Cited by 219

The DOI matches its Crossref record; 3 of the 3 references it cites were found in a registry or an index.

Revisiting the Relationship between Transposable Elements and the Eukaryotic Stress Response

Horváth, Vivien, Merenciano, Miriam, González, Josefa·2017·Trends in Genetics

Abstract

A relationship between transposable elements (TEs) and the eukaryotic stress response was suggested in the first publications describing TEs. Since then, it has often been assumed that TEs are activated by stress, and that this activation is often beneficial for the organism. In recent years, the availability of new high-throughput experimental techniques has allowed further interrogation of the relationship between TEs and stress. By reviewing the recent literature, we conclude that although there is evidence for a beneficial effect of TE activation under stress conditions, the relationship between TEs and the eukaryotic stress response is quite complex.

Overview

Integrity signals

Registry

Crossref · 10.1016/j.tig.2017.08.007

Cites

3 of 3 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 3 references

Research works printed but not linked: 74

  1. Wicker, 2007, A unified classification system for eukaryotic transposable elements, Nat. Rev. Genet., 8, 973, 10.1038/nrg2165 · DOI
  2. Hua-Van, 2011, The struggle for life of the genome’s selfish architects, Biol. Direct, 6, 19, 10.1186/1745-6150-6-19 · DOI
  3. Dej, 1998, A hotspot for the Drosophila gypsy retroelement in the ovo locus, Nucleic Acids Res., 26, 4019, 10.1093/nar/26.17.4019 · DOI
  4. Nefedova, 2017, Mechanisms of LTR-retroelement transposition: lessons from Drosophila melanogaster, Viruses, 9, 10.3390/v9040081 · DOI
  5. Gonzalez, 2012, Evolution of genome content: population dynamics of transposable elements in flies and humans, Methods Mol. Biol., 855, 361, 10.1007/978-1-61779-582-4_13 · DOI
  6. Izsvak, 2009, Efficient stable gene transfer into human cells by the Sleeping Beauty transposon vectors, Methods, 49, 287, 10.1016/j.ymeth.2009.07.001 · DOI
  7. Rebollo, 2012, Transposable elements: an abundant and natural source of regulatory sequences for host genes, Annu. Rev. Genet., 46, 21, 10.1146/annurev-genet-110711-155621 · DOI
  8. Elbarbary, 2016, Retrotransposons as regulators of gene expression, Science, 351, aac7247, 10.1126/science.aac7247 · DOI
  9. Mieczkowski, 2006, Recombination between retrotransposons as a source of chromosome rearrangements in the yeast Saccharomyces cerevisiae, DNA Repair (Amst), 5, 1010, 10.1016/j.dnarep.2006.05.027 · DOI
  10. Lee, 2015, Role of transposable elements in genomic rearrangement, evolution, gene regulation and epigenetics in primates, Genes Genet. Syst., 90, 245, 10.1266/ggs.15-00016 · DOI
  11. Zamudio, 2010, Transposable elements in the mammalian germline: a comfortable niche or a deadly trap?, Heredity (Edinb), 105, 92, 10.1038/hdy.2010.53 · DOI
  12. Magwire, 2011, Successive increases in the resistance of Drosophila to viral infection through a transposon insertion followed by a duplication, PLoS Genet., 7, e1002337, 10.1371/journal.pgen.1002337 · DOI
  13. Guio, 2014, The transposable element Bari-Jheh mediates oxidative stress response in Drosophila, Mol. Ecol., 23, 2020, 10.1111/mec.12711 · DOI
  14. Mateo, 2014, A transposable element insertion confers xenobiotic resistance in Drosophila, PLoS Genet., 10, e1004560, 10.1371/journal.pgen.1004560 · DOI
  15. Aminetzach, 2005, Pesticide resistance via transposition-mediated adaptive gene truncation in Drosophila, Science, 309, 764, 10.1126/science.1112699 · DOI
  16. Daborn, 2002, A single p450 allele associated with insecticide resistance in Drosophila, Science, 297, 2253, 10.1126/science.1074170 · DOI
  17. Ellison, 2013, Dosage compensation via transposable element mediated rewiring of a regulatory network, Science, 342, 846, 10.1126/science.1239552 · DOI
  18. Emera, 2012, Transformation of a transposon into a derived prolactin promoter with function during human pregnancy, Proc. Natl. Acad. Sci. U. S. A., 109, 11246, 10.1073/pnas.1118566109 · DOI
  19. Choi, 2017, Deficiency of microRNA miR-34a expands cell fate potential in pluripotent stem cells, Science, 355, eaag1927, 10.1126/science.aag1927 · DOI
  20. McClintock, 1984, The significance of responses of the genome to challenge, Science, 226, 792, 10.1126/science.15739260 · DOI
  21. Capy, 2000, Stress and transposable elements: co-evolution or useful parasites?, Heredity (Edinb), 85, 101, 10.1046/j.1365-2540.2000.00751.x · DOI
  22. Fablet, 2011, Evolvability, epigenetics and transposable elements, Biomol. Concepts, 2, 333, 10.1515/BMC.2011.035 · DOI
  23. Chenais, 2012, The impact of transposable elements on eukaryotic genomes: from genome size increase to genetic adaptation to stressful environments, Gene, 509, 7, 10.1016/j.gene.2012.07.042 · DOI
  24. Casacuberta, 2013, The impact of transposable elements in environmental adaptation, Mol. Ecol., 22, 1503, 10.1111/mec.12170 · DOI
  25. Negi, 2016, Moving through the stressed genome: emerging regulatory roles for transposons in plant stress response, Front. Plant Sci., 7, 1448, 10.3389/fpls.2016.01448 · DOI
  26. Rey, 2016, Adaptation to global change: a transposable element-epigenetics perspective, Trends Ecol. Evol., 31, 514, 10.1016/j.tree.2016.03.013 · DOI
  27. Cowley, 2013, Transposable elements re-wire and fine-tune the transcriptome, PLoS Genet., 9, e1003234, 10.1371/journal.pgen.1003234 · DOI
  28. de Souza, 2013, Exaptation of transposable elements into novel cis-regulatory elements: is the evidence always strong?, Mol. Biol. Evol., 30, 1239, 10.1093/molbev/mst045 · DOI
  29. Elliott, 2014, Conceptual and empirical challenges of ascribing functions to transposable elements, Am. Nat., 184, 14, 10.1086/676588 · DOI
  30. Brunet, 2015, Multilevel selection theory and the evolutionary functions of transposable elements, Genome Biol. Evol., 7, 2445, 10.1093/gbe/evv152 · DOI
  31. Rahman, 2015, Unique transposon landscapes are pervasive across Drosophila melanogaster genomes, Nucleic Acids Res., 43, 10655, 10.1093/nar/gkv1193 · DOI
  32. Rishishwar, 2017, Population and clinical genetics of human transposable elements in the (post) genomic era, Mob. Genet. Elements, 7, 1, 10.1080/2159256X.2017.1280116 · DOI
  33. Voronova, 2014, Stress-induced transcriptional activation of retrotransposon-like sequences in the Scots pine (Pinus sylvestris L.) genome, Tree Genet. Genomes, 10, 937, 10.1007/s11295-014-0733-1 · DOI
  34. Bundo, 2014, Increased l1 retrotransposition in the neuronal genome in schizophrenia, Neuron, 81, 306, 10.1016/j.neuron.2013.10.053 · DOI
  35. Ryan, 2016, Hsp90 and physiological stress are linked to autonomous transposon mobility and heritable genetic change in nematodes, Genome Biol. Evol., 8, 3794
  36. Hummel, 2017, The evolutionary capacitor HSP90 buffers the regulatory effects of mammalian endogenous retroviruses, Nat. Struct. Mol. Biol., 24, 234, 10.1038/nsmb.3368 · DOI
  37. Zovoilis, 2016, Destabilization of B2 RNA by EZH2 activates the stress response, Cell, 167, 10.1016/j.cell.2016.11.041 · DOI
  38. Romero-Soriano, 2016, Expression of the retrotransposon Helena Reveals a complex pattern of TE deregulation in Drosophila hybrids, PLoS One, 11, e0147903, 10.1371/journal.pone.0147903 · DOI
  39. Shpyleva, 2017, Overexpression of LINE-1 retrotransposons in autism brain, Mol. Neurobiol.
  40. Huang, 2017, EARE-1, a transcriptionally active Ty1/copia-like retrotransposon has colonized the genome of Excoecaria agallocha through horizontal transfer, Front. Plant Sci., 8, 45
  41. Hunter, 2012, Acute stress and hippocampal histone H3 lysine 9 trimethylation, a retrotransposon silencing response, Proc. Natl. Acad. Sci. U. S. A., 109, 17657, 10.1073/pnas.1215810109 · DOI
  42. Secco, 2015, Stress induced gene expression drives transient DNA methylation changes at adjacent repetitive elements, Elife, 4, e09343, 10.7554/eLife.09343 · DOI
  43. Lapp, 2016, The dynamic genome: transposons and environmental adaptation in the nervous system, Epigenomics, 8, 237, 10.2217/epi.15.107 · DOI
  44. Barah, 2013, Genome scale transcriptional response diversity among ten ecotypes of Arabidopsis thaliana during heat stress, Front. Plant Sci., 4, 532, 10.3389/fpls.2013.00532 · DOI
  45. Trivedi, 2014, Morphine induces redox-based changes in global DNA methylation and retrotransposon transcription by inhibition of excitatory amino acid transporter type 3-mediated cysteine uptake, Mol. Pharmacol., 85, 747, 10.1124/mol.114.091728 · DOI
  46. Menees, 1996, Cellular stress inhibits transposition of the yeast retrovirus-like element Ty3 by a ubiquitin-dependent block of virus-like particle formation, Proc. Natl. Acad. Sci. U. S. A., 93, 5629, 10.1073/pnas.93.11.5629 · DOI
  47. Le, 2014, DNA demethylases target promoter transposable elements to positively regulate stress responsive genes in Arabidopsis, Genome Biol., 15, 458, 10.1186/s13059-014-0458-3 · DOI
  48. Makarevitch, 2015, Transposable elements contribute to activation of maize genes in response to abiotic stress, PLoS Genet., 11, e1004915, 10.1371/journal.pgen.1004915 · DOI
  49. Persson, 2016, Regulating retrotransposon activity through the use of alternative transcription start sites, EMBO Rep., 17, 753, 10.15252/embr.201541866 · DOI
  50. Forestan, 2016, Stress-induced and epigenetic-mediated maize transcriptome regulation study by means of transcriptome reannotation and differential expression analysis, Sci. Rep., 6, 10.1038/srep30446 · DOI
  51. Bouttier, 2016, Alu repeats as transcriptional regulatory platforms in macrophage responses to M. tuberculosis infection, Nucleic Acids Res., 44, 10571, 10.1093/nar/gkw782 · DOI
  52. Garg, 2015, Divergent DNA methylation patterns associated with gene expression in rice cultivars with contrasting drought and salinity stress response, Sci. Rep., 5, 14922, 10.1038/srep14922 · DOI
  53. Zhao, 2014, Identification of a retroelement from the resurrection plant Boea hygrometrica that confers osmotic and alkaline tolerance in Arabidopsis thaliana, PLoS One, 9, e98098, 10.1371/journal.pone.0098098 · DOI
  54. Merenciano, 2016, Multiple independent retroelement insertions in the promoter of a stress response gene have variable molecular and functional effects in Drosophila, PLoS Genet., 12, e1006249, 10.1371/journal.pgen.1006249 · DOI
  55. Mao, 2015, A transposable element in a NAC gene is associated with drought tolerance in maize seedlings, Nat. Commun., 6, 8326, 10.1038/ncomms9326 · DOI
  56. Ullastres, 2015, Exploring the phenotypic space and the evolutionary history of a natural mutation in Drosophila melanogaster, Mol. Biol. Evol., 32, 1800, 10.1093/molbev/msv061 · DOI
  57. Wang, 2017, Transposable elements (TEs) contribute to stress-related long intergenic noncoding RNAs in plants, Plant J., 90, 133, 10.1111/tpj.13481 · DOI
  58. Chuong, 2016, Regulatory activities of transposable elements: from conflicts to benefits, Nat. Rev. Genet., 18, 71, 10.1038/nrg.2016.139 · DOI · Paper page
  59. Scott, 2016, A hot L1 retrotransposon evades somatic repression and initiates human colorectal cancer, Genome Res., 26, 745, 10.1101/gr.201814.115 · DOI
  60. Kondo, 2003, Enrichment for histone H3 lysine 9 methylation at Alu repeats in human cells, J. Biol. Chem., 278, 27658, 10.1074/jbc.M304072200 · DOI
  61. Sentmanat, 2012, Ectopic assembly of heterochromatin in Drosophila melanogaster triggered by transposable elements, Proc. Natl. Acad. Sci. U. S. A., 109, 14104, 10.1073/pnas.1207036109 · DOI
  62. Friedli, 2015, The developmental control of transposable elements and the evolution of higher species, Annu. Rev. Cell Dev. Biol., 31, 429, 10.1146/annurev-cellbio-100814-125514 · DOI
  63. Martens, 2005, The profile of repeat-associated histone lysine methylation states in the mouse epigenome, EMBO J., 24, 800, 10.1038/sj.emboj.7600545 · DOI
  64. Clapier, 2009, The biology of chromatin remodeling complexes, Annu. Rev. Biochem., 78, 273, 10.1146/annurev.biochem.77.062706.153223 · DOI
  65. Bartholomew, 2014, Regulating the chromatin landscape: structural and mechanistic perspectives, Annu. Rev. Biochem., 83, 671, 10.1146/annurev-biochem-051810-093157 · DOI
  66. Girard, 2008, Conserved themes in small-RNA-mediated transposon control, Trends Cell Biol., 18, 136, 10.1016/j.tcb.2008.01.004 · DOI
  67. Law, 2010, Establishing, maintaining and modifying DNA methylation patterns in plants and animals, Nat. Rev. Genet., 11, 204, 10.1038/nrg2719 · DOI
  68. Mahfouz, 2010, RNA-directed DNA methylation: mechanisms and functions, Plant Signal. Behav., 5, 806, 10.4161/psb.5.7.11695 · DOI
  69. Wheeler, 2013, Small RNAs, big impact: small RNA pathways in transposon control and their effect on the host stress response, Chromosome Res., 21, 587, 10.1007/s10577-013-9394-4 · DOI
  70. He, 2014, Non-coding RNA transcription and RNA-directed DNA methylation in Arabidopsis, Mol. Plant, 7, 1406, 10.1093/mp/ssu075 · DOI
  71. Toth, 2016, The piRNA pathway guards the germline genome against transposable elements, Adv. Exp. Med. Biol., 886, 51, 10.1007/978-94-017-7417-8_4 · DOI
  72. Clark, 2014, Piwi proteins and piRNAs step onto the systems biology stage, Adv. Exp. Med. Biol., 825, 159, 10.1007/978-1-4939-1221-6_5 · DOI
  73. Buchon, 2006, RNAi: a defensive RNA-silencing against viruses and transposable elements, Heredity (Edinb), 96, 195, 10.1038/sj.hdy.6800789 · DOI
  74. Obbard, 2009, The evolution of RNAi as a defence against viruses and transposable elements, Philos. Trans. R. Soc. Lond. B Biol. Sci., 364, 99, 10.1098/rstb.2008.0168 · DOI

Cited by

Sorted by citations

Metadata

Authors
Horváth, V., Merenciano, M., & González, J.
Venue
Trends in Genetics
Publisher
Elsevier BV
Published
2017-11
Volume
33
Issue
11
Pages
832-841
ISSN
0168-9525
Cited by
219
References
3
Language
en
Funders
  • European Research Council
  • Spanish Ministry of Economy and Competitivity

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