CoChat
Sign Up
Cited by 1,489

The DOI matches its Crossref record; 20 of the 20 references it cites were found in a registry or an index.

Regulatory activities of transposable elements: from conflicts to benefits

Chuong, Edward B., Elde, Nels C., Feschotte, Cédric·2017·Nature Reviews Genetics
DOI 10.1038/nrg.2016.139PMC PMC5498291
Open this paper in CoChat — free account

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 · 10.1038/nrg.2016.139

Cites

20 of 20 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

Research works printed but not linked: 165

  1. McClintock, B. Intranuclear systems controlling gene action and mutation. Brookhaven Symp. Biol. 8, 58–74 (1956).
  2. Britten, R. J. & Kohne, D. E. Repeated sequences in DNA. Hundreds of thousands of copies of DNA sequences have been incorporated into the genomes of higher organisms. Science 161, 529–540 (1968). · DOI
  3. Britten, R. J. & Davidson, E. H. Repetitive and non-repetitive DNA sequences and a speculation on the origins of evolutionary novelty. Q. Rev. Biol. 46, 111–138 (1971). · DOI · Paper page
  4. Orgel, L. E., Crick, F. H. & Sapienza, C. Selfish DNA. Nature 288, 645–646 (1980). · DOI
  5. Doolittle, W. F. & Sapienza, C. Selfish genes, the phenotype paradigm and genome evolution. Nature 284, 601–603 (1980). · DOI
  6. Lynch, M. The Origins of Genome Architecture (Sinauer Associates Incorporated, 2007).
  7. Mager, D. L. & Stoye, J. P. Mammalian endogenous retroviruses. Microbiol. Spectr. 3, MDNA3-0009-2014 (2015). · DOI
  8. Richardson, S. R. et al. The influence of LINE-1 and SINE retrotransposons on mammalian genomes. Microbiol. Spectr. 3, MDNA3-0061-2014 (2015). · DOI
  9. Speek, M. Antisense promoter of human L1 retrotransposon drives transcription of adjacent cellular genes. Mol. Cell. Biol. 21, 1973–1985 (2001). · DOI
  10. Lander, E. S. et al. Initial sequencing and analysis of the human genome. Nature 409, 860–921 (2001). · DOI · Paper page
  11. Feschotte, C., Zhang, X. & Wessler, S. R. Mobile DNA II (eds Craig, N. L., Craigie, R., Gellert, M. & Lambowitz, A. M.) 1147–1158 (ASM Press, 2002). · DOI · Paper page
  12. Faulkner, G. J. et al. The regulated retrotransposon transcriptome of mammalian cells. Nat. Genet. 41, 563–571 (2009). · DOI
  13. Lisch, D. How important are transposons for plant evolution? Nat. Rev. Genet. 14, 49–61 (2013). · DOI
  14. Feschotte, C. Transposable elements and the evolution of regulatory networks. Nat. Rev. Genet. 9, 397–405 (2008). · DOI
  15. Bourque, G. et al. Evolution of the mammalian transcription factor binding repertoire via transposable elements. Genome Res. 18, 1752–1762 (2008). · DOI
  16. Roman, A. C., Benitez, D. A., Carvajal-Gonzalez, J. M. & Fernandez-Salguero, P. M. Genome-wide B1 retrotransposon binds the transcription factors dioxin receptor and Slug and regulates gene expression in vivo. Proc. Natl Acad. Sci. USA 105, 1632–1637 (2008). · DOI
  17. Kunarso, G. et al. Transposable elements have rewired the core regulatory network of human embryonic stem cells. Nat. Genet. 42, 631–634 (2010). · DOI
  18. Testori, A. et al. The role of transposable elements in shaping the combinatorial interaction of transcription factors. BMC Genomics 13, 400 (2012). · DOI
  19. Sundaram, V. et al. Widespread contribution of transposable elements to the innovation of gene regulatory networks. Genome Res. 24, 1963–1976 (2014). This is the most comprehensive assessment so far of the contribution of TEs to the genomic landscape of transcription factor binding in human and mouse cells. · DOI · Paper page
  20. Teng, L., He, B., Gao, P., Gao, L. & Tan, K. Discover context-specific combinatorial transcription factor interactions by integrating diverse ChIP-Seq data sets. Nucleic Acids Res. 42, e24 (2014). · DOI
  21. Thompson, P. J., Macfarlan, T. S. & Lorincz, M. C. Long terminal repeats: from parasitic elements to building blocks of the transcriptional regulatory repertoire. Mol. Cell 62, 766–776 (2016). · DOI
  22. Lisch, D. & Damon, L. Regulation of transposable elements in maize. Curr. Opin. Plant Biol. 15, 511–516 (2012). · DOI
  23. Gerdes, P., Richardson, S. R., Mager, D. L. & Faulkner, G. J. Transposable elements in the mammalian embryo: pioneers surviving through stealth and service. Genome Biol. 17, 100 (2016). · DOI · Paper page
  24. Kazazian, H. H. Jr. Mobile DNA transposition in somatic cells. BMC Biol. 9, 62 (2011). · DOI
  25. Perrat, P. N. et al. Transposition-driven genomic heterogeneity in the Drosophila brain. Science 340, 91–95 (2013). · DOI
  26. Levin, H. L. & Moran, J. V. Dynamic interactions between transposable elements and their hosts. Nat. Rev. Genet. 12, 615–627 (2011). · DOI · Paper page
  27. Liu, S. et al. Mu transposon insertion sites and meiotic recombination events co-localize with epigenetic marks for open chromatin across the maize genome. PLoS Genet. 5, e1000733 (2009). · DOI
  28. Naito, K. et al. Unexpected consequences of a sudden and massive transposon amplification on rice gene expression. Nature 461, 1130–1134 (2009). · DOI
  29. Leem, Y.-E. et al. Retrotransposon Tf1 is targeted to Pol II promoters by transcription activators. Mol. Cell 30, 98–107 (2008). · DOI
  30. Liao, G.-C., Rehm, E. J. & Rubin, G. M. Insertion site preferences of the P transposable element in Drosophila melanogaster. Proc. Natl Acad. Sci. 97, 3347–3351 (2000). · DOI
  31. Schröder, A. R. W. et al. HIV-1 integration in the human genome favors active genes and local hotspots. Cell 110, 521–529 (2002). · DOI · Paper page
  32. Friedli, M. & Trono, D. The developmental control of transposable elements and the evolution of higher species. Annu. Rev. Cell Dev. Biol. 31, 429–451 (2015). · DOI
  33. Wolf, G., Greenberg, D. & Macfarlan, T. S. Spotting the enemy within: targeted silencing of foreign DNA in mammalian genomes by the Krüppel-associated box zinc finger protein family. Mob. DNA 6, 17 (2015). · DOI
  34. Rebollo, R., Farivar, S. & Mager, D. L. C-GATE — catalogue of genes affected by transposable elements. Mob. DNA 3, 9 (2012). · DOI
  35. Hirsch, C. D. & Springer, N. M. Transposable element influences on gene expression in plants. Biochim. Biophys. Acta http://dx.doi.org/10.1016/j.bbagrm.2016.05.010 (2016). · DOI
  36. Elbarbary, R. A., Lucas, B. A. & Maquat, L. E. Retrotransposons as regulators of gene expression. Science 351, aac7247 (2016). · DOI
  37. Macfarlan, T. S. et al. Embryonic stem cell potency fluctuates with endogenous retrovirus activity. Nature 487, 57–63 (2012). References 17 and 38 are seminal studies hinting at the recurrent regulatory co-option of ERVs in mammalian early development. · DOI · Paper page
  38. Batut, P., Dobin, A., Plessy, C., Carninci, P. & Gingeras, T. R. High-fidelity promoter profiling reveals widespread alternative promoter usage and transposon-driven developmental gene expression. Genome Res. 23, 169–180 (2013). · DOI
  39. Jacques, P.-É., Jeyakani, J. & Bourque, G. The majority of primate-specific regulatory sequences are derived from transposable elements. PLoS Genet. 9, e1003504 (2013). · DOI
  40. Wang, T. et al. Species-specific endogenous retroviruses shape the transcriptional network of the human tumor suppressor protein p53. Proc. Natl Acad. Sci. USA 104, 18613–18618 (2007). · DOI
  41. Van Bortle, K. & Corces, V. G. The role of chromatin insulators in nuclear architecture and genome function. Curr. Opin. Genet. Dev. 23, 212–218 (2013). · DOI
  42. Schmidt, D. et al. Waves of retrotransposon expansion remodel genome organization and CTCF binding in multiple mammalian lineages. Cell 148, 335–348 (2012). · DOI
  43. Crepaldi, L. et al. Binding of TFIIIC to sine elements controls the relocation of activity-dependent neuronal genes to transcription factories. PLoS Genet. 9, e1003699 (2013). · DOI
  44. Wang, J. et al. MIR retrotransposon sequences provide insulators to the human genome. Proc. Natl Acad. Sci. USA 112, E4428–E4437 (2015). References 45–47 show that SINEs frequently have properties of architectural elements partitioning the mammalian genome into distinct topological domains. · DOI
  45. Rao, S. S. P. et al. A 3D map of the human genome at kilobase resolution reveals principles of chromatin looping. Cell 159, 1665–1680 (2014). · DOI · Paper page
  46. Cournac, A., Koszul, R. & Mozziconacci, J. The 3D folding of metazoan genomes correlates with the association of similar repetitive elements. Nucleic Acids Res. 44, 245–255 (2016). · DOI
  47. Mateo, L., Ullastres, A. & Gonzalez, J. A transposable element insertion confers xenobiotic resistance in Drosophila. PLoS Genet. 10, e1004560 (2014). This is a meticulous investigation of the physiological effect of a TE insertion with adaptive regulatory effects in D. melanogaster. · DOI
  48. Lippman, Z. et al. Role of transposable elements in heterochromatin and epigenetic control. Nature 430, 471–476 (2004). · DOI · Paper page
  49. Rebollo, R. et al. Retrotransposon-induced heterochromatin spreading in the mouse revealed by insertional polymorphisms. PLoS Genet. 7, e1002301 (2011). · DOI
  50. de Souza, F. S. J., Franchini, L. F. & Rubinstein, M. Exaptation of transposable elements into novel cis-regulatory elements: is the evidence always strong? Mol. Biol. Evol. 30, 1239–1251 (2013). · DOI
  51. del Rosario, R. C. H., Rayan, N. A. & Shyam, P. Noncoding origins of anthropoid traits and a new null model of transposon functionalization. Genome Res. 24, 1469–1484 (2014). · DOI
  52. Brosius, J. & Gould, S. J. On 'genomenclature': a comprehensive (and respectful) taxonomy for pseudogenes and other 'junk DNA'. Proc. Natl Acad. Sci. USA 89, 10706–10710 (1992). · DOI
  53. Miller, W. J., McDonald, J. F. & Pinsker, W. Molecular domestication of mobile elements. Genetica 100, 261–270 (1997). · DOI
  54. Lowe, C. B. & Haussler, D. 29 mammalian genomes reveal novel exaptations of mobile elements for likely regulatory functions in the human genome. PLoS ONE 7, e43128 (2012). · DOI
  55. Bejerano, G. et al. A distal enhancer and an ultraconserved exon are derived from a novel retroposon. Nature 441, 87–90 (2006). · DOI
  56. Samstein, R. M., Josefowicz, S. Z., Arvey, A., Treuting, P. M. & Rudensky, A. Y. Extrathymic generation of regulatory T cells in placental mammals mitigates maternal–fetal conflict. Cell 150, 29–38 (2012). This is a careful study tracing the origination of an enhancer that is essential for extrathymic regulatory T cell differentiation to an ancient TE insertion that was co-opted in the common ancestor of placental mammals. · DOI
  57. Lam, D. D. et al. Partially redundant enhancers cooperatively maintain mammalian Pomc expression above a critical functional threshold. PLoS Genet. 11, e1004935 (2015). · DOI
  58. Notwell, J. H., Chung, T., Heavner, W. & Bejerano, G. A family of transposable elements co-opted into developmental enhancers in the mouse neocortex. Nat. Commun. 6, 6644 (2015). · DOI
  59. Nishihara, H. et al. Coordinately co-opted multiple transposable elements constitute an enhancer for wnt5a expression in the mammalian secondary palate. PLOS Genet. 12, e1006380 (2016). · DOI
  60. Ahituv, N. et al. Deletion of ultraconserved elements yields viable mice. PLoS Biol. 5, e234 (2007). · DOI
  61. Stone, E. A., Cooper, G. M. & Sidow, A. Trade-offs in detecting evolutionarily constrained sequence by comparative genomics. Annu. Rev. Genomics Hum. Genet. 6, 143–164 (2005). · DOI
  62. Boffelli, D. et al. Phylogenetic shadowing of primate sequences to find functional regions of the human genome. Science 299, 1391–1394 (2003). · DOI · Paper page
  63. Weirauch, M. T. & Hughes, T. R. Conserved expression without conserved regulatory sequence: the more things change, the more they stay the same. Trends Genet. 26, 66–74 (2010). · DOI
  64. Kapusta, A. & Feschotte, C. Volatile evolution of long noncoding RNA repertoires: mechanisms and biological implications. Trends Genet. 30, 439–452 (2014). · DOI
  65. Ting, C.-N., Rosenberg, M. P., Snow, C. M., Samuelson, L. C. & Meisler, M. H. Endogenous retroviral sequences are required for tissue-specific expression of a human salivary amylase gene. Genes Dev. 6, 1457–1465 (1992). · DOI
  66. Emera, D. & Wagner, G. P. Transformation of a transposon into a derived prolactin promoter with function during human pregnancy. Proc. Natl Acad. Sci. USA 109, 11246–11251 (2012). · DOI
  67. Gerlo, S., Davis, J. R. E., Mager, D. L. & Kooijman, R. Prolactin in man: a tale of two promoters. Bioessays 28, 1051–1055 (2006). · DOI
  68. Sasaki, T. et al. Possible involvement of SINEs in mammalian-specific brain formation. Proc. Natl Acad. Sci. USA 105, 4220–4225 (2008). · DOI
  69. Flemr, M. et al. A retrotransposon-driven dicer isoform directs endogenous small interfering RNA production in mouse oocytes. Cell 155, 807–816 (2013). This is a compelling study using TALEN editing to show the phenotypic importance of a lineage-specific TE insertion driving the emergence of an alternative protein isoform with a novel function. · DOI
  70. Ferreira, L. M. R. et al. A distant trophoblast-specific enhancer controls HLA-G expression at the maternal–fetal interface. Proc. Natl Acad. Sci. USA 113, 5364–5369 (2016). · DOI
  71. Studer, A., Zhao, Q., Ross-Ibarra, J. & Doebley, J. Identification of a functional transposon insertion in the maize domestication gene tb1. Nat. Genet. 43, 1160–1163 (2011). · DOI
  72. Butelli, E. et al. Retrotransposons control fruit-specific, cold-dependent accumulation of anthocyanins in blood oranges. Plant Cell 24, 1242–1255 (2012). · DOI
  73. Sun, W., Shen, Y.-H., Han, M.-J., Cao, Y.-F. & Zhang, Z. An adaptive transposable element insertion in the regulatory region of the EO gene in the domesticated silkworm, Bombyx mori. Mol. Biol. Evol. 31, 3302–3313 (2014). · DOI
  74. Klütsch, C. F. C. & de Caprona, M. D. C. The IGF1 small dog haplotype is derived from Middle Eastern grey wolves: a closer look at statistics, sampling, and the alleged Middle Eastern origin of small dogs. BMC Biol. 8, 119 (2010). · DOI
  75. Clark, L. A., Wahl, J. M., Rees, C. A. & Murphy, K. E. Retrotransposon insertion in SILV is responsible for merle patterning of the domestic dog. Proc. Natl Acad. Sci. USA 103, 1376–1381 (2006). · DOI
  76. David, V. A. et al. Endogenous retrovirus insertion in the KIT oncogene determines White and White spotting in domestic cats. G3 (Bethesda) 4, 1881–1891 (2014). · DOI
  77. Van't Hof, A. E. et al. The industrial melanism mutation in British peppered moths is a transposable element. Nature 534, 102–105 (2016). This is a classic example of environmental adaptation traced to a TE insertion with cis -regulatory effect. · DOI
  78. Swinnen, G., Goossens, A. & Pauwels, L. Lessons from domestication: targeting cis-regulatory elements for crop improvement. Trends Plant Sci. 21, 506–515 (2016). · DOI
  79. Sorrells, T. R. & Johnson, A. D. Making sense of transcription networks. Cell 161, 714–723 (2015). · DOI
  80. Chuong, E. B., Rumi, M. A. K., Soares, M. J. & Baker, J. C. Endogenous retroviruses function as species-specific enhancer elements in the placenta. Nat. Genet. 45, 325–329 (2013). · DOI · Paper page
  81. Chuong, E. B. Retroviruses facilitate the rapid evolution of the mammalian placenta. Bioessays 35, 853–861 (2013). · DOI
  82. Xie, M. et al. DNA hypomethylation within specific transposable element families associates with tissue-specific enhancer landscape. Nat. Genet. 45, 836–841 (2013). · DOI
  83. Lynch, V. J. et al. Ancient transposable elements transformed the uterine regulatory landscape and transcriptome during the evolution of mammalian pregnancy. Cell Rep. 10, 551–561 (2015). · DOI
  84. Dewannieux, M., Dupressoir, A., Harper, F., Pierron, G. & Heidmann, T. Identification of autonomous IAP LTR retrotransposons mobile in mammalian cells. Nat. Genet. 36, 534–539 (2004). · DOI
  85. Brady, T. et al. Integration target site selection by a resurrected human endogenous retrovirus. Genes Dev. 23, 633–642 (2009). · DOI
  86. Fontanillas, P., Hartl, D. L. & Reuter, M. Genome organization and gene expression shape the transposable element distribution in the Drosophila melanogaster euchromatin. PLoS Genet. 3, e210 (2007). · DOI
  87. McVicker, G. & Green, P. Genomic signatures of germline gene expression. Genome Res. 20, 1503–1511 (2010). · DOI
  88. Zhang, Y., Ying, Z. & Mager, D. L. Gene properties and chromatin state influence the accumulation of transposable elements in genes. PLoS ONE 7, e30158 (2012). · DOI
  89. Sironi, M. et al. Gene function and expression level influence the insertion/fixation dynamics of distinct transposon families in mammalian introns. Genome Biol. 7, R120 (2006). · DOI
  90. Simons, C., Pheasant, M., Makunin, I. V. & Mattick, J. S. Transposon-free regions in mammalian genomes. Genome Res. 16, 164–172 (2006). · DOI
  91. Kvikstad, E. M. & Makova, K. D. The (r)evolution of SINE versus LINE distributions in primate genomes: sex chromosomes are important. Genome Res. 20, 600–613 (2010). · DOI
  92. Zhang, Y., Romanish, M. T. & Mager, D. L. Distributions of transposable elements reveal hazardous zones in mammalian introns. PLoS Comput. Biol. 7, e1002046 (2011). · DOI
  93. Nellåker, C. et al. The genomic landscape shaped by selection on transposable elements across 18 mouse strains. Genome Biol. 13, R45 (2012). · DOI
  94. Campos-Sánchez, R., Cremona, M. A., Pini, A., Chiaromonte, F. & Makova, K. D. Integration and fixation preferences of human and mouse endogenous retroviruses uncovered with functional data analysis. PLoS Comput. Biol. 12, e1004956 (2016). · DOI
  95. Ellison, C. E. & Bachtrog, D. Dosage compensation via transposable element mediated rewiring of a regulatory network. Science 342, 846–850 (2013). · DOI
  96. Lyon, M. F. X-Chromosome inactivation: a repeat hypothesis. Cytogenet. Cell Genet. 80, 133–137 (1998). · DOI
  97. Chow, J. C. et al. LINE-1 activity in facultative heterochromatin formation during X chromosome inactivation. Cell 141, 956–969 (2010). · DOI
  98. Belancio, V. P., Roy-Engel, A. M. & Deininger, P. L. All y'all need to know 'bout retroelements in cancer. Semin. Cancer Biol. 20, 200–210 (2010). · DOI
  99. Sudmant, P. H. et al. An integrated map of structural variation in 2,504 human genomes. Nature 526, 75–81 (2015). · DOI · Paper page
  100. Sekar, A. et al. Schizophrenia risk from complex variation of complement component 4. Nature 530, 177–183 (2016). · DOI · Paper page
  101. Leboyer, M., Tamouza, R., Charron, D., Faucard, R. & Perron, H. Human endogenous retrovirus type W (HERV-W) in schizophrenia: a new avenue of research at the gene–environment interface. World J. Biol. Psychiatry 14, 80–90 (2013). · DOI
  102. Rodic´, N. et al. Long interspersed element-1 protein expression is a hallmark of many human cancers. Am. J. Pathol. 184, 1280–1286 (2014). · DOI
  103. Kassiotis, G. Endogenous retroviruses and the development of cancer. J. Immunol. 192, 1343–1349 (2014). · DOI
  104. van der Kuyl, A. C. HIV infection and HERV expression: a review. Retrovirology 9, 6 (2012). · DOI
  105. Mourier, T., Nielsen, L. P., Hansen, A. J. & Willerslev, E. Transposable elements in cancer as a by-product of stress-induced evolvability. Front. Genet. 5, 156 (2014). · DOI
  106. Rodic´, N. & Burns, K. H. Long interspersed element-1 (LINE-1): passenger or driver in human neoplasms? PLoS Genet. 9, e1003402 (2013). · DOI
  107. Magiorkinis, G., Belshaw, R. & Katzourakis, A. 'There and back again': revisiting the pathophysiological roles of human endogenous retroviruses in the post-genomic era. Philos. Trans. R. Soc. B 368, 20120504 (2013). · DOI
  108. Lee, E. et al. Landscape of somatic retrotransposition in human cancers. Science 337, 967–971 (2012). · DOI · Paper page
  109. Rodic´, N. et al. Retrotransposon insertions in the clonal evolution of pancreatic ductal adenocarcinoma. Nat. Med. 21, 1060–1064 (2015). · DOI
  110. Doucet-O'Hare, T. T. et al. LINE-1 expression and retrotransposition in Barrett's esophagus and esophageal carcinoma. Proc. Natl Acad. Sci. USA 112, E4894–E4900 (2015). · DOI
  111. Shukla, R. et al. Endogenous retrotransposition activates oncogenic pathways in hepatocellular carcinoma. Cell 153, 101–111 (2013). · DOI
  112. Scott, E. C. et al. A hot L1 retrotransposon evades somatic repression and initiates human colorectal cancer. Genome Res. 26, 745–755 (2016). · DOI
  113. Duperray, A. et al. Inflammatory response of endothelial cells to a human endogenous retrovirus associated with multiple sclerosis is mediated by TLR4. Int. Immunol. 27, 545–553 (2015). · DOI
  114. Conrad, B. et al. A human endogenous retroviral superantigen as candidate autoimmune gene in type I diabetes. Cell 90, 303–313 (1997). · DOI
  115. Yu, P. The potential role of retroviruses in autoimmunity. Immunol. Rev. 269, 85–99 (2015). · DOI
  116. Hurst, T. P. & Magiorkinis, G. Activation of the innate immune response by endogenous retroviruses. J. Gen. Virol. 96, 1207–1218 (2015). · DOI
  117. Volkman, H. E. & Stetson, D. B. The enemy within: endogenous retroelements and autoimmune disease. Nat. Immunol. 15, 415–422 (2014). · DOI · Paper page
  118. Lock, F. E. et al. Distinct isoform of FABP7 revealed by screening for retroelement-activated genes in diffuse large B-cell lymphoma. Proc. Natl Acad. Sci. USA 111, E3534–E3543 (2014). · DOI
  119. Babaian, A. et al. Onco-exaptation of an endogenous retroviral LTR drives IRF5 expression in Hodgkin lymphoma. Oncogene 35, 2542–2546 (2016). References 134–136 provide clear instances in which the derepression of LTR elements leads to the activation of proto-oncogenes in human lymphoma. · DOI · Paper page
  120. Babaian, A. & Mager, D. L. Endogenous retroviral promoter exaptation in human cancer. Mob. DNA in press.
  121. Hashimoto, K. et al. CAGE profiling of ncRNAs in hepatocellular carcinoma reveals widespread activation of retroviral LTR promoters in virus-induced tumors. Genome Res. 25, 1812–1824 (2015). · DOI · Paper page
  122. Flockhart, R. J. et al. BRAFV600E remodels the melanocyte transcriptome and induces BANCR to regulate melanoma cell migration. Genome Res. 22, 1006–1014 (2012). · DOI · Paper page
  123. Gibb, E. A. et al. Activation of an endogenous retrovirus-associated long non-coding RNA in human adenocarcinoma. Genome Med. 7, 22 (2015). · DOI
  124. Ong-Abdullah, M. et al. Loss of Karma transposon methylation underlies the mantled somaclonal variant of oil palm. Nature 525, 533–537 (2015). This is a striking case of epigenetic derepression of a TE associated with a deleterious phenotype that has long plagued the palm oil industry. · DOI
  125. Man, S. M. et al. Critical role for the DNA sensor AIM2 in stem cell proliferation and cancer. Cell 162, 45–58 (2015). · DOI
  126. Man, S. M., Karki, R. & Kanneganti, T.-D. AIM2 inflammasome in infection, cancer, and autoimmunity: role in DNA sensing, inflammation, and innate immunity. Eur. J. Immunol. 46, 269–280 (2016). · DOI · Paper page
  127. Woerner, S. M. et al. The putative tumor suppressor AIM2 is frequently affected by different genetic alterations in microsatellite unstable colon cancers. Genes Chromosomes Cancer 46, 1080–1089 (2007). · DOI
  128. Villar, D. et al. Enhancer evolution across 20 mammalian species. Cell 160, 554–566 (2015). · DOI · Paper page
  129. Emera, D., Yin, J., Reilly, S. K., Gockley, J. & Noonan, J. P. Origin and evolution of developmental enhancers in the mammalian neocortex. Proc. Natl Acad. Sci. USA 113, E2617–E2626 (2016). · DOI
  130. Casacuberta, E. & González, J. The impact of transposable elements in environmental adaptation. Mol. Ecol. 22, 1503–1517 (2013). · DOI
  131. Quadrana, L. et al. The Arabidopsis thaliana mobilome and its impact at the species level. eLife 5, e15716 (2016). · DOI
  132. Feng, G., Leem, Y.-E. & Levin, H. L. Transposon integration enhances expression of stress response genes. Nucleic Acids Res. 41, 775–789 (2013). · DOI
  133. Barroso-Batista, J. et al. The first steps of adaptation of Escherichia coli to the gut are dominated by soft sweeps. PLoS Genet. 10, e1004182 (2014). · DOI
  134. Reilly, M. T., Faulkner, G. J., Dubnau, J., Ponomarev, I. & Gage, F. H. The role of transposable elements in health and diseases of the central nervous system. J. Neurosci. 33, 17577–17586 (2013). · DOI · Paper page
  135. Goke, J. et al. Dynamic transcription of distinct classes of endogenous retroviral elements marks specific populations of early human embryonic cells. Cell Stem Cell 16, 135–141 (2015). · DOI
  136. Grow, E. J. et al. Intrinsic retroviral reactivation in human preimplantation embryos and pluripotent cells. Nature 522, 221–225 (2015). This study reports that the HERV-K family is precisely activated during early human development and expresses proteins promoting the formation of retroviral particles and potentially modulating embryonic gene expression. · DOI
  137. Fort, A. et al. Deep transcriptome profiling of mammalian stem cells supports a regulatory role for retrotransposons in pluripotency maintenance. Nat. Genet. 46, 558–566 (2014). · DOI
  138. Wang, J. et al. Primate-specific endogenous retrovirus-driven transcription defines naive-like stem cells. Nature 516, 405–409 (2014). · DOI
  139. Santoni, F. A., Guerra, J. & Luban, J. HERV-H RNA is abundant in human embryonic stem cells and a precise marker for pluripotency. Retrovirology 9, 111 (2012). · DOI
  140. Ohnuki, M. et al. Dynamic regulation of human endogenous retroviruses mediates factor-induced reprogramming and differentiation potential. Proc. Natl Acad. Sci. USA 111, 12426–12431 (2014). · DOI
  141. Loewer, S. et al. Large intergenic non-coding RNA-RoR modulates reprogramming of human induced pluripotent stem cells. Nat. Genet. 42, 1113–1117 (2010). · DOI
  142. Wang, Y. et al. Endogenous miRNA sponge lincRNA-RoR regulates Oct4, Nanog, and Sox2 in human embryonic stem cell self-renewal. Dev. Cell 25, 69–80 (2013). · DOI
  143. Lu, X. et al. The retrovirus HERVH is a long noncoding RNA required for human embryonic stem cell identity. Nat. Struct. Mol. Biol. 21, 423–425 (2014). · DOI
  144. Durruthy-Durruthy, J. et al. The primate-specific noncoding RNA HPAT5 regulates pluripotency during human preimplantation development and nuclear reprogramming. Nat. Genet. 48, 44–52 (2015). · DOI
  145. Izsvák, Z., Wang, J., Singh, M., Mager, D. L. & Hurst, L. D. Pluripotency and the endogenous retrovirus HERVH: conflict or serendipity? Bioessays 38, 109–117 (2016). · DOI
  146. Casola, C., Hucks, D. & Feschotte, C. Convergent domestication of pogo-like transposases into centromere-binding proteins in fission yeast and mammals. Mol. Biol. Evol. 25, 29–41 (2007). · DOI
  147. Cornelis, G. et al. Retroviral envelope gene captures and syncytin exaptation for placentation in marsupials. Proc. Natl Acad. Sci. USA 112, E487–E496 (2015). · DOI
  148. Gong, C. & Maquat, L. E. lncRNAs transactivate STAU1-mediated mRNA decay by duplexing with 3' UTRs via Alu elements. Nature 470, 284–288 (2011). · DOI
  149. Hu, S.-B. et al. Protein arginine methyltransferase CARM1 attenuates the paraspeckle-mediated nuclear retention of mRNAs containing IRAlus. Genes Dev. 29, 630–645 (2015). · DOI
  150. Shen, S. et al. Widespread establishment and regulatory impact of Alu exons in human genes. Proc. Natl Acad. Sci. USA 108, 2837–2842 (2011). · DOI
  151. Roberts, J. T., Cardin, S. E. & Borchert, G. M. Burgeoning evidence indicates that microRNAs were initially formed from transposable element sequences. Mob. Genet. Elements 4, e29255 (2014). · DOI
  152. Liang, D. & Wilusz, J. E. Short intronic repeat sequences facilitate circular RNA production. Genes Dev. 28, 2233–2247 (2014). · DOI
  153. Johnson, R. & Guigó, R. The RIDL hypothesis: transposable elements as functional domains of long noncoding RNAs. RNA 20, 959–976 (2014). · DOI
  154. Spengler, R. M., Oakley, C. K. & Davidson, B. L. Functional microRNAs and target sites are created by lineage-specific transposition. Hum. Mol. Genet. 23, 1783–1793 (2014). · DOI
  155. Creasey, K. M. et al. miRNAs trigger widespread epigenetically activated siRNAs from transposons in Arabidopsis. Nature 508, 411–415 (2014). · DOI
  156. Kelley, D. R., Hendrickson, D. G., Tenen, D. & Rinn, J. L. Transposable elements modulate human RNA abundance and splicing via specific RNA-protein interactions. Genome Biol. 15, 537 (2014). · DOI
  157. González, J., Lenkov, K., Lipatov, M., Michael Macpherson, J. & Petrov, D. A. High rate of recent transposable element-induced adaptation in Drosophila melanogaster. PLoS Biol. 6, e251 (2008). · DOI
  158. Ellison, C. E. & Bachtrog, D. Non-allelic gene conversion enables rapid evolutionary change at multiple regulatory sites encoded by transposable elements. eLife 4, e05899 (2015). This study reveals a gene conversion-like process by which cis -regulatory sequences derived from related TE copies may be rapidly ameliorated to fine-tune their binding affinity for a trans -regulatory protein. · DOI
  159. Romanish, M. T., Lock, W. M., van de Lagemaat, L. N., Dunn, C. A. & Mager, D. L. Repeated recruitment of LTR retrotransposons as promoters by the anti-apoptotic locus NAIP during mammalian mvolution. PLoS Genet. 3, e10 (2007). · DOI
  160. Tuan, D. & Pi, W. In human β-globin gene locus, ERV-9 LTR retrotransposon interacts with and activates β-but not γ-globin gene. Blood 124, 2686 (2014). · DOI
  161. Lunyak, V. V. et al. Developmentally regulated activation of a SINE B2 repeat as a domain boundary in organogenesis. Science 317, 248–251 (2007). · DOI
  162. Emera, D. et al. Convergent evolution of endometrial prolactin expression in primates, mice, and elephants through the independent recruitment of transposable elements. Mol. Biol. Evol. 29, 239–247 (2012). · DOI
  163. Chung, H. et al. Cis-regulatory elements in the Accord retrotransposon result in tissue-specific expression of the Drosophila melanogaster insecticide resistance gene Cyp6g1. Genetics 175, 1071–1077 (2007). · DOI
  164. Guio, L., Barrón, M. G. & González, J. The transposable element Bari-Jheh mediates oxidative stress response in Drosophila. Mol. Ecol. 23, 2020–2030 (2014). · DOI
  165. Ding, Y. et al. Natural courtship song variation caused by an intronic retroelement in an ion channel gene. Nature 536, 329–332 (2016). This study uses an elegant mix of genetic mapping and genome editing to show that a polymorphic TE insertion within an intron of an ion channel gene is responsible for driving courtship song variation in Drosophila simulans. · DOI

Cited by

Sorted by citations

See all 1,489

Metadata

Authors
Chuong, E. B., Elde, N. C., & Feschotte, C.
Venue
Nature Reviews Genetics
Publisher
Springer Science and Business Media LLC
Published
2016-11-21
Volume
18
Issue
2
Pages
71-86
ISSN
  • 1471-0056
  • 1471-0064
DOI
10.1038/nrg.2016.139
PMC
PMC5498291
Cited by
1,489
References
20
Language
en
Licence
www.springer.com/tdm (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