CoChat
Sign Up
Cited by 95

The DOI matches its Crossref record; 5 of the 5 references it cites were found in a registry or an index.

Transposable element small RNAs as regulators of gene expression

McCue, Andrea D., Slotkin, R. Keith·2012·Trends in Genetics
DOI 10.1016/j.tig.2012.09.001
Open this paper in CoChat — free account

Abstract

Transposable elements (TEs) are a source of endogenous small RNAs in animals and plants. These TE-derived small RNAs have been traditionally treated as functionally distinct from gene-regulating small RNAs, such as miRNAs. Two recent reports in Drosophila and Arabidopsis have blurred the lines of this distinction. In both examples, epigenetically and developmentally regulated bursts in TE expression produce gene-regulating small RNAs. In the Drosophila early embryo, maternally deposited TE-derived PIWI-interacting small RNAs (piRNAs) play a role in regulating the nanos mRNA through small RNA binding sites in the nanos 3' untranslated region (UTR). In Arabidopsis, when Athila retrotransposons are epigenetically activated, their transcripts are processed into small RNAs, which directly target the 3'UTR of the genic oligouridylate binding protein 1B (UBP1b) mRNA. Based on these two examples, we suggest that other TE-derived small RNAs regulate additional genes and propose that, through small RNAs, the epigenetic status of TEs could widely influence the genic transcriptome.

Overview

Integrity signals

Registry

Crossref · 10.1016/j.tig.2012.09.001

Cites

5 of 5 references verified0 citation errors · 0 not checkable

Statistics

Recomputing p-values needs the paper’s full text.

Verification

Claims the paper makes

This paper’s full text isn’t openly available, so its claims and self-check weren’t run. The registry and citation checks still apply.

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?

Citations

Cites

Show all 5 references

Research works printed but not linked: 80

  1. Saito, 2010, Small RNA-mediated quiescence of transposable elements in animals, Dev. Cell, 19, 1, 10.1016/j.devcel.2010.10.011 · DOI
  2. Czech, 2010, Small RNA sorting: matchmaking for Argonautes, Nat. Rev. Genet., 12, 19, 10.1038/nrg2916 · DOI · Paper page
  3. Zilberman, 2003, ARGONAUTE4 control of locus-specific siRNA accumulation and DNA and histone methylation, Science, 299, 1, 10.1126/science.1079695 · DOI · Paper page
  4. Xie, 2004, Genetic and functional diversification of small RNA pathways in plants, PLoS Biol., 2, 1, 10.1371/journal.pbio.0020104 · DOI
  5. Aravin, 2008, Small RNA guides for de novo DNA methylation in mammalian germ cells, Genes Dev., 22, 1, 10.1101/gad.1669408 · DOI
  6. Wang, 2011, Drosophila Piwi functions downstream of piRNA production mediating a chromatin-based transposon silencing mechanism in female germ line, Proc. Natl. Acad. Sci. U.S.A., 108, 1, 10.1073/pnas.1107892109 · DOI · Paper page
  7. Cropley, 2007, Controlling elements are wild cards in the epigenomic deck, Proc. Natl. Acad. Sci. U.S.A., 104, 18879, 10.1073/pnas.0708872104 · DOI
  8. Pfeffer, 2004, Identification of virus-encoded microRNAs, Science, 304, 734, 10.1126/science.1096781 · DOI
  9. Dölken, 2007, Mouse cytomegalovirus microRNAs dominate the cellular small RNA profile during lytic infection and show features of posttranscriptional regulation, J. Virol., 81, 13771, 10.1128/JVI.01313-07 · DOI
  10. Parameswaran, 2010, Six RNA viruses and forty-one hosts: viral small RNAs and modulation of small RNA repertoires in vertebrate and invertebrate systems, PLoS Pathog., 6, e1000764, 10.1371/journal.ppat.1000764 · DOI
  11. Smalheiser, 2005, Mammalian microRNAs derived from genomic repeats, Trends Genet., 21, 1, 10.1016/j.tig.2005.04.008 · DOI · Paper page
  12. Allen, 2004, Evolution of microRNA genes by inverted duplication of target gene sequences in Arabidopsis thaliana, Nat. Genet., 36, 1, 10.1038/ng1478 · DOI · Paper page
  13. Slotkin, 2005, Heritable transposon silencing initiated by a naturally occurring transposon inverted duplication, Nat. Genet., 37, 641, 10.1038/ng1576 · DOI · Paper page
  14. Piriyapongsa, 2008, Dual coding of siRNAs and miRNAs by plant transposable elements, RNA, 14, 814, 10.1261/rna.916708 · DOI
  15. Piriyapongsa, 2006, Origin and evolution of human microRNAs from transposable elements, Genetics, 176, 1323, 10.1534/genetics.107.072553 · DOI
  16. Zhang, 2011, Evolution of microRNA genes in Oryza sativa and Arabidopsis thaliana: an update of the inverted duplication model, PLoS ONE, 6, e28073, 10.1371/journal.pone.0028073 · DOI
  17. Li, 2011, Domestication of transposable elements into MicroRNA genes in plants, PLoS ONE, 6, 1
  18. Yan, 2011, Small RNAs from MITE-derived stem-loop precursors regulate abscisic acid signaling and abiotic stress responses in rice, Plant J., 65, 820, 10.1111/j.1365-313X.2010.04467.x · DOI
  19. Jiang, 2011, Pack-Mutator-like transposable elements (Pack-MULEs) induce directional modification of genes through biased insertion and DNA acquisition, Proc. Natl. Acad. Sci. U.S.A., 108, 1537, 10.1073/pnas.1010814108 · DOI
  20. Piriyapongsa, 2007, Origin and evolution of human microRNAs from transposable elements, Genetics, 176, 1, 10.1534/genetics.107.072553 · DOI
  21. Rouget, 2010, Maternal mRNA deadenylation and decay by the piRNA pathway in the early Drosophila embryo, Nature, 467, 1, 10.1038/nature09465 · DOI
  22. Zaessinger, 2006, Oskar allows nanos mRNA translation in Drosophila embryos by preventing its deadenylation by Smaug/CCR4, Development, 133, 4573, 10.1242/dev.02649 · DOI
  23. McCue, 2012, Gene expression and stress response mediated by the epigenetic regulation of a transposable element small RNA, PLoS Genet., 8, e1002474, 10.1371/journal.pgen.1002474 · DOI
  24. Calarco, 2011, Genome reprogramming and small interfering RNA in the Arabidopsis germline, Curr. Opin. Genet. Dev., 21, 134, 10.1016/j.gde.2011.01.014 · DOI
  25. Hirochika, 2000, Silencing of retrotransposons in Arabidopsis and reactivation by the ddm1 mutation, Plant Cell, 12, 357, 10.1105/tpc.12.3.357 · DOI
  26. Slotkin, 2009, Epigenetic reprogramming and small RNA silencing of transposable elements in pollen, Cell, 136, 461, 10.1016/j.cell.2008.12.038 · DOI · Paper page
  27. Slotkin, 2010, The epigenetic control of the Athila family of retrotransposons in Arabidopsis, Epigenetics, 5, 483, 10.4161/epi.5.6.12119 · DOI
  28. Chapman, 2007, Specialization and evolution of endogenous small RNA pathways, Nat. Rev. Genet., 8, 1, 10.1038/nrg2179 · DOI
  29. Dunoyer, 2005, DICER-LIKE 4 is required for RNA interference and produces the 21-nucleotide small interfering RNA component of the plant cell-to-cell silencing signal, Nat. Genet., 37, 1356, 10.1038/ng1675 · DOI
  30. Deleris, 2006, Hierarchical action and inhibition of plant Dicer-like proteins in antiviral defense, Science, 313, 68, 10.1126/science.1128214 · DOI
  31. Garcia-Ruiz, 2010, Arabidopsis RNA-dependent RNA polymerases and Dicer-like proteins in antiviral defense and small interfering RNA biogenesis during Turnip Mosaic Virus infection, Plant Cell, 22, 481, 10.1105/tpc.109.073056 · DOI
  32. Arteaga-Vázquez, 2006, A family of microRNAs present in plants and animals, Plant Cell, 18, 3355, 10.1105/tpc.106.044420 · DOI
  33. Weber, 2008, Plant stress granules and mRNA processing bodies are distinct from heat stress granules, Plant J., 56, 517, 10.1111/j.1365-313X.2008.03623.x · DOI
  34. Schott, 2012, Differential effects of viral silencing suppressors on siRNA and miRNA loading support the existence of two distinct cellular pools of ARGONAUTE1, EMBO J., 31, 2553, 10.1038/emboj.2012.92 · DOI
  35. Pillai, 2012, piRNAs and their involvement in male germline development in mice, Dev. Growth Differ., 54, 78, 10.1111/j.1440-169X.2011.01320.x · DOI
  36. Galli, 2003, Expression of the Arabidopsis transposable element Tag1 is targeted to developing gametophytes, Genetics, 165, 2093, 10.1093/genetics/165.4.2093 · DOI
  37. Gehring, 2009, Extensive demethylation of repetitive elements during seed development underlies gene imprinting, Science, 324, 1447, 10.1126/science.1171609 · DOI
  38. Chambeyron, 2008, piRNA-mediated nuclear accumulation of retrotransposon transcripts in the Drosophila female germline, Proc. Natl. Acad. Sci. U.S.A., 105, 14964, 10.1073/pnas.0805943105 · DOI
  39. Malone, 2009, Specialized piRNA pathways act in germline and somatic tissues of the Drosophila ovary, Cell, 137, 522, 10.1016/j.cell.2009.03.040 · DOI
  40. Shpiz, 2011, Mechanism of the piRNA-mediated silencing of Drosophila telomeric retrotransposons, Nucleic Acids Res., 39, 8703, 10.1093/nar/gkr552 · DOI
  41. Lisch, 2012, Regulation of transposable elements in maize, Curr. Opin. Plant Biol., 13, 1
  42. Lisch, 1995, Genetic characterization of the Mutator system in maize: behavior and regulation of Mu transposons in a minimal line, Genetics, 139, 1777, 10.1093/genetics/139.4.1777 · DOI
  43. McCarty, 2005, Steady-state transposon mutagenesis in inbred maize, Plant J., 44, 52, 10.1111/j.1365-313X.2005.02509.x · DOI
  44. Takumi, 2007, Epigenetic silencing and unstable inheritance of MuDR activity monitored at four bz2–mu alleles in maize (Zea mays L.), Genes Genet. Syst., 82, 387, 10.1266/ggs.82.387 · DOI
  45. Skibbe, 2009, Mutator transposon activity reprograms the transcriptomes and proteomes of developing maize anthers, Plant J., 59, 622, 10.1111/j.1365-313X.2009.03901.x · DOI
  46. Brennecke, 2008, An epigenetic role for maternally inherited piRNAs in transposon silencing, Science, 322, 1, 10.1126/science.1165171 · DOI
  47. Dobigny, 2006, Absence of hypomethylation and LINE–1 amplification in a white x black rhinoceros hybrid, Genetica, 127, 81, 10.1007/s10709-005-2483-3 · DOI
  48. Metcalfe, 2007, Genomic instability within centromeres of interspecific marsupial hybrids, Genetics, 177, 2507, 10.1534/genetics.107.082313 · DOI
  49. Greaves, 2012, Trans chromosomal methylation in Arabidopsis hybrids, Proc. Natl. Acad. Sci. U.S.A., 109, 1, 10.1073/pnas.1201043109 · DOI
  50. Shivaprasad, 2011, Extraordinary transgressive phenotypes of hybrid tomato are influenced by epigenetics and small silencing RNAs, EMBO J., 31, 257, 10.1038/emboj.2011.458 · DOI
  51. Wilke, 1992, The population biology and evolutionary significance of Ty elements in Saccharomyces cerevisiae, Genetica, 86, 155, 10.1007/BF00133718 · DOI
  52. Giraud, 1996, Somatic activity of the mariner transposable element in natural populations of Drosophila simulans, Proc. R. Soc. B, 263, 1481, 10.1098/rspb.1996.0216 · DOI
  53. Akagi, 2008, Extensive variation between inbred mouse strains due to endogenous L1 retrotransposition, Genome Res., 18, 869, 10.1101/gr.075770.107 · DOI
  54. McClintock, 1956, Intranuclear systems controlling gene action and mutation, Brookhaven Symp. Biol., 8, 58
  55. McClintock, 1984, The significance of responses of the genome to challenge, Science, 226, 792, 10.1126/science.15739260 · DOI
  56. Lisch, 2011, Strategies for silencing and escape: the ancient struggle between transposable elements and their hosts, Int. Rev. Cell Mol. Biol., 292, 119, 10.1016/B978-0-12-386033-0.00003-7 · DOI
  57. Liu, 2011, PAPI, a novel TUDOR-domain protein, complexes with AGO3, ME31B and TRAL in the nuage to silence transposition, Development, 138, 1863, 10.1242/dev.059287 · DOI
  58. Kedersha, 1999, RNA-binding proteins TIA-1 and TIAR link the phosphorylation of eIF–2 alpha to the assembly of mammalian stress granules, J. Cell Biol., 147, 1431, 10.1083/jcb.147.7.1431 · DOI
  59. Beckham, 2008, P bodies, stress granules, and viral life cycles, Cell Host Microbe, 3, 206, 10.1016/j.chom.2008.03.004 · DOI
  60. Li, 2002, Cell proteins TIA-1 and TIAR interact with the 3′ stem-loop of the West Nile Virus complementary minus-strand RNA and facilitate virus replication, J. Virol., 76, 11989, 10.1128/JVI.76.23.11989-12000.2002 · DOI
  61. Qin, 2009, Mammalian orthoreovirus particles induce and are recruited into stress granules at early times postinfection, J. Virol., 83, 11090, 10.1128/JVI.01239-09 · DOI
  62. Lindquist, 2010, Respiratory syncytial virus induces host RNA stress granules to facilitate viral replication, J. Virol., 84, 12274, 10.1128/JVI.00260-10 · DOI
  63. Zeller, 2009, Stress-induced changes in the Arabidopsis thaliana transcriptome analyzed using whole-genome tiling arrays, Plant J., 58, 1068, 10.1111/j.1365-313X.2009.03835.x · DOI
  64. Ito, 2011, An siRNA pathway prevents transgenerational retrotransposition in plants subjected to stress, Nature, 472, 115, 10.1038/nature09861 · DOI
  65. Dahanukar, 1996, The Nanos gradient in Drosophila embryos is generated by translational regulation, Genes Dev., 10, 2610, 10.1101/gad.10.20.2610 · DOI
  66. Law, 2010, Establishing, maintaining and modifying DNA methylation patterns in plants and animals, Nat. Rev. Genet., 11, 1, 10.1038/nrg2719 · DOI
  67. Qi, 2006, Distinct catalytic and non-catalytic roles of ARGONAUTE4 in RNA-directed DNA methylation, Nature, 443, 1008, 10.1038/nature05198 · DOI
  68. Wierzbicki, 2008, Noncoding transcription by RNA polymerase Pol IVb/Pol V mediates transcriptional silencing of overlapping and adjacent genes, Cell, 135, 1, 10.1016/j.cell.2008.09.035 · DOI
  69. Chung, 2008, Endogenous RNA interference provides a somatic defense against Drosophila transposons, Curr. Biol., 18, 795, 10.1016/j.cub.2008.05.006 · DOI
  70. Ghildiyal, 2008, Endogenous siRNAs derived from transposons and mRNAs in Drosophila somatic cells, Science, 320, 1077, 10.1126/science.1157396 · DOI · Paper page
  71. Czech, 2008, An endogenous small interfering RNA pathway in Drosophila, Nature, 453, 798, 10.1038/nature07007 · DOI
  72. Kawamura, 2008, Drosophila endogenous small RNAs bind to Argonaute 2 in somatic cells, Nature, 453, 793, 10.1038/nature06938 · DOI
  73. Senti, 2010, The piRNA pathway: a fly's perspective on the guardian of the genome, Trends Genet., 26, 499, 10.1016/j.tig.2010.08.007 · DOI
  74. Vazquez, 2004, Endogenous trans-acting siRNAs regulate the accumulation of Arabidopsis mRNAs, Mol. Cell, 16, 69, 10.1016/j.molcel.2004.09.028 · DOI
  75. Allen, 2005, microRNA-directed phasing during trans-acting siRNA biogenesis in plants, Cell, 121, 207, 10.1016/j.cell.2005.04.004 · DOI
  76. Ding, 2010, RNA-based antiviral immunity, Nat. Rev. Immunol., 10, 632, 10.1038/nri2824 · DOI
  77. Felippes, 2009, Triggering the formation of tasiRNAs in Arabidopsis thaliana: the role of microRNA miR173, EMBO Rep., 10, 1, 10.1038/embor.2008.247 · DOI
  78. Montgomery, 2008, Specificity of ARGONAUTE7-mir390 interaction and dual functionality in TAS3 trans-acting siRNA formation, Cell, 133, 128, 10.1016/j.cell.2008.02.033 · DOI
  79. Chang, 2012, RNA interference pathways in fungi: mechanisms and functions, Annu. Rev. Microbiol., 66, 305, 10.1146/annurev-micro-092611-150138 · DOI
  80. Senti, 2010, The piRNA pathway: a fly's perspective on the guardian of the genome, Trends Genet., 26, 499, 10.1016/j.tig.2010.08.007 · DOI

Cited by

Sorted by citations

Metadata

Authors
McCue, A. D., & Slotkin, R. K.
Venue
Trends in Genetics
Publisher
Elsevier BV
Published
2012-12
Volume
28
Issue
12
Pages
616-623
ISSN
0168-9525
DOI
10.1016/j.tig.2012.09.001
Cited by
95
References
5
Language
en
Licence
www.elsevier.com/tdm/userlicense/1.0/ (tdm)

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