Long non-coding RNAs: A new frontier in the study of human diseases

Cancer Letters - Tập 339 - Trang 159-166 - 2013
Xuefei Shi1, Ming Sun2, Hongbing Liu1, Yanwen Yao1, Yong Song1
1Department of Respiratory Medicine, Jinling Hospital, Nanjing University School of Medicine, Nanjing, China
2Department of Biochemistry and Molecular Biology, Nanjing Medical University, Nanjing, China

Tài liệu tham khảo

Mercer, 2009, Long non-coding RNAs: insights into functions, Nat. Rev. Genet., 10, 155, 10.1038/nrg2521 Wapinski, 2011, Long noncoding RNAs and human disease, Trends Cell Biol., 21, 354, 10.1016/j.tcb.2011.04.001 Tsai, 2011, Long intergenic noncoding RNAs: new links in cancer progression, Cancer Res., 71, 3, 10.1158/0008-5472.CAN-10-2483 Mattick, 2004, RNA regulation: a new genetics?, Nat. Rev. Genet., 5, 316, 10.1038/nrg1321 Derrien, 2012, The GENCODE v7 catalog of human long noncoding RNAs: analysis of their gene structure, evolution, and expression, Genome Res., 22, 1775, 10.1101/gr.132159.111 Kapranov, 2007, RNA maps reveal new RNA classes and a possible function for pervasive transcription, Science, 316, 1484, 10.1126/science.1138341 Spizzo, 2012, Long non-coding RNAs and cancer: a new frontier of translational research?, Oncogene, 31, 4577, 10.1038/onc.2011.621 Ponting, 2009, Evolution and functions of long noncoding RNAs, Cell, 136, 629, 10.1016/j.cell.2009.02.006 Wang, 2011, The long arm of long noncoding RNAs: roles as sensors regulating gene transcriptional programs, Cold Spring Harb. Perspect. Biol., 3, a003756, 10.1101/cshperspect.a003756 van Bakel, 2009, Establishing legitimacy and function in the new transcriptome, Brief Funct. Genomic Proteomic, 8, 424, 10.1093/bfgp/elp037 Gutschner, 2012, The hallmarks of cancer: a long non-coding RNA point of view, RNA Biol., 9, 703, 10.4161/rna.20481 Wilusz, 2009, Long noncoding RNAs: functional surprises from the RNA world, Genes Dev., 23, 1494, 10.1101/gad.1800909 Gibb, 2011, The functional role of long non-coding RNA in human carcinomas, Mol. Cancer, 10, 38, 10.1186/1476-4598-10-38 Moran, 2012, Emerging functional and mechanistic paradigms of mammalian long non-coding RNAs, Nucleic Acids Res., 40, 6391, 10.1093/nar/gks296 Huarte, 2010, Large non-coding RNAs: missing links in cancer?, Hum. Mol. Genet., 19, R152, 10.1093/hmg/ddq353 Korneev, 2008, Novel noncoding antisense RNA transcribed from human anti-NOS2A locus is differentially regulated during neuronal differentiation of embryonic stem cells, RNA, 14, 2030, 10.1261/rna.1084308 Folkersen, 2009, Relationship between CAD risk genotype in the chromosome 9p21 locus and gene expression. Identification of eight new ANRIL splice variants, PLoS ONE, 4, e7677, 10.1371/journal.pone.0007677 Pasmant, 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, 10.1158/0008-5472.CAN-06-2004 Yap, 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, 10.1016/j.molcel.2010.03.021 Yu, 2008, Epigenetic silencing of tumour suppressor gene p15 by its antisense RNA, Nature, 451, 202, 10.1038/nature06468 Chen, 1997, Expression of neural BC200 RNA in human tumours, J. Pathol., 183, 345, 10.1002/(SICI)1096-9896(199711)183:3<345::AID-PATH930>3.0.CO;2-8 Iacoangeli, 2004, BC200 RNA in invasive and preinvasive breast cancer, Carcinogenesis, 25, 2125, 10.1093/carcin/bgh228 Faghihi, 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, 10.1038/nm1784 Mourtada-Maarabouni, 2009, GAS5, a non-protein-coding RNA, controls apoptosis and is downregulated in breast cancer, Oncogene, 28, 195, 10.1038/onc.2008.373 Matouk, 2009, Highly upregulated in liver cancer noncoding RNA is overexpressed in hepatic colorectal metastasis, Eur. J. Gastroenterol. Hepatol., 21, 688, 10.1097/MEG.0b013e328306a3a2 Panzitt, 2007, Characterization of HULC, a novel gene with striking up-regulation in hepatocellular carcinoma, as noncoding RNA, Gastroenterology, 132, 330, 10.1053/j.gastro.2006.08.026 Moseley, 2006, Bidirectional expression of CUG and CAG expansion transcripts and intranuclear polyglutamine inclusions in spinocerebellar ataxia type 8, Nat. Genet., 38, 758, 10.1038/ng1827 Berteaux, 2004, Hormonal regulation of H19 gene expression in prostate epithelial cells, J. Endocrinol., 183, 69, 10.1677/joe.1.05696 Brannan, 1990, The product of the H19 gene may function as an RNA, Mol. Cell. Biol., 10, 28, 10.1128/MCB.10.1.28 Gabory, 2010, The H19 locus: role of an imprinted non-coding RNA in growth and development, BioEssays, 32, 473, 10.1002/bies.200900170 Hibi, 1996, Loss of H19 imprinting in esophageal cancer, Cancer Res., 56, 480 Pasic, 2010, Recurrent focal copy-number changes and loss of heterozygosity implicate two noncoding RNAs and one tumor suppressor gene at chromosome 3q13.31 in osteosarcoma, Cancer Res., 70, 160, 10.1158/0008-5472.CAN-09-1902 Poliseno, 2010, A coding-independent function of gene and pseudogene mRNAs regulates tumour biology, Nature, 465, 1033, 10.1038/nature09144 Guo, 2010, Inhibition of metastasis-associated lung adenocarcinoma transcript 1 in CaSki human cervical cancer cells suppresses cell proliferation and invasion, Acta Biochim. Biophys. Sin. (Shanghai), 42, 224, 10.1093/abbs/gmq008 Ji, 2003, MALAT-1, a novel noncoding RNA, and thymosin beta4 predict metastasis and survival in early-stage non-small cell lung cancer, Oncogene, 22, 8031, 10.1038/sj.onc.1206928 Lin, 2007, A large noncoding RNA is a marker for murine hepatocellular carcinomas and a spectrum of human carcinomas, Oncogene, 26, 851, 10.1038/sj.onc.1209846 Miyoshi, 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 Cells, 5, 211, 10.1046/j.1365-2443.2000.00320.x Zhang, 2010, Maternally expressed gene 3 (MEG3) noncoding ribonucleic acid: isoform structure, expression, and functions, Endocrinology, 151, 939, 10.1210/en.2009-0657 Zhang, 2003, A pituitary-derived MEG3 isoform functions as a growth suppressor in tumor cells, J. Clin. Endocrinol. Metab., 88, 5119, 10.1210/jc.2003-030222 Khalil, 2008, A novel RNA transcript with antiapoptotic function is silenced in fragile X syndrome, PLoS ONE, 3, e1486, 10.1371/journal.pone.0001486 Zalfa, 2005, Fragile X mental retardation protein (FMRP) binds specifically to the brain cytoplasmic RNAs BC1/BC200 via a novel RNA-binding motif, J. Biol. Chem., 280, 33403, 10.1074/jbc.M504286200 Petrovics, 2004, Elevated expression of PCGEM1, a prostate-specific gene with cell growth-promoting function, is associated with high-risk prostate cancer patients, Oncogene, 23, 605, 10.1038/sj.onc.1207069 Srikantan, 2000, PCGEM1, a prostate-specific gene, is overexpressed in prostate cancer, Proc. Natl. Acad. Sci. USA, 97, 12216, 10.1073/pnas.97.22.12216 Chooniedass-Kothari, 2004, The steroid receptor RNA activator is the first functional RNA encoding a protein, FEBS Lett., 566, 43, 10.1016/j.febslet.2004.03.104 Leygue, 1999, Expression of the steroid receptor RNA activator in human breast tumors, Cancer Res., 59, 4190 Yu, 2009, High expression of ncRAN, a novel non-coding RNA mapped to chromosome 17q25.1, is associated with poor prognosis in neuroblastoma, Int. J. Oncol., 34, 931 Zhu, 2011, ncRAN, a newly identified long noncoding RNA, enhances human bladder tumor growth, invasion, and survival, Urology, 77 Wang, 2006, Rapid identification of UCA1 as a very sensitive and specific unique marker for human bladder carcinoma, Clin. Cancer Res., 12, 4851, 10.1158/1078-0432.CCR-06-0134 Rinn, 2007, Functional demarcation of active and silent chromatin domains in human HOX loci by noncoding RNAs, Cell, 129, 1311, 10.1016/j.cell.2007.05.022 Prensner, 2011, The emergence of lncRNAs in cancer biology, Cancer Discov., 1, 391, 10.1158/2159-8290.CD-11-0209 Prensner, 2011, Transcriptome sequencing across a prostate cancer cohort identifies PCAT-1, an unannotated lincRNA implicated in disease progression, Nat. Biotechnol., 29, 742, 10.1038/nbt.1914 Askarian-Amiri, 2011, SNORD-host RNA Zfas1 is a regulator of mammary development and a potential marker for breast cancer, RNA, 17, 878, 10.1261/rna.2528811 Maida, 2009, An RNA-dependent RNA polymerase formed by TERT and the RMRP RNA, Nature, 461, 230, 10.1038/nature08283 Makitie, 1993, Cartilage-hair hypoplasia–clinical manifestations in 108 Finnish patients, Eur. J. Pediatr., 152, 211, 10.1007/BF01956147 Yochum, 2007, An antisense transcript induced by Wnt/beta-catenin signaling decreases E2F4, J. Biol. Chem., 282, 871, 10.1074/jbc.M609391200 Redrup, 2009, The long noncoding RNA Kcnq1ot1 organises a lineage-specific nuclear domain for epigenetic gene silencing, Development, 136, 525, 10.1242/dev.031328 Chan, 2002, Identification of a novel gene NCRMS on chromosome 12q21 with differential expression between rhabdomyosarcoma subtypes, Oncogene, 21, 3029, 10.1038/sj.onc.1205460 Huang, 2011, Epigenetics in breast cancer: what’s new?, Breast Cancer Res., 13, 225, 10.1186/bcr2925 Feinberg, 2007, Phenotypic plasticity and the epigenetics of human disease, Nature, 447, 433, 10.1038/nature05919 Ellis, 2009, Epigenetics in cancer: targeting chromatin modifications, Mol. Cancer Ther., 8, 1409, 10.1158/1535-7163.MCT-08-0860 Atkinson, 2012, Exploring long non-coding RNAs through sequencing, Semin. Cell Dev. Biol., 23, 200, 10.1016/j.semcdb.2011.12.003 He, 2011, The sequence, structure and evolutionary features of HOTAIR in mammals, BMC Evol. Biol., 11, 102, 10.1186/1471-2148-11-102 Chisholm, 2012, Detection of long non-coding RNA in archival tissue: correlation with polycomb protein expression in primary and metastatic breast carcinoma, PLoS ONE, 7, e47998, 10.1371/journal.pone.0047998 Kogo, 2011, Long noncoding RNA HOTAIR regulates polycomb-dependent chromatin modification and is associated with poor prognosis in colorectal cancers, Cancer Res., 71, 6320, 10.1158/0008-5472.CAN-11-1021 Li, 2013, Long intergenic noncoding RNA HOTAIR is overexpressed and regulates PTEN methylation in laryngeal squamous cell carcinoma, Am. J. Pathol., 182, 64, 10.1016/j.ajpath.2012.08.042 Gupta, 2010, Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis, Nature, 464, 1071, 10.1038/nature08975 Tsai, 2010, Long noncoding RNA as modular scaffold of histone modification complexes, Science, 329, 689, 10.1126/science.1192002 Brown, 1991, A gene from the region of the human X inactivation centre is expressed exclusively from the inactive X chromosome, Nature, 349, 38, 10.1038/349038a0 Zhao, 2008, Polycomb proteins targeted by a short repeat RNA to the mouse X chromosome, Science, 322, 750, 10.1126/science.1163045 Amort, 2013, Long non-coding RNAs as targets for cytosine methylation, RNA Biol., 10, 10.4161/rna.24454 Ogawa, 2008, Intersection of the RNA interference and X-inactivation pathways, Science, 320, 1336, 10.1126/science.1157676 Ganesan, 2002, BRCA1 supports XIST RNA concentration on the inactive X chromosome, Cell, 111, 393, 10.1016/S0092-8674(02)01052-8 Kawakami, 2004, XIST unmethylated DNA fragments in male-derived plasma as a tumour marker for testicular cancer, Lancet, 363, 40, 10.1016/S0140-6736(03)15170-7 Richardson, 2006, X chromosomal abnormalities in basal-like human breast cancer, Cancer Cell, 9, 121, 10.1016/j.ccr.2006.01.013 Yildirim, 2013, Xist RNA is a potent suppressor of hematologic cancer in mice, Cell, 152, 727, 10.1016/j.cell.2013.01.034 Koerner, 2009, The function of non-coding RNAs in genomic imprinting, Development, 136, 1771, 10.1242/dev.030403 Sleutels, 2002, The non-coding Air RNA is required for silencing autosomal imprinted genes, Nature, 415, 810, 10.1038/415810a Mohammad, 2009, Epigenetics of imprinted long noncoding RNAs, Epigenetics, 4, 277, 10.4161/epi.4.5.9242 Oliva, 2009, The regulation of non-coding RNA expression in the liver of mice fed DDC, Exp. Mol. Pathol., 87, 12, 10.1016/j.yexmp.2009.03.006 Feng, 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, 10.1101/gad.1416106 Bond, 2009, Balanced gene regulation by an embryonic brain ncRNA is critical for adult hippocampal GABA circuitry, Nat. Neurosci., 12, 1020, 10.1038/nn.2371 Cooper, 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, 10.1093/nar/gkp441 Kawashima, 2003, A novel steroid receptor co-activator protein (SRAP) as an alternative form of steroid receptor RNA-activator gene: expression in prostate cancer cells and enhancement of androgen receptor activity, Biochem. J., 369, 163, 10.1042/bj20020743 Martianov, 2007, Repression of the human dihydrofolate reductase gene by a non-coding interfering transcript, Nature, 445, 666, 10.1038/nature05519 Bertozzi, 2011, Characterization of novel antisense HIF-1alpha transcripts in human cancers, Cell Cycle, 10, 3189, 10.4161/cc.10.18.17183 Rossignol, 2002, Natural antisense transcripts of hypoxia-inducible factor 1alpha are detected in different normal and tumour human tissues, Gene, 299, 135, 10.1016/S0378-1119(02)01049-1 Cayre, 2003, AHIF but not HIF-1alpha transcript is a poor prognostic marker in human breast cancer, Breast Cancer Res., 5, R223, 10.1186/bcr652 Nogalska, 2010, Increased BACE1 mRNA and noncoding BACE1-antisense transcript in sporadic inclusion-body myositis muscle fibers–possibly caused by endoplasmic reticulum stress, Neurosci. Lett., 474, 140, 10.1016/j.neulet.2010.03.023 Schmidt, 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, 10.1097/JTO.0b013e3182307eac Tripathi, 2010, The nuclear-retained noncoding RNA MALAT1 regulates alternative splicing by modulating SR splicing factor phosphorylation, Mol. Cell, 39, 925, 10.1016/j.molcel.2010.08.011 Eissmann, 2012, Loss of the abundant nuclear non-coding RNA MALAT1 is compatible with life and development, RNA Biol., 9, 1076, 10.4161/rna.21089 Zhang, 2012, The lncRNA Malat1 is dispensable for mouse development but its transcription plays a cis-regulatory role in the adult, Cell Rep., 2, 111, 10.1016/j.celrep.2012.06.003 Yoon, 2012, Posttranscriptional gene regulation by long noncoding RNA, J. Mol. Biol. Huarte, 2010, A large intergenic noncoding RNA induced by p53 mediates global gene repression in the p53 response, Cell, 142, 409, 10.1016/j.cell.2010.06.040 Yoon, 2012, LincRNA-p21 suppresses target mRNA translation, Mol. Cell, 47, 648, 10.1016/j.molcel.2012.06.027 Bartel, 2009, MicroRNAs: target recognition and regulatory functions, Cell, 136, 215, 10.1016/j.cell.2009.01.002 Salmena, 2011, A ceRNA hypothesis: the Rosetta Stone of a hidden RNA language?, Cell, 146, 353, 10.1016/j.cell.2011.07.014 Thomas, 2010, Desperately seeking microRNA targets, Nat. Struct. Mol. Biol., 17, 1169, 10.1038/nsmb.1921 Seitz, 2009, Redefining microRNA targets, Curr. Biol., 19, 870, 10.1016/j.cub.2009.03.059 Sarver, 2012, Competing endogenous RNA database, Bioinformation, 8, 731, 10.6026/97320630008731 Wang, 2010, CREB up-regulates long non-coding RNA, HULC expression through interaction with microRNA-372 in liver cancer, Nucleic Acids Res., 38, 5366, 10.1093/nar/gkq285 Cesana, 2011, A long noncoding RNA controls muscle differentiation by functioning as a competing endogenous RNA, Cell, 147, 358, 10.1016/j.cell.2011.09.028 Gu, 2009, Biological basis for restriction of microRNA targets to the 3′ untranslated region in mammalian mRNAs, Nat. Struct. Mol. Biol., 16, 144, 10.1038/nsmb.1552 Fang, 2012, Versican 3′-untranslated region (3′-UTR) functions as a ceRNA in inducing the development of hepatocellular carcinoma by regulating miRNA activity, FASEB J. Nakamura, 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 Genet. Cytogenet., 182, 144, 10.1016/j.cancergencyto.2008.01.013 Roberts, 2012, Mutation of Rubie, a novel long non-coding RNA located upstream of Bmp4, causes vestibular malformation in mice, PLoS ONE, 7, e29495, 10.1371/journal.pone.0029495 Ohno, 1997, Significance of rearrangement of the BCL6 gene in B-cell lymphoid neoplasms, Leuk. Lymphoma, 27, 53, 10.3109/10428199709068271 Smith, 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, Mol. Cell. Biol., 18, 6897, 10.1128/MCB.18.12.6897