator of the metastasis phenotype of lung cancer cells. Cancer Res 73:1180-1189
110. Xu C, Yang M, Tian J, Wang X, Li Z (2011) MALAT-1: a long non-coding RNA and its important 3 end functional motif in colorectal cancer metastasis. Int J Oncol 39:169-175
111. Lee GL, Dobi A, Srivastava S (2011) Prostate cancer: diagnostic performance of the PCA3 urine test. Nat Rev Urol 8:123-124
112. Poliseno L, Salmena L, Zhang J, Carver B, Haveman WJ, Pandolfi PP (2010) A coding-independent function of gene and pseudogene mRNAs regulates tumour biology. Nature 465:1033-1038
113. Colley SM, Leedman PJ (2011) Steroid receptor RNA activator - a nuclear receptor coregulator with multiple partners: Insights and challenges. Biochimie 93:1966-1972
114. Cooper C, Guo J, Yan Y, Chooniedass-Kothari S, Hube F, Hamedani MK, Murphy LC, Myal Y, Leygue E (2009) Increasing the relative expression of endogenous non-coding steroid receptor RNA activator (SRA) in human breast cancer cells using modified oligonucleotides. Nucleic Acids Res 37:4518-4531
115. Redon S, Zemp I, Lingner J (2013) A three-state model for the regulation of telomerase by TERRA and hnRNPA1. Nucleic Acids Res 41:9117-9128
116. Ritter O, Haase H, Schulte HD, Lange PE, Morano I (1999) Remodeling of the hypertrophied human myocardium by cardiac bHLH transcription factors. J Cell Biochem 74:551-561
117. Ishii N et al (2006) Identification of a novel non-coding RNA, MIAT, that confers risk of myocardial infarction. J Hum Genet 51:1087-1099
118. Rapicavoli NA, Poth EM, Blackshaw S (2010) The long noncoding RNA RNCR2 directs mouse retinal cell specification. BMC Dev Biol 10:49
119. Haddad F, Bodell PW, Qin AX, Giger JM, Baldwin KM (2003) Role of antisense RNA in coordinating cardiac myosin heavy chain gene switching. J Biol Chem 278:37132-37138
120. Chubb JE, Bradshaw NJ, Soares DC, Porteous DJ, Millar JK (2008) The DISC locus in psychiatric illness. Mol Psychiatry 13:36-64
121. Scheele C et al (2007) Altered regulation of the PINK1 locus: a link between type 2 diabetes and neurodegeneration? FASEB J 21:3653-3665
122. Chen WL, Lin JW, Huang HJ, Wang SM, Su MT, Lee-Chen GJ, Chen CM, Hsieh-Li HM (2008) SCA8 mRNA expression suggests an antisense regulation of KLHL1 and correlates to SCA8 pathology. Brain Res 1233:176-184