Long noncoding RNAs and human disease

Crick, 1961, General nature of the genetic code for proteins, Nature, 192, 1227, 10.1038/1921227a0 Yanofsky, 2007, Establishing the triplet nature of the genetic code, Cell, 128, 815, 10.1016/j.cell.2007.02.029 Guttman, 2009, Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals, Nature, 458, 223, 10.1038/nature07672 Guttman, 2010, Ab initio reconstruction of cell type-specific transcriptomes in mouse reveals the conserved multi-exonic structure of lincRNAs, Nat. Biotechnol., 28, 503, 10.1038/nbt.1633 Marques, 2009, Catalogues of mammalian long noncoding RNAs: modest conservation and incompleteness, Genome Biol., 10, R124, 10.1186/gb-2009-10-11-r124 Ponting, 2009, Evolution and functions of long noncoding RNAs, Cell, 136, 629, 10.1016/j.cell.2009.02.006 Zhao, 2010, Genome-wide identification of polycomb-associated RNAs by RIP-seq, Mol. Cell, 40, 939, 10.1016/j.molcel.2010.12.011 Mattick, 2003, Challenging the dogma: the hidden layer of non-protein-coding RNAs in complex organisms, Bioessays, 25, 930, 10.1002/bies.10332 Dinger, 2008, Long noncoding RNAs in mouse embryonic stem cell pluripotency and differentiation, Genome Res., 18, 1433, 10.1101/gr.078378.108 Mercer, 2008, Specific expression of long noncoding RNAs in the mouse brain, Proc. Natl. Acad. Sci. U.S.A., 105, 716, 10.1073/pnas.0706729105 Mattick, 2009, The genetic signatures of noncoding RNAs, PLoS Genet., 5, e1000459, 10.1371/journal.pgen.1000459 Mattick, 2006, Non-coding RNA, Hum. Mol. Genet., 15, R17, 10.1093/hmg/ddl046 Qureshi, 2010, Long non-coding RNAs in nervous system function and disease, Brain Res., 1338, 20, 10.1016/j.brainres.2010.03.110 Wilusz, 2009, Long noncoding RNAs: functional surprises from the RNA world, Genes Dev., 23, 1494, 10.1101/gad.1800909 Pasmant, 2010, ANRIL, a long, noncoding RNA, is an unexpected major hotspot in GWAS, FASEB J., 25, 444, 10.1096/fj.10-172452 Yap, 2010, Molecular Interplay of the non coding 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 Harismendy, 2011, 9p21 DNA variants associated with coronary artery disease impair interferon-γ signalling response, Nature, 470, 264, 10.1038/nature09753 Burd, 2010, Expression of linear and novel circular forms of an INK4/ARF-associated non-coding RNA correlates with atherosclerosis risk, PLoS Genet., 6, e1001233, 10.1371/journal.pgen.1001233 Tsai, 2010, Long noncoding RNA as modular scaffold of histone modification complexes, Science, 329, 689, 10.1126/science.1192002 Gupta, 2010, Long non-coding RNA HOTAIR reprograms chromatin state to promote cancer metastasis, Nature, 464, 1071, 10.1038/nature08975 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 Bernard, 2010, A long nuclear-retained non-coding RNA regulates synaptogenesis by modulating gene expression, EMBO J., 29, 3082, 10.1038/emboj.2010.199 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 Long, 2009, The SR protein family of splicing factors: master regulators of gene expression, Biochem. J., 417, 15, 10.1042/BJ20081501 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 Kino, 2010, Noncoding RNA gas5 is a growth arrest- and starvation-associated repressor of the glucocorticoid receptor, Sci. Signal., 3, ra8, 10.1126/scisignal.2000568 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 Webster, 2002, Dexamethasone and tumor necrosis factor-alpha act together to induce the cellular inhibitor of apoptosis-2 gene and prevent apoptosis in a variety of cell types, Endocrinology, 143, 3866, 10.1210/en.2002-220188 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 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 Halvorsen, 2010, Disease-associated mutations that alter the RNA structural ensemble, PLoS Genet., 6, e1001074, 10.1371/journal.pgen.1001074 Calin, 2007, Ultraconserved regions encoding ncRNAs are altered in human leukemias and carcinomas, Cancer Cell, 12, 215, 10.1016/j.ccr.2007.07.027 Millar, 2000, Disruption of two novel genes by a translocation co-segregating with schizophrenia, Hum. Mol. Genet., 9, 1415, 10.1093/hmg/9.9.1415 Devon, 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, Psychiatr. Genet., 11, 71, 10.1097/00041444-200106000-00003 Ekelund, 2004, Replication of 1q42 linkage in Finnish schizophrenia pedigrees, Mol. Psychiatry, 9, 1037, 10.1038/sj.mp.4001536 Mutsuddi, 2005, Molecular genetics of spinocerebellar ataxia type 8 (SCA8), RNA Biol., 2, 249, 10.4161/rna.2.2.1682 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 Daughters, 2009, RNA gain-of-function in spinocerebellar ataxia type 8, PLoS Genet., 5, e1000600, 10.1371/journal.pgen.1000600 Scott, 2007, A genome-wide association study of type 2 diabetes in Finns detects multiple susceptibility variants, Science, 316, 1341, 10.1126/science.1142382 Broadbent, 2008, Susceptibility to coronary artery disease and diabetes is encoded by distinct, tightly linked SNPs in the ANRIL locus on chromosome 9p, Hum. Mol. Genet., 17, 806, 10.1093/hmg/ddm352 Wojcik, 2010, Non-coding RNA sequence variations in human chronic lymphocytic leukemia and colorectal cancer, Carcinogenesis, 31, 208, 10.1093/carcin/bgp209 Lagier-Tourenne, 2009, Rethinking ALS: the FUS about TDP-43, Cell, 136, 1001, 10.1016/j.cell.2009.03.006 Kwiatkowski, 2009, Mutations in the FUS/TLS gene on chromosome 16 cause familial amyotrophic lateral sclerosis, Science, 323, 1205, 10.1126/science.1166066 Vance, 2009, Mutations in FUS, an RNA processing protein, cause familial amyotrophic lateral sclerosis type 6, Science, 323, 1208, 10.1126/science.1165942 Wang, 2008, Induced ncRNAs allosterically modify RNA-binding proteins in cis to inhibit transcription, Nature, 454, 126, 10.1038/nature06992 Bagni, 2005, From mRNP trafficking to spine dysmorphogenesis: the roots of fragile X syndrome, Nat. Rev. Neurosci., 6, 376, 10.1038/nrn1667 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 Johnson, 2006, Role of Pur alpha in targeting mRNA to sites of translation in hippocampal neuronal dendrites, J. Neurosci. Res., 83, 929, 10.1002/jnr.20806 Khanam, 2006, Poly(A)-binding protein binds to A-rich sequences via RNA-binding domains 1+2 and 3+4, RNA Biol., 3, 170, 10.4161/rna.3.4.4075 Mus, 2007, Dendritic BC200 RNA in aging and in Alzheimer's disease, Proc. Natl. Acad. Sci. U.S.A., 104, 10679, 10.1073/pnas.0701532104