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