Evolution and Functions of Long Noncoding RNAs

Allen, 2004, The SINE-encoded mouse B2 RNA represses mRNA transcription in response to heat shock, Nat. Struct. Mol. Biol., 11, 816, 10.1038/nsmb813

Babak, 2007, Considerations in the identification of functional RNA structural elements in genomic alignments, BMC Bioinformatics, 8, 33, 10.1186/1471-2105-8-33

Bartolomei, 1991, Parental imprinting of the mouse H19 gene, Nature, 351, 153, 10.1038/351153a0

Bertone, 2004, Global identification of human transcribed sequences with genome tiling arrays, Science, 306, 2242, 10.1126/science.1103388

Birney, 2007, Identification and analysis of functional elements in 1% of the human genome by the ENCODE pilot project, Nature, 447, 799, 10.1038/nature05874

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

Brockdorff, 1991, Conservation of position and exclusive expression of mouse Xist from the inactive X chromosome, Nature, 351, 329, 10.1038/351329a0

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

Brown, 1994, The human X-inactivation centre is not required for maintenance of X-chromosome inactivation, Nature, 368, 154, 10.1038/368154a0

Cai, 2007, The imprinted H19 noncoding RNA is a primary microRNA precursor, RNA, 13, 313, 10.1261/rna.351707

Cao, 2006, Noncoding RNAs in the mammalian central nervous system, Annu. Rev. Neurosci., 29, 77, 10.1146/annurev.neuro.29.051605.112839

Carninci, 2005, The transcriptional landscape of the mammalian genome, Science, 309, 1559, 10.1126/science.1112014

Carninci, 2006, Genome-wide analysis of mammalian promoter architecture and evolution, Nat. Genet., 38, 626, 10.1038/ng1789

Cawley, 2004, Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs, Cell, 116, 499, 10.1016/S0092-8674(04)00127-8

Chaumeil, 2006, A novel role for Xist RNA in the formation of a repressive nuclear compartment into which genes are recruited when silenced, Genes Dev., 20, 2223, 10.1101/gad.380906

Chen, 2005, Genome-wide analysis of coordinate expression and evolution of human cis-encoded sense-antisense transcripts, Trends Genet., 21, 326, 10.1016/j.tig.2005.04.006

Cheng, 2005, Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution, Science, 308, 1149, 10.1126/science.1108625

Chotalia, 2009, Transcription is required for establishment of germline methylation marks at imprinted genes, Genes Dev., 23, 105, 10.1101/gad.495809

Ciaudo, 2006, Nuclear mRNA degradation pathway(s) are implicated in Xist regulation and X chromosome inactivation, PLoS Genet., 2, e94, 10.1371/journal.pgen.0020094

Clemson, 1996, XIST RNA paints the inactive X chromosome at interphase: evidence for a novel RNA involved in nuclear/chromosome structure, J. Cell Biol., 132, 259, 10.1083/jcb.132.3.259

Conley, 2008, Human cis natural antisense transcripts initiated by transposable elements, Trends Genet., 24, 53, 10.1016/j.tig.2007.11.008

Dinger, 2009, NRED: a database of long noncoding RNA expression, Nucleic Acids Res., 37, D122, 10.1093/nar/gkn617

Dinger, 2008, Differentiating protein-coding and noncoding RNA: challenges and ambiguities, PLoS Comput. Biol., 4, e1000176, 10.1371/journal.pcbi.1000176

Dreszer, 2007, Biased clustered substitutions in the human genome: the footprints of male-driven biased gene conversion, Genome Res., 17, 1420, 10.1101/gr.6395807

Duret, 2006, The Xist RNA gene evolved in eutherians by pseudogenization of a protein-coding gene, Science, 312, 1653, 10.1126/science.1126316

Dutrow, 2008, Dynamic transcriptome of Schizosaccharomyces pombe shown by RNA-DNA hybrid mapping, Nat. Genet., 40, 977, 10.1038/ng.196

Ebisuya, 2008, Ripples from neighbouring transcription, Nat. Cell Biol., 10, 1106, 10.1038/ncb1771

Elisaphenko, 2008, A dual origin of the Xist gene from a protein-coding gene and a set of transposable elements, PLoS ONE, 3, e2521, 10.1371/journal.pone.0002521

Espinoza, 2004, B2 RNA binds directly to RNA polymerase II to repress transcript synthesis, Nat. Struct. Mol. Biol., 11, 822, 10.1038/nsmb812

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

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

Fitzpatrick, 2002, Regional loss of imprinting and growth deficiency in mice with a targeted deletion of KvDMR1, Nat. Genet., 32, 426, 10.1038/ng988

Galtier, 2007, Adaptation or biased gene conversion? Extending the null hypothesis of molecular evolution, Trends Genet., 23, 273, 10.1016/j.tig.2007.03.011

Gerstein, 2007, What is a gene, post-ENCODE? History and updated definition, Genome Res., 17, 669, 10.1101/gr.6339607

Gingeras, 2007, Origin of phenotypes: genes and transcripts, Genome Res., 17, 682, 10.1101/gr.6525007

Goni, 2004, Triplex-forming oligonucleotide target sequences in the human genome, Nucleic Acids Res., 32, 354, 10.1093/nar/gkh188

Goodrich, 2006, Non-coding-RNA regulators of RNA polymerase II transcription, Nat. Rev. Mol. Cell Biol., 7, 612, 10.1038/nrm1946

Green, 2007, A developmental window of opportunity for imprinted gene silencing mediated by DNA methylation and the Kcnq1ot1 noncoding RNA, Mamm. Genome, 18, 32, 10.1007/s00335-006-0092-9

Gribnau, 2000, Intergenic transcription and developmental remodeling of chromatin subdomains in the human beta-globin locus, Mol. Cell, 5, 377, 10.1016/S1097-2765(00)80432-3

Gruber, 2008, Invertebrate 7SK snRNAs, J. Mol. Evol., 66, 107, 10.1007/s00239-007-9052-6

Guttman, 2009, Chromatin signature reveals over a thousand highly conserved large non-coding RNAs in mammals, Nature, 10.1038/nature07672

Hirota, 2008, Stepwise chromatin remodelling by a cascade of transcription initiation of non-coding RNAs, Nature, 456, 130, 10.1038/nature07348

Hutchinson, 2007, A screen for nuclear transcripts identifies two linked noncoding RNAs associated with SC35 splicing domains, BMC Genomics, 8, 39, 10.1186/1471-2164-8-39

Hyashizaki, 2004, Mouse transcriptome: Neutral evolution of ‘non-coding’ complementary DNAs, Nature, 431, 757, 10.1038/nature03017

Jonkers, 2008, Xist RNA is confined to the nuclear territory of the silenced X chromosome throughout the cell cycle, Mol. Cell. Biol., 28, 5583, 10.1128/MCB.02269-07

Kampa, 2004, Novel RNAs identified from an in-depth analysis of the transcriptome of human chromosomes 21 and 22, Genome Res., 14, 331, 10.1101/gr.2094104

Kapranov, 2007, RNA maps reveal new RNA classes and a possible function for pervasive transcription, Science, 316, 1484, 10.1126/science.1138341

Kapranov, 2007, Genome-wide transcription and the implications for genomic organization, Nat. Rev. Genet., 8, 413, 10.1038/nrg2083

Katayama, 2005, Antisense transcription in the mammalian transcriptome, Science, 309, 1564, 10.1126/science.1112009

Khaitovich, 2006, Functionality of intergenic transcription: an evolutionary comparison, PLoS Genet., 2, e171, 10.1371/journal.pgen.0020171

Killian, 2000, M6P/IGF2R imprinting evolution in mammals, Mol. Cell, 5, 707, 10.1016/S1097-2765(00)80249-X

Koob, 1999, An untranslated CTG expansion causes a novel form of spinocerebellar ataxia (SCA8), Nat. Genet., 21, 379, 10.1038/7710

Lapidot, 2006, Genome-wide natural antisense transcription: coupling its regulation to its different regulatory mechanisms, EMBO Rep., 7, 1216, 10.1038/sj.embor.7400857

Lewejohann, 2004, Role of a neuronal small non-messenger RNA: behavioural alterations in BC1 RNA-deleted mice, Behav. Brain Res., 154, 273, 10.1016/j.bbr.2004.02.015

Lewis, 2006, Epigenetic dynamics of the Kcnq1 imprinted domain in the early embryo, Development, 133, 4203, 10.1242/dev.02612

Lewis, 2004, Imprinting on distal chromosome 7 in the placenta involves repressive histone methylation independent of DNA methylation, Nat. Genet., 36, 1291, 10.1038/ng1468

Louro, 2008, Conserved tissue expression signatures of intronic noncoding RNAs transcribed from human and mouse loci, Genomics, 92, 18, 10.1016/j.ygeno.2008.03.013

Mancini-Dinardo, 2006, Elongation of the Kcnq1ot1 transcript is required for genomic imprinting of neighboring genes, Genes Dev., 20, 1268, 10.1101/gad.1416906

Mariner, 2008, Human Alu RNA is a modular transacting repressor of mRNA transcription during heat shock, Mol. Cell, 29, 499, 10.1016/j.molcel.2007.12.013

Martens, 2004, Intergenic transcription is required to repress the Saccharomyces cerevisiae SER3 gene, Nature, 429, 571, 10.1038/nature02538

Martianov, 2007, Repression of the human dihydrofolate reductase gene by a non-coding interfering transcript, Nature, 445, 666, 10.1038/nature05519

Mattick, 2006, Non-coding RNA, Hum. Mol. Genet., 15, R17, 10.1093/hmg/ddl046

Mercer, 2008, Specific expression of long noncoding RNAs in the mouse brain, Proc. Natl. Acad. Sci. USA, 105, 716, 10.1073/pnas.0706729105

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

Mus, 2007, Dendritic BC200 RNA in aging and in Alzheimer's disease, Proc. Natl. Acad. Sci. USA, 104, 10679, 10.1073/pnas.0701532104

Nagalakshmi, 2008, The transcriptional landscape of the yeast genome defined by RNA sequencing, Science, 320, 1344, 10.1126/science.1158441

Nagano, 2008, The Air noncoding RNA epigenetically silences transcription by targeting G9a to chromatin, Science, 322, 1717, 10.1126/science.1163802

Nesterova, 2008, Dicer regulates Xist promoter methylation in ES cells indirectly through transcriptional control of Dnmt3a, Epigenetics Chromatin, 1, 2, 10.1186/1756-8935-1-2

Nguyen, 2001, 7SK small nuclear RNA binds to and inhibits the activity of CDK9/cyclin T complexes, Nature, 414, 322, 10.1038/35104581

Ogawa, 2008, Intersection of the RNA interference and X-inactivation pathways, Science, 320, 1336, 10.1126/science.1157676

Osato, 2007, Transcriptional interferences in cis natural antisense transcripts of humans and mice, Genetics, 176, 1299, 10.1534/genetics.106.069484

Pandey, 2008, Kcnq1ot1 antisense noncoding RNA mediates lineage-specific transcriptional silencing through chromatin-level regulation, Mol. Cell, 32, 232, 10.1016/j.molcel.2008.08.022

Pang, 2006, Rapid evolution of noncoding RNAs: lack of conservation does not mean lack of function, Trends Genet., 22, 1, 10.1016/j.tig.2005.10.003

Pauler, 2007, Silencing by imprinted noncoding RNAs: is transcription the answer?, Trends Genet., 23, 284, 10.1016/j.tig.2007.03.018

Peters, 2008, Imprinted noncoding RNAs, Mamm. Genome., 19, 493, 10.1007/s00335-008-9139-4

Pollard, 2006, An RNA gene expressed during cortical development evolved rapidly in humans, Nature, 443, 167, 10.1038/nature05113

Ponjavic, 2007, The long and the short of RNA maps, Bioessays, 29, 1077, 10.1002/bies.20669

Ponjavic, 2007, Functionality or transcriptional noise? Evidence for selection within long noncoding RNAs, Genome Res., 17, 556, 10.1101/gr.6036807

Ponting, 2008, The functional repertoires of metazoan genomes, Nat. Rev. Genet., 9, 689, 10.1038/nrg2413

Ranum, 2006, RNA-mediated neuromuscular disorders, Annu. Rev. Neurosci., 29, 259, 10.1146/annurev.neuro.29.051605.113014

Ravasi, 2006, Experimental validation of the regulated expression of large numbers of non-coding RNAs from the mouse genome, Genome Res., 16, 11, 10.1101/gr.4200206

Redrup, 2009, The long noncoding RNA Kcnq1ot1 organises a lineage-specific nuclear domain for epigenetic gene silencing, Development, 136, 525, 10.1242/dev.031328

Regha, 2007, Active and repressive chromatin are interspersed without spreading in an imprinted gene cluster in the Mamm. Genome, Mol. Cell, 27, 353, 10.1016/j.molcel.2007.06.024

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

Seidl, 2006, The imprinted Air ncRNA is an atypical RNAPII transcript that evades splicing and escapes nuclear export, EMBO J., 25, 3565, 10.1038/sj.emboj.7601245

Shamovsky, 2006, RNA-mediated response to heat shock in mammalian cells, Nature, 440, 556, 10.1038/nature04518

Shin, 2008, Two distinct mechanisms of silencing by the KvDMR1 imprinting control region, EMBO J., 27, 168, 10.1038/sj.emboj.7601960

Sleutels, 2002, The non-coding Air RNA is required for silencing autosomal imprinted genes, Nature, 415, 810, 10.1038/415810a

Smits, 2008, Conservation of the H19 noncoding RNA and H19–IGF2 imprinting mechanism in therians, Nat. Genet., 40, 971, 10.1038/ng.168

Sone, 2007, The mRNA-like noncoding RNA Gomafu constitutes a novel nuclear domain in a subset of neurons, J. Cell Sci., 120, 2498, 10.1242/jcs.009357

Szymanski, 2005, A new frontier for molecular medicine: noncoding RNAs, Biochim. Biophys. Acta, 1756, 65

Terranova, 2008, Polycomb group proteins Ezh2 and Rnf2 direct genomic contraction and imprinted repression in early mouse embryos, Dev. Cell, 15, 668, 10.1016/j.devcel.2008.08.015

Tian, 2005, A large-scale analysis of mRNA polyadenylation of human and mouse genes, Nucleic Acids Res., 33, 201, 10.1093/nar/gki158

Umlauf, 2004, Imprinting along the Kcnq1 domain on mouse chromosome 7 involves repressive histone methylation and recruitment of Polycomb group complexes, Nat. Genet., 36, 1296, 10.1038/ng1467

Wang, 2004, Mouse transcriptome: neutral evolution of ‘non-coding’ complementary DNAs, Nature, 431, 757, 10.1038/nature03016

Wang, 2008, Induced ncRNAs allosterically modify RNA-binding proteins in cis to inhibit transcription, Nature, 454, 126, 10.1038/nature06992

Wilhelm, 2008, Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution, Nature, 453, 1239, 10.1038/nature07002

Willingham, 2005, A strategy for probing the function of noncoding RNAs finds a repressor of NFAT, Science, 309, 1570, 10.1126/science.1115901

Wutz, 2007, X inactivation Xplained, Curr. Opin. Genet. Dev., 17, 387, 10.1016/j.gde.2007.08.001

Wutz, 2000, A shift from reversible to irreversible X inactivation is triggered during ES cell differentiation, Mol. Cell, 5, 695, 10.1016/S1097-2765(00)80248-8

Wutz, 1997, Imprinted expression of the Igf2r gene depends on an intronic CpG island, Nature, 389, 745, 10.1038/39631

Yang, 2001, The 7SK small nuclear RNA inhibits the CDK9/cyclin T1 kinase to control transcription, Nature, 414, 317, 10.1038/35104575

Zalfa, 2003, The fragile X syndrome protein FMRP associates with BC1 RNA and regulates the translation of specific mRNAs at synapses, Cell, 112, 317, 10.1016/S0092-8674(03)00079-5

Zhao, 2008, Polycomb proteins targeted by a short repeat RNA to the mouse X chromosome, Science, 322, 750, 10.1126/science.1163045