Cited by 4,208

The DOI matches its Crossref record; 8 of the 8 references it cites were found in a registry or an index.

Evolution and Functions of Long Noncoding RNAs

Ponting, Chris P., Oliver, Peter L., Reik, Wolf·2009·Cell

Overview

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1016/j.cell.2009.02.006

Cites

8 of 8 references verified0 citation errors · 0 not checkable

Statistics

Verification

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Citations

Cites

Flagged first, then by citations

Show all 8 references

Research works printed but not linked: 96

  1. 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 · DOI
  2. Babak, 2007, Considerations in the identification of functional RNA structural elements in genomic alignments, BMC Bioinformatics, 8, 33, 10.1186/1471-2105-8-33 · DOI
  3. Bartolomei, 1991, Parental imprinting of the mouse H19 gene, Nature, 351, 153, 10.1038/351153a0 · DOI
  4. Bertone, 2004, Global identification of human transcribed sequences with genome tiling arrays, Science, 306, 2242, 10.1126/science.1103388 · DOI
  5. 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 · DOI · Paper page
  6. 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 · DOI
  7. Brockdorff, 1991, Conservation of position and exclusive expression of mouse Xist from the inactive X chromosome, Nature, 351, 329, 10.1038/351329a0 · DOI
  8. 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 · DOI
  9. Brown, 1994, The human X-inactivation centre is not required for maintenance of X-chromosome inactivation, Nature, 368, 154, 10.1038/368154a0 · DOI
  10. Cai, 2007, The imprinted H19 noncoding RNA is a primary microRNA precursor, RNA, 13, 313, 10.1261/rna.351707 · DOI
  11. Cao, 2006, Noncoding RNAs in the mammalian central nervous system, Annu. Rev. Neurosci., 29, 77, 10.1146/annurev.neuro.29.051605.112839 · DOI · Paper page
  12. Carninci, 2005, The transcriptional landscape of the mammalian genome, Science, 309, 1559, 10.1126/science.1112014 · DOI
  13. 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 · DOI
  14. 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 · DOI
  15. Cheng, 2005, Transcriptional maps of 10 human chromosomes at 5-nucleotide resolution, Science, 308, 1149, 10.1126/science.1108625 · DOI
  16. Chotalia, 2009, Transcription is required for establishment of germline methylation marks at imprinted genes, Genes Dev., 23, 105, 10.1101/gad.495809 · DOI
  17. 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 · DOI
  18. 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 · DOI
  19. Conley, 2008, Human cis natural antisense transcripts initiated by transposable elements, Trends Genet., 24, 53, 10.1016/j.tig.2007.11.008 · DOI
  20. Dinger, 2009, NRED: a database of long noncoding RNA expression, Nucleic Acids Res., 37, D122, 10.1093/nar/gkn617 · DOI
  21. Dinger, 2008, Differentiating protein-coding and noncoding RNA: challenges and ambiguities, PLoS Comput. Biol., 4, e1000176, 10.1371/journal.pcbi.1000176 · DOI
  22. 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 · DOI · Paper page
  23. Dutrow, 2008, Dynamic transcriptome of Schizosaccharomyces pombe shown by RNA-DNA hybrid mapping, Nat. Genet., 40, 977, 10.1038/ng.196 · DOI
  24. Ebisuya, 2008, Ripples from neighbouring transcription, Nat. Cell Biol., 10, 1106, 10.1038/ncb1771 · DOI
  25. 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 · DOI
  26. Espinoza, 2004, B2 RNA binds directly to RNA polymerase II to repress transcript synthesis, Nat. Struct. Mol. Biol., 11, 822, 10.1038/nsmb812 · DOI
  27. 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 · DOI · Paper page
  28. Fitzpatrick, 2002, Regional loss of imprinting and growth deficiency in mice with a targeted deletion of KvDMR1, Nat. Genet., 32, 426, 10.1038/ng988 · DOI
  29. 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 · DOI
  30. Gerstein, 2007, What is a gene, post-ENCODE? History and updated definition, Genome Res., 17, 669, 10.1101/gr.6339607 · DOI
  31. Gingeras, 2007, Origin of phenotypes: genes and transcripts, Genome Res., 17, 682, 10.1101/gr.6525007 · DOI
  32. Goni, 2004, Triplex-forming oligonucleotide target sequences in the human genome, Nucleic Acids Res., 32, 354, 10.1093/nar/gkh188 · DOI
  33. Goodrich, 2006, Non-coding-RNA regulators of RNA polymerase II transcription, Nat. Rev. Mol. Cell Biol., 7, 612, 10.1038/nrm1946 · DOI · Paper page
  34. 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 · DOI
  35. 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 · DOI
  36. Gruber, 2008, Invertebrate 7SK snRNAs, J. Mol. Evol., 66, 107, 10.1007/s00239-007-9052-6 · DOI
  37. Hirota, 2008, Stepwise chromatin remodelling by a cascade of transcription initiation of non-coding RNAs, Nature, 456, 130, 10.1038/nature07348 · DOI
  38. 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 · DOI
  39. Hyashizaki, 2004, Mouse transcriptome: Neutral evolution of ‘non-coding’ complementary DNAs, Nature, 431, 757, 10.1038/nature03017 · DOI
  40. 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 · DOI
  41. 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 · DOI
  42. Kapranov, 2007, RNA maps reveal new RNA classes and a possible function for pervasive transcription, Science, 316, 1484, 10.1126/science.1138341 · DOI
  43. Kapranov, 2007, Genome-wide transcription and the implications for genomic organization, Nat. Rev. Genet., 8, 413, 10.1038/nrg2083 · DOI
  44. Katayama, 2005, Antisense transcription in the mammalian transcriptome, Science, 309, 1564, 10.1126/science.1112009 · DOI
  45. Khaitovich, 2006, Functionality of intergenic transcription: an evolutionary comparison, PLoS Genet., 2, e171, 10.1371/journal.pgen.0020171 · DOI
  46. Killian, 2000, M6P/IGF2R imprinting evolution in mammals, Mol. Cell, 5, 707, 10.1016/S1097-2765(00)80249-X · DOI · Paper page
  47. Koob, 1999, An untranslated CTG expansion causes a novel form of spinocerebellar ataxia (SCA8), Nat. Genet., 21, 379, 10.1038/7710 · DOI
  48. Lapidot, 2006, Genome-wide natural antisense transcription: coupling its regulation to its different regulatory mechanisms, EMBO Rep., 7, 1216, 10.1038/sj.embor.7400857 · DOI
  49. 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 · DOI
  50. Lewis, 2006, Epigenetic dynamics of the Kcnq1 imprinted domain in the early embryo, Development, 133, 4203, 10.1242/dev.02612 · DOI
  51. 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 · DOI
  52. 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 · DOI
  53. Mancini-Dinardo, 2006, Elongation of the Kcnq1ot1 transcript is required for genomic imprinting of neighboring genes, Genes Dev., 20, 1268, 10.1101/gad.1416906 · DOI
  54. 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 · DOI
  55. Martens, 2004, Intergenic transcription is required to repress the Saccharomyces cerevisiae SER3 gene, Nature, 429, 571, 10.1038/nature02538 · DOI
  56. Martianov, 2007, Repression of the human dihydrofolate reductase gene by a non-coding interfering transcript, Nature, 445, 666, 10.1038/nature05519 · DOI
  57. Mattick, 2006, Non-coding RNA, Hum. Mol. Genet., 15, R17, 10.1093/hmg/ddl046 · DOI
  58. 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 · DOI
  59. Mus, 2007, Dendritic BC200 RNA in aging and in Alzheimer's disease, Proc. Natl. Acad. Sci. USA, 104, 10679, 10.1073/pnas.0701532104 · DOI
  60. Nagalakshmi, 2008, The transcriptional landscape of the yeast genome defined by RNA sequencing, Science, 320, 1344, 10.1126/science.1158441 · DOI · Paper page
  61. Nagano, 2008, The Air noncoding RNA epigenetically silences transcription by targeting G9a to chromatin, Science, 322, 1717, 10.1126/science.1163802 · DOI
  62. 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 · DOI
  63. Nguyen, 2001, 7SK small nuclear RNA binds to and inhibits the activity of CDK9/cyclin T complexes, Nature, 414, 322, 10.1038/35104581 · DOI
  64. Ogawa, 2008, Intersection of the RNA interference and X-inactivation pathways, Science, 320, 1336, 10.1126/science.1157676 · DOI
  65. Osato, 2007, Transcriptional interferences in cis natural antisense transcripts of humans and mice, Genetics, 176, 1299, 10.1534/genetics.106.069484 · DOI
  66. 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 · DOI
  67. 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 · DOI
  68. Pauler, 2007, Silencing by imprinted noncoding RNAs: is transcription the answer?, Trends Genet., 23, 284, 10.1016/j.tig.2007.03.018 · DOI
  69. Peters, 2008, Imprinted noncoding RNAs, Mamm. Genome., 19, 493, 10.1007/s00335-008-9139-4 · DOI
  70. Ponjavic, 2007, The long and the short of RNA maps, Bioessays, 29, 1077, 10.1002/bies.20669 · DOI
  71. Ponjavic, 2007, Functionality or transcriptional noise? Evidence for selection within long noncoding RNAs, Genome Res., 17, 556, 10.1101/gr.6036807 · DOI
  72. Ponting, 2008, The functional repertoires of metazoan genomes, Nat. Rev. Genet., 9, 689, 10.1038/nrg2413 · DOI
  73. Ranum, 2006, RNA-mediated neuromuscular disorders, Annu. Rev. Neurosci., 29, 259, 10.1146/annurev.neuro.29.051605.113014 · DOI
  74. 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 · DOI
  75. Redrup, 2009, The long noncoding RNA Kcnq1ot1 organises a lineage-specific nuclear domain for epigenetic gene silencing, Development, 136, 525, 10.1242/dev.031328 · DOI
  76. 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 · DOI
  77. 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 · DOI
  78. 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 · DOI
  79. Shamovsky, 2006, RNA-mediated response to heat shock in mammalian cells, Nature, 440, 556, 10.1038/nature04518 · DOI
  80. Shin, 2008, Two distinct mechanisms of silencing by the KvDMR1 imprinting control region, EMBO J., 27, 168, 10.1038/sj.emboj.7601960 · DOI
  81. Sleutels, 2002, The non-coding Air RNA is required for silencing autosomal imprinted genes, Nature, 415, 810, 10.1038/415810a · DOI
  82. Smits, 2008, Conservation of the H19 noncoding RNA and H19–IGF2 imprinting mechanism in therians, Nat. Genet., 40, 971, 10.1038/ng.168 · DOI
  83. 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 · DOI
  84. Szymanski, 2005, A new frontier for molecular medicine: noncoding RNAs, Biochim. Biophys. Acta, 1756, 65
  85. 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 · DOI
  86. Tian, 2005, A large-scale analysis of mRNA polyadenylation of human and mouse genes, Nucleic Acids Res., 33, 201, 10.1093/nar/gki158 · DOI
  87. 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 · DOI
  88. Wang, 2004, Mouse transcriptome: neutral evolution of ‘non-coding’ complementary DNAs, Nature, 431, 757, 10.1038/nature03016 · DOI
  89. Wang, 2008, Induced ncRNAs allosterically modify RNA-binding proteins in cis to inhibit transcription, Nature, 454, 126, 10.1038/nature06992 · DOI
  90. Wilhelm, 2008, Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution, Nature, 453, 1239, 10.1038/nature07002 · DOI
  91. Willingham, 2005, A strategy for probing the function of noncoding RNAs finds a repressor of NFAT, Science, 309, 1570, 10.1126/science.1115901 · DOI
  92. Wutz, 2007, X inactivation Xplained, Curr. Opin. Genet. Dev., 17, 387, 10.1016/j.gde.2007.08.001 · DOI
  93. 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 · DOI
  94. Wutz, 1997, Imprinted expression of the Igf2r gene depends on an intronic CpG island, Nature, 389, 745, 10.1038/39631 · DOI
  95. Yang, 2001, The 7SK small nuclear RNA inhibits the CDK9/cyclin T1 kinase to control transcription, Nature, 414, 317, 10.1038/35104575 · DOI
  96. Zhao, 2008, Polycomb proteins targeted by a short repeat RNA to the mouse X chromosome, Science, 322, 750, 10.1126/science.1163045 · DOI

Cited by

Sorted by citations

See all 4,208

Metadata

Authors
Ponting, C. P., Oliver, P. L., & Reik, W.
Venue
Cell
Publisher
Elsevier BV
Published
2009-02
Volume
136
Issue
4
Pages
629-641
ISSN
0092-8674
Cited by
4,208
References
8
Language
en

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review