CoChat
Sign Up
Cited by 18Chromosomal and Genetic VariationsGenomics and Chromatin DynamicsEpigenetics and DNA Methylation

All Quiet on the TE Front? The Role of Chromatin in Transposable Element Silencing

Open access
Di Stefano, Luisa·2022·Cells
DOI 10.3390/cells11162501PMC PMC9406493
Open this paper in CoChat — free accountOpen PDF

Abstract

Transposable elements (TEs) are mobile genetic elements that constitute a sizeable portion of many eukaryotic genomes. Through their mobility, they represent a major source of genetic variation, and their activation can cause genetic instability and has been linked to aging, cancer and neurodegenerative diseases. Accordingly, tight regulation of TE transcription is necessary for normal development. Chromatin is at the heart of TE regulation; however, we still lack a comprehensive understanding of the precise role of chromatin marks in TE silencing and how chromatin marks are established and maintained at TE loci. In this review, I discuss evidence documenting the contribution of chromatin-associated proteins and histone marks in TE regulation across different species with an emphasis on Drosophila and mammalian systems.

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 · 10.3390/cells11162501

Cites

11 of 11 references verified0 citation errors · 0 not checkable

Statistics

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.

Cites

Flagged first, then by citations

Research works printed but not linked: 209

  1. [1]Kazazian H.H. Jr. Wong C. Youssoufian H. Scott A.F. Phillips D.G. Antonarakis S.E. Haemophilia A resulting from de novo insertion of L1 sequences represents a novel mechanism for mutation in man Nature 1988 332 164 166 10.1038/332164a0 2831458 · DOI
  2. [2]Hancks D.C. Kazazian H.H. Jr. Roles for retrotransposon insertions in human disease Mob. DNA 2016 7 9 10.1186/s13100-016-0065-9 27158268 PMC4859970 · DOI · Paper page
  3. [3]Robberecht C. Voet T. Zamani Esteki M. Nowakowska B.A. Vermeesch J.R. Nonallelic homologous recombination between retrotransposable elements is a driver of de novo unbalanced translocations Genome Res. 2013 23 411 418 10.1101/gr.145631.112 23212949 PMC3589530 · DOI
  4. [4]Naville M. Henriet S. Warren I. Sumic S. Reeve M. Volff J.N. Chourrout D. Massive Changes of Genome Size Driven by Expansions of Non-autonomous Transposable Elements Curr. Biol. 2019 29 1161 1168.e6 10.1016/j.cub.2019.01.080 30880010 · DOI
  5. [5]Shao F. Han M. Peng Z. Evolution and diversity of transposable elements in fish genomes Sci. Rep. 2019 9 15399 10.1038/s41598-019-51888-1 31659260 PMC6817897 · DOI
  6. [6]Serrato-Capuchina A. Matute D.R. The Role of Transposable Elements in Speciation Genes 2018 9 254 10.3390/genes9050254 PMC5977194 29762547 · DOI
  7. [7]Bourque G. Burns K.H. Gehring M. Gorbunova V. Seluanov A. Hammell M. Imbeault M. Izsvak Z. Levin H.L. Macfarlan T.S. Ten things you should know about transposable elements Genome Biol. 2018 19 199 10.1186/s13059-018-1577-z 30454069 PMC6240941 · DOI · Paper page
  8. [8]Mi S. Lee X. Li X. Veldman G.M. Finnerty H. Racie L. LaVallie E. Tang X.Y. Edouard P. Howes S. Syncytin is a captive retroviral envelope protein involved in human placental morphogenesis Nature 2000 403 785 789 10.1038/35001608 10693809 · DOI
  9. [9]Percharde M. Lin C.J. Yin Y. Guan J. Peixoto G.A. Bulut-Karslioglu A. Biechele S. Huang B. Shen X. Ramalho-Santos M. A LINE1-Nucleolin Partnership Regulates Early Development and ESC Identity Cell 2018 174 391 405.e19 10.1016/j.cell.2018.05.043 29937225 PMC6046266 · DOI
  10. [10]Goerner-Potvin P. Bourque G. Computational tools to unmask transposable elements Nat. Rev. Genet. 2018 19 688 704 10.1038/s41576-018-0050-x 30232369 · DOI
  11. [12]Gualdrini F. Polletti S. Simonatto M. Prosperini E. Pileri F. Natoli G. H3K9 trimethylation in active chromatin restricts the usage of functional CTCF sites in SINE B2 repeats Genes Dev. 2022 36 414 432 10.1101/gad.349282.121 35361678 PMC9067402 · DOI
  12. [13]Kaaij L.J.T. Mohn F. van der Weide R.H. de Wit E. Buhler M. The ChAHP Complex Counteracts Chromatin Looping at CTCF Sites that Emerged from SINE Expansions in Mouse Cell 2019 178 1437 1451.e14 10.1016/j.cell.2019.08.007 31491387 · DOI
  13. [14]Sentmanat M.F. Elgin S.C. Ectopic assembly of heterochromatin in Drosophila melanogaster triggered by transposable elements Proc. Natl. Acad. Sci. USA 2012 109 14104 14109 10.1073/pnas.1207036109 22891327 PMC3435190 · DOI
  14. [15]Etchegaray E. Naville M. Volff J.N. Haftek-Terreau Z. Transposable element-derived sequences in vertebrate development Mob. DNA 2021 12 1 10.1186/s13100-020-00229-5 33407840 PMC7786948 · DOI
  15. [16]Ninova M. Chen Y.A. Godneeva B. Rogers A.K. Luo Y. Fejes Toth K. Aravin A.A. Su(var)2-10 and the SUMO Pathway Link piRNA-Guided Target Recognition to Chromatin Silencing Mol. Cell 2020 77 556 570.e556 10.1016/j.molcel.2019.11.012 31901446 PMC7007863 · DOI
  16. [17]Lee Y.C.G. Karpen G.H. Pervasive epigenetic effects of Drosophila euchromatic transposable elements impact their evolution Elife 2017 6 e25762 10.7554/eLife.25762 28695823 PMC5505702 · DOI
  17. [18]Kapitonov V.V. Koonin E.V. Evolution of the RAG1-RAG2 locus: Both proteins came from the same transposon Biol. Direct 2015 10 20 10.1186/s13062-015-0055-8 25928409 PMC4411706 · DOI
  18. [19]Lanciano S. Cristofari G. Measuring and interpreting transposable element expression Nat. Rev. Genet. 2020 21 721 736 10.1038/s41576-020-0251-y 32576954 · DOI
  19. [21]Wicker T. Sabot F. Hua-Van A. Bennetzen J.L. Capy P. Chalhoub B. Flavell A. Leroy P. Morgante M. Panaud O. A unified classification system for eukaryotic transposable elements Nat. Rev. Genet. 2007 8 973 982 10.1038/nrg2165 17984973 · DOI
  20. [22]Makalowski W. Gotea V. Pande A. Makalowska I. Transposable Elements: Classification, Identification, and Their Use As a Tool For Comparative Genomics Methods Mol. Biol. 2019 1910 177 207 10.1007/978-1-4939-9074-0_6 31278665 · DOI · Paper page
  21. [24]Sheng W. LaFleur M.W. Nguyen T.H. Chen S. Chakravarthy A. Conway J.R. Li Y. Chen H. Yang H. Hsu P.-H. LSD1 Ablation Stimulates Anti-tumor Immunity and Enables Checkpoint Blockade Cell 2018 174 549 563.e19 10.1016/j.cell.2018.05.052 29937226 PMC6063761 · DOI · Paper page
  22. [25]Aravin A.A. Naumova N.M. Tulin A.V. Vagin V.V. Rozovsky Y.M. Gvozdev V.A. Double-stranded RNA-mediated silencing of genomic tandem repeats and transposable elements in the D. melanogaster germline Curr. Biol. 2001 11 1017 1027 10.1016/S0960-9822(01)00299-8 11470406 · DOI
  23. [26]Aravin A.A. Sachidanandam R. Bourc’His D. Schaefer C. Pezic D. Toth K.F. Bestor T. Hannon G.J. A piRNA Pathway Primed by Individual Transposons Is Linked to De Novo DNA Methylation in Mice Mol. Cell 2008 31 785 799 10.1016/j.molcel.2008.09.003 18922463 PMC2730041 · DOI
  24. [27]Vagin V.V. Sigova A. Li C. Seitz H. Gvozdev V. Zamore P.D. A Distinct Small RNA Pathway Silences Selfish Genetic Elements in the Germline Science 2006 313 320 324 10.1126/science.1129333 16809489 · DOI
  25. [28]Girard A. Sachidanandam R. Hannon G.J. Carmell M.A. A germline-specific class of small RNAs binds mammalian Piwi proteins Nature 2006 442 199 202 10.1038/nature04917 16751776 · DOI · Paper page
  26. [29]Lau N.C. Seto A.G. Kim J. Kuramochi-Miyagawa S. Nakano T. Bartel D.P. Kingston R.E. Characterization of the piRNA Complex from Rat Testes Science 2006 313 363 367 10.1126/science.1130164 16778019 · DOI
  27. [30]Aravin A. Gaidatzis D. Pfeffer S. Lagos-Quintana M. Landgraf P. Iovino N. Morris P. Brownstein M.J. Kuramochi-Miyagawa S. Nakano T. A novel class of small RNAs bind to MILI protein in mouse testes Nature 2006 442 203 207 10.1038/nature04916 16751777 · DOI · Paper page
  28. [31]Grivna S.T. Beyret E. Wang Z. Lin H. A novel class of small RNAs in mouse spermatogenic cells Genes Dev. 2006 20 1709 1714 10.1101/gad.1434406 16766680 PMC1522066 · DOI
  29. [32]Saito K. Nishida K.M. Mori T. Kawamura Y. Miyoshi K. Nagami T. Siomi H. Siomi M.C. Specific association of Piwi with rasiRNAs derived from retrotransposon and heterochromatic regions in the Drosophila genome Genes Dev. 2006 20 2214 2222 10.1101/gad.1454806 16882972 PMC1553205 · DOI
  30. [33]Houwing S. Kamminga L.M. Berezikov E. Cronembold D. Girard A. van den Elst H. Filippov D.V. Blaser H. Raz E. Moens C.B. A Role for Piwi and piRNAs in Germ Cell Maintenance and Transposon Silencing in Zebrafish Cell 2007 129 69 82 10.1016/j.cell.2007.03.026 17418787 · DOI
  31. [34]Watanabe T. Takeda A. Tsukiyama T. Mise K. Okuno T. Sasaki H. Minami N. Imai H. Identification and characterization of two novel classes of small RNAs in the mouse germline: Retrotransposon-derived siRNAs in oocytes and germline small RNAs in testes Genes Dev. 2006 20 1732 1743 10.1101/gad.1425706 16766679 PMC1522070 · DOI
  32. [35]Sienski G. Dönertas D. Brennecke J. Transcriptional Silencing of Transposons by Piwi and Maelstrom and Its Impact on Chromatin State and Gene Expression Cell 2012 151 964 980 10.1016/j.cell.2012.10.040 23159368 PMC3504300 · DOI
  33. [36]Le Thomas A. Rogers A.K. Webster A. Marinov G.K. Liao S.E. Perkins E.M. Hur J.K. Aravin A.A. Tóth K.F. Piwi induces piRNA-guided transcriptional silencing and establishment of a repressive chromatin state Genes Dev. 2013 27 390 399 10.1101/gad.209841.112 23392610 PMC3589556 · DOI
  34. [37]Rozhkov N.V. Hammell M. Hannon G.J. Multiple roles for Piwi in silencing Drosophila transposons Genes Dev. 2013 27 400 412 10.1101/gad.209767.112 23392609 PMC3589557 · DOI
  35. [38]Yamashiro H. Siomi M.C. PIWI-Interacting RNA in Drosophila: Biogenesis, Transposon Regulation, and Beyond Chem Rev. 2018 118 4404 4421 10.1021/acs.chemrev.7b00393 29281264 · DOI
  36. [39]Kuramochi-Miyagawa S. Watanabe T. Gotoh K. Totoki Y. Toyoda A. Ikawa M. Asada N. Kojima K. Yamaguchi Y. Ijiri T.W. DNA methylation of retrotransposon genes is regulated by Piwi family members MILI and MIWI2 in murine fetal testes Genes Dev. 2008 22 908 917 10.1101/gad.1640708 18381894 PMC2279202 · DOI
  37. [40]Pezic D. Manakov S.A. Sachidanandam R. Aravin A.A. piRNA pathway targets active LINE1 elements to establish the repressive H3K9me3 mark in germ cells Genes Dev. 2014 28 1410 1428 10.1101/gad.240895.114 24939875 PMC4083086 · DOI
  38. [41]Molaro A. Malik H.S. Hide and seek: How chromatin-based pathways silence retroelements in the mammalian germline Curr. Opin. Genet. Dev. 2016 37 51 58 10.1016/j.gde.2015.12.001 26821364 PMC4914476 · DOI
  39. [42]Onishi R. Yamanaka S. Siomi M.C. piRNA- and siRNA-mediated transcriptional repression in Drosophila, mice, and yeast: New insights and biodiversity EMBO Rep. 2021 22 e53062 10.15252/embr.202153062 34347367 PMC8490990 · DOI
  40. [43]Ozata D.M. Gainetdinov I. Zoch A. O’Carroll D. Zamore P.D. PIWI-interacting RNAs: Small RNAs with big functions Nat. Rev. Genet. 2018 20 89 108 10.1038/s41576-018-0073-3 30446728 · DOI
  41. [44]Czech B. Munafo M. Ciabrelli F. Eastwood E.L. Fabry M.H. Kneuss E. Hannon G.J. piRNA-Guided Genome Defense: From Biogenesis to Silencing Annu. Rev. Genet. 2018 52 131 157 10.1146/annurev-genet-120417-031441 30476449 PMC10784713 · DOI
  42. [46]Greenberg M.V.C. Bourc’His D. The diverse roles of DNA methylation in mammalian development and disease Nat. Rev. Mol. Cell Biol. 2019 20 590 607 10.1038/s41580-019-0159-6 31399642 · DOI
  43. [47]Jeltsch A. Phylogeny of Methylomes Science 2010 328 837 838 10.1126/science.1190738 20466912 · DOI
  44. [48]Dor Y. Cedar H. Principles of DNA methylation and their implications for biology and medicine Lancet 2018 392 777 786 10.1016/S0140-6736(18)31268-6 30100054 · DOI · Paper page
  45. [49]Tsukahara S. Kobayashi A. Kawabe A. Mathieu O. Miura A. Kakutani T. Bursts of retrotransposition reproduced in Arabidopsis Nature 2009 461 423 426 10.1038/nature08351 19734880 · DOI
  46. [50]Lippman Z. Gendrel A.-V. Black M. Vaughn M. Dedhia N. McCombie W.R. Lavine K. Mittal V. May B. Kasschau K.D. Role of transposable elements in heterochromatin and epigenetic control Nature 2004 430 471 476 10.1038/nature02651 15269773 · DOI
  47. [51]Zhou Y. Cambareri E.B. Kinsey J.A. DNA methylation inhibits expression and transposition of the Neurospora Tad retrotransposon Mol. Genet. Genom. 2001 265 748 754 10.1007/s004380100472 11459196 · DOI
  48. [52]Chernyavskaya Y. Mudbhary R. Tokarz D. Jacob V. Gopinath S. Zhang C. Sun X. Wang S. Magnani E. Madakashira B.P. Loss of DNA methylation in zebrafish embryos activates retrotransposons to trigger antiviral signaling Development 2017 144 2925 2939 10.1242/dev.147629 28698226 PMC5592811 · DOI
  49. [53]Walsh C. Chaillet J.R. Bestor T.H. Transcription of IAP endogenous retroviruses is constrained by cytosine methylation Nat. Genet. 1998 20 116 117 10.1038/2413 9771701 · DOI · Paper page
  50. [54]Barau J. Teissandier A. Zamudio N. Roy S. Nalesso V. Hérault Y. Guillou F. Bourc’His D. The DNA methyltransferase DNMT3C protects male germ cells from transposon activity Science 2016 354 909 912 10.1126/science.aah5143 27856912 · DOI
  51. [55]Haubold B. Wiehe T. How repetitive are genomes? BMC Bioinformat. 2006 7 541 10.1186/1471-2105-7-541 PMC1769404 17187668 · DOI
  52. [56]Cuellar T.L. Herzner A.-M. Zhang X. Goyal Y. Watanabe C. Friedman B.A. Janakiraman V. Durinck S. Stinson J. Arnott D. Silencing of retrotransposons by SETDB1 inhibits the interferon response in acute myeloid leukemia J. Cell Biol. 2017 216 3535 3549 10.1083/jcb.201612160 28887438 PMC5674883 · DOI
  53. [57]Sanchez-Luque F.J. Kempen M.-J.H. Gerdes P. Vargas-Landin D.B. Richardson S.R. Troskie R.-L. Jesuadian J.S. Cheetham S.W. Carreira P.E. Salvador-Palomeque C. LINE-1 Evasion of Epigenetic Repression in Humans Mol. Cell 2019 75 590 604.e12 10.1016/j.molcel.2019.05.024 31230816 · DOI · Paper page
  54. [59]Burns K.H. Transposable elements in cancer Nat. Cancer 2017 17 415 424 10.1038/nrc.2017.35 28642606 · DOI · Paper page
  55. [60]Lander E.S. Linton L.M. Birren B. Nusbaum C. Zody M.C. Baldwin J. Devon K. Dewar K. Doyle M. FitzHugh W. Initial sequencing and analysis of the human genome Nature 2001 409 860 921 Correction in Nature 2001, 412, 565–566; Erratum in Nature 2001, 7, 720 10.1038/35057062 11237011 · DOI · Paper page
  56. [61]Roulois D. Loo Yau H. Singhania R. Wang Y. Danesh A. Shen S.Y. Han H. Liang G. Jones P.A. Pugh T.J. DNA-Demethylating Agents Target Colorectal Cancer Cells by Inducing Viral Mimicry by Endogenous Transcripts Cell 2015 162 961 973 10.1016/j.cell.2015.07.056 26317465 PMC4843502 · DOI · Paper page
  57. [62]Wu T.P. Wang T. Seetin M.G. Lai Y. Zhu S. Lin K. Liu Y. Byrum S.D. Mackintosh S.G. Zhong M. DNA methylation on N6-adenine in mammalian embryonic stem cells Nature 2016 532 329 333 10.1038/nature17640 27027282 PMC4977844 · DOI · Paper page
  58. [63]Yao B. Cheng Y. Wang Z. Li Y. Chen L. Huang L. Zhang W. Chen D. Wu H. Tang B. DNA N6-methyladenine is dynamically regulated in the mouse brain following environmental stress Nat. Commun. 2017 8 1 10 10.1038/s41467-017-01195-y 29066820 PMC5654764 · DOI
  59. [64]Zhu S. Beaulaurier J. Deikus G. Wu T.P. Strahl M. Hao Z. Luo G. Gregory J. Chess A. He C. Mapping and characterizing N6-methyladenine in eukaryotic genomes using single-molecule real-time sequencing Genome Res. 2018 28 1067 1078 10.1101/gr.231068.117 29764913 PMC6028124 · DOI
  60. [65]Deniz Ö. Frost J.M. Branco M.R. Regulation of transposable elements by DNA modifications Nat. Rev. Genet. 2019 20 417 431 10.1038/s41576-019-0106-6 30867571 · DOI
  61. [66]Jansz N. DNA methylation dynamics at transposable elements in mammals Essays Biochem. 2019 63 677 689 10.1042/ebc20190039 31654072 · DOI
  62. [67]Allshire R. Madhani H.D. Ten principles of heterochromatin formation and function Nat. Rev. Mol. Cell Biol. 2017 19 229 244 10.1038/nrm.2017.119 29235574 PMC6822695 · DOI
  63. [68]Barnes C.E. English D.M. Cowley S.M. Acetylation & Co: An expanding repertoire of histone acylations regulates chromatin and transcription Essays Biochem. 2019 63 97 107 10.1042/ebc20180061 30940741 PMC6484784 · DOI
  64. [69]Talbert P.B. Henikoff S. The Yin and Yang of Histone Marks in Transcription Annu. Rev. Genom. Hum. Genet. 2021 22 147 170 10.1146/annurev-genom-120220-085159 33781079 · DOI
  65. [71]Matsui T. Leung D. Miyashita H. Maksakova I.A. Miyachi H. Kimura H. Tachibana M. Lorincz M.C. Shinkai Y. Proviral silencing in embryonic stem cells requires the histone methyltransferase ESET Nature 2010 464 927 931 10.1038/nature08858 20164836 · DOI
  66. [72]Zhao Z. Shilatifard A. Epigenetic modifications of histones in cancer Genome Biol. 2019 20 1 16 10.1186/s13059-019-1870-5 31747960 PMC6868810 · DOI
  67. [73]modENCODE Consortium Roy S. Ernst J. Kharchenko P.V. Kheradpour P. Negre N. Eaton M.L. Landolin J.M. Bristow C.A. Ma L. Identification of functional elements and regulatory circuits by Drosophila modENCODE Science 2010 330 1787 1797 10.1126/science.1198374 21177974 PMC3192495 · DOI
  68. [74]Strahl B.D. Allis C.D. The language of covalent histone modifications Nature 2000 403 41 45 10.1038/47412 10638745 · DOI · Paper page
  69. [75]Jenuwein T. Allis C.D. Translating the histone code Science 2001 293 1074 1080 10.1126/science.1063127 11498575 · DOI · Paper page
  70. [76]Fu K. Bonora G. Pellegrini M. Interactions between core histone marks and DNA methyltransferases predict DNA methylation patterns observed in human cells and tissues Epigenetics 2019 15 272 282 10.1080/15592294.2019.1666649 31509087 PMC7028327 · DOI
  71. [77]Li Y. Chen X. Lu C. The interplay between DNA and histone methylation: Molecular mechanisms and disease implications EMBO Rep. 2021 22 e51803 10.15252/embr.202051803 33844406 PMC8097341 · DOI · Paper page
  72. [78]Walter M. Teissandier A. Pérez-Palacios R. Bourc’His D. An epigenetic switch ensures transposon repression upon dynamic loss of DNA methylation in embryonic stem cells eLife 2016 5 e11418 10.7554/eLife.11418 26814573 PMC4769179 · DOI · Paper page
  73. [79]Berrens R.V. Andrews S. Spensberger D. Santos F. Dean W. Gould P. Sharif J. Olova N. Chandra T. Koseki H. An endosiRNA-Based Repression Mechanism Counteracts Transposon Activation during Global DNA Demethylation in Embryonic Stem Cells Cell Stem Cell 2017 21 694 703.e7 10.1016/j.stem.2017.10.004 29100015 PMC5678422 · DOI
  74. [80]Molaro A. Falciatori I. Hodges E. Aravin A.A. Marran K. Rafii S. McCombie W.R. Smith A.D. Hannon G.J. Two waves of de novo methylation during mouse germ cell development Genes Dev. 2014 28 1544 1549 10.1101/gad.244350.114 25030694 PMC4102761 · DOI
  75. [81]Fadloun A. Eid A. Torres-Padilla M.E. Mechanisms and dynamics of heterochromatin formation during mammalian development: Closed paths and open questions Curr. Top. Dev. Biol. 2013 104 1 45 10.1016/B978-0-12-416027-9.00001-2 23587237 · DOI
  76. [82]Soares L.M. He P.C. Chun Y. Suh H. Kim T. Buratowski S. Determinants of Histone H3K4 Methylation Patterns Mol. Cell 2017 68 773 785.e6 10.1016/j.molcel.2017.10.013 29129639 PMC5706784 · DOI · Paper page
  77. [83]Rada-Iglesias A. Is H3K4me1 at enhancers correlative or causative? Nat. Genet. 2018 50 4 5 10.1038/s41588-017-0018-3 29273804 · DOI
  78. [84]Wang Z. Zang C. Rosenfeld J.A. Schones D.E. Barski A. Cuddapah S. Cui K. Roh T.-Y. Peng W. Zhang M.Q. Combinatorial patterns of histone acetylations and methylations in the human genome Nat. Genet. 2008 40 897 903 10.1038/ng.154 18552846 PMC2769248 · DOI · Paper page
  79. [85]Bernstein B.E. Mikkelsen T.S. Xie X. Kamal M. Huebert D.J. Cuff J. Fry B. Meissner A. Wernig M. Plath K. A Bivalent Chromatin Structure Marks Key Developmental Genes in Embryonic Stem Cells Cell 2006 125 315 326 10.1016/j.cell.2006.02.041 16630819 · DOI · Paper page
  80. [86]Nicetto D. Donahue G. Jain T. Peng T. Sidoli S. Sheng L. Montavon T. Becker J.S. Grindheim J.M. Blahnik K. H3K9me3-heterochromatin loss at protein-coding genes enables developmental lineage specification Science 2019 363 294 297 10.1126/science.aau0583 30606806 PMC6664818 · DOI
  81. [87]Methot S.P. Padeken J. Brancati G. Zeller P. Delaney C.E. Gaidatzis D. Kohler H. van Oudenaarden A. Großhans H. Gasser S.M. H3K9me selectively blocks transcription factor activity and ensures differentiated tissue integrity Nature 2021 23 1163 1175 10.1038/s41556-021-00776-w PMC8572725 34737442 · DOI
  82. [88]Bannister A.J. Zegerman P. Partridge J.F. Miska E.A. Thomas J.O. Allshire R.C. Kouzarides T. Selective recognition of methylated lysine 9 on histone H3 by the HP1 chromo domain Nature 2001 410 120 124 10.1038/35065138 11242054 · DOI · Paper page
  83. [89]Lachner M. O’Carroll D. Rea S. Mechtler K. Jenuwein T. Methylation of histone H3 lysine 9 creates a binding site for HP1 proteins Nature 2001 410 116 120 10.1038/35065132 11242053 · DOI · Paper page
  84. [90]Nakayama J.-I. Rice J.C. Strahl B.D. Allis C.D. Grewal S.I.S. Role of Histone H3 Lysine 9 Methylation in Epigenetic Control of Heterochromatin Assembly Science 2001 292 110 113 10.1126/science.1060118 11283354 · DOI · Paper page
  85. [91]Grewal S.I.S. Jia S. Heterochromatin revisited Nat. Rev. Genet. 2007 8 35 46 10.1038/nrg2008 17173056 · DOI · Paper page
  86. [92]Elgin S.C. Reuter G. Position-Effect Variegation, Heterochromatin Formation, and Gene Silencing in Drosophila Cold Spring Harb. Perspect. Biol. 2013 5 a017780 10.1101/cshperspect.a017780 23906716 PMC3721279 · DOI · Paper page
  87. [93]Montavon T. Shukeir N. Erikson G. Engist B. Onishi-Seebacher M. Ryan D. Musa Y. Mittler G. Meyer A.G. Genoud C. Complete loss of H3K9 methylation dissolves mouse heterochromatin organization Nat. Commun. 2021 12 1 16 10.1038/s41467-021-24532-8 34272378 PMC8285382 · DOI
  88. [94]Padeken J. Zeller P. Towbin B. Katic I. Kalck V. Methot S.P. Gasser S.M. Synergistic lethality between BRCA1 and H3K9me2 loss reflects satellite derepression Genes Dev. 2019 33 436 451 10.1101/gad.322495.118 30804228 PMC6446544 · DOI
  89. [95]Penke T.J. McKay D.J. Strahl B.D. Matera A.G. Duronio R.J. Direct interrogation of the role of H3K9 in metazoan heterochromatin function Genes Dev. 2016 30 1866 1880 10.1101/gad.286278.116 27566777 PMC5024684 · DOI · Paper page
  90. [96]Tachibana M. Sugimoto K. Nozaki M. Ueda J. Ohta T. Ohki M. Fukuda M. Takeda N. Niida H. Kato H. G9a histone methyltransferase plays a dominant role in euchromatic histone H3 lysine 9 methylation and is essential for early embryogenesis Genes Dev. 2002 16 1779 1791 10.1101/gad.989402 12130538 PMC186403 · DOI
  91. [98]Agger K. Christensen J. Cloos P.A. Helin K. The emerging functions of histone demethylases Curr. Opin. Genet. Dev. 2008 18 159 168 10.1016/j.gde.2007.12.003 18281209 · DOI
  92. [99]Cloos P.A. Christensen J. Agger K. Helin K. Erasing the methyl mark: Histone demethylases at the center of cellular differentiation and disease Genes Dev. 2008 22 1115 1140 10.1101/gad.1652908 18451103 PMC2732404 · DOI
  93. [100]Nottke A. Colaiácovo M.P. Shi Y. Developmental roles of the histone lysine demethylases Development 2009 136 879 889 10.1242/dev.020966 19234061 PMC2692332 · DOI
  94. [101]Metzger E. Wissmann M. Yin N. Müller J.M. Schneider R. Peters A.H.F.M. Günther T. Buettner R. Schüle R. LSD1 demethylates repressive histone marks to promote androgen-receptor-dependent transcription Nature 2005 437 436 439 10.1038/nature04020 16079795 · DOI
  95. [102]Zeller P. Padeken J. van Schendel R. Kalck V. Tijsterman M. Gasser S.M. Histone H3K9 methylation is dispensable for Caenorhabditis elegans development but suppresses RNA:DNA hybrid-associated repeat instability Nat. Genet. 2016 48 1385 1395 10.1038/ng.3672 27668659 · DOI · Paper page
  96. [103]Jacobs F.M. Greenberg D. Nguyen N. Haeussler M. Ewing A.D. Katzman S. Paten B. Salama S.R. Haussler D. An evolutionary arms race between KRAB zinc-finger genes ZNF91/93 and SVA/L1 retrotransposons Nature 2014 516 242 245 10.1038/nature13760 25274305 PMC4268317 · DOI · Paper page
  97. [104]Ecco G. Cassano M. Kauzlaric A. Duc J. Coluccio A. Offner S. Imbeault M. Rowe H.M. Turelli P. Trono D. Transposable Elements and Their KRAB-ZFP Controllers Regulate Gene Expression in Adult Tissues Dev. Cell 2016 36 611 623 10.1016/j.devcel.2016.02.024 27003935 PMC4896391 · DOI
  98. [105]Tan X. Xu X. Elkenani M. Smorag L. Zechner U. Nolte J. Engel W. Pantakani D.K. Zfp819, a novel KRAB-zinc finger protein, interacts with KAP1 and functions in genomic integrity maintenance of mouse embryonic stem cells Stem Cell Res. 2013 11 1045 1059 10.1016/j.scr.2013.07.006 23954693 · DOI
  99. [107]Friedman J.R. Fredericks W.J. Jensen D.E. Speicher D.W. Huang X.P. Neilson E.G. Rauscher F.J. KAP-1, a novel corepressor for the highly conserved KRAB repression domain Genes Dev. 1996 10 2067 2078 10.1101/gad.10.16.2067 8769649 · DOI
  100. [108]Peng H. Begg G.E. Harper S.L. Friedman J.R. Speicher D.W. Rauscher F.J. Biochemical Analysis of the Kruppel-associated Box (KRAB) Transcriptional Repression Domain J. Biol. Chem. 2000 275 18000 18010 10.1074/jbc.M001499200 10748030 · DOI
  101. [110]Ecco G. Rowe H.M. Trono D. A Large-Scale Functional Screen to Identify Epigenetic Repressors of Retrotransposon Expression Transposons Retrotransposons 2016 1400 403 417 10.1007/978-1-4939-3372-3_25 26895067 · DOI
  102. [112]Ivanov A.V. Peng H. Yurchenko V. Yap K.L. Negorev D.G. Schultz D.C. Psulkowski E. Fredericks W.J. White D.E. Maul G.G. PHD Domain-Mediated E3 Ligase Activity Directs Intramolecular Sumoylation of an Adjacent Bromodomain Required for Gene Silencing Mol. Cell 2007 28 823 837 10.1016/j.molcel.2007.11.012 18082607 PMC4348069 · DOI · Paper page
  103. [113]Rowe H.M. Friedli M. Offner S. Verp S. Mesnard D. Marquis J. Aktas T. Trono D. De novo DNA methylation of endogenous retroviruses is shaped by KRAB-ZFPs/KAP1 and ESET Development 2013 140 519 529 10.1242/dev.087585 23293284 PMC4892343 · DOI
  104. [114]Tchasovnikarova I.A. Timms R.T. Douse C.H. Roberts R.C. Dougan G. Kingston R.E. Modis Y. Lehner P.J. Hyperactivation of HUSH complex function by Charcot-Marie-Tooth disease mutation in MORC2 Nat. Genet. 2017 49 1035 1044 10.1038/ng.3878 28581500 PMC5493197 · DOI
  105. [115]Tchasovnikarova I.A. Timms R.T. Matheson N.J. Wals K. Antrobus R. Göttgens B. Dougan G. Dawson M.A. Lehner P.J. Epigenetic silencing by the HUSH complex mediates position-effect variegation in human cells Science 2015 348 1481 1485 10.1126/science.aaa7227 26022416 PMC4487827 · DOI
  106. [116]Robbez-Masson L. Tie C.H.C. Conde L. Tunbak H. Husovsky C. Tchasovnikarova I.A. Timms R.T. Herrero J. Lehner P.J. Rowe H.M. The HUSH complex cooperates with TRIM28 to repress young retrotransposons and new genes Genome Res. 2018 28 836 845 10.1101/gr.228171.117 29728366 PMC5991525 · DOI · Paper page
  107. [117]Seczynska M. Bloor S. Cuesta S.M. Lehner P.J. Genome surveillance by HUSH-mediated silencing of intronless mobile elements Nature 2021 601 440 445 10.1038/s41586-021-04228-1 34794168 PMC8770142 · DOI
  108. [118]Akkouche A. Mugat B. Barckmann B. Varela-Chavez C. Li B. Raffel R. Pélisson A. Chambeyron S. Piwi Is Required during Drosophila Embryogenesis to License Dual-Strand piRNA Clusters for Transposon Repression in Adult Ovaries Mol. Cell 2017 66 411 419.e4 10.1016/j.molcel.2017.03.017 28457744 · DOI
  109. [119]Gu T. Elgin S.C.R. Maternal Depletion of Piwi, a Component of the RNAi System, Impacts Heterochromatin Formation in Drosophila PLoS Genet. 2013 9 e1003780 10.1371/journal.pgen.1003780 24068954 PMC3777992 · DOI
  110. [120]Yu Y. Gu J. Jin Y. Luo Y. Preall J.B. Ma J. Czech B. Hannon G.J. Panoramix enforces piRNA-dependent cotranscriptional silencing Science 2015 350 339 342 10.1126/science.aab0700 26472911 PMC4722808 · DOI
  111. [121]Dönertas D. Sienski G. Brennecke J. Drosophila Gtsf1 is an essential component of the Piwi-mediated transcriptional silencing complex Genes Dev. 2013 27 1693 1705 10.1101/gad.221150.113 23913922 PMC3744727 · DOI
  112. [122]Muerdter F. Guzzardo P.M. Gillis J. Luo Y. Yu Y. Chen C. Fekete R. Hannon G.J. A Genome-wide RNAi Screen Draws a Genetic Framework for Transposon Control and Primary piRNA Biogenesis in Drosophila Mol. Cell 2013 50 736 748 10.1016/j.molcel.2013.04.006 23665228 PMC3724422 · DOI
  113. [123]Ohtani H. Iwasaki Y.W. Shibuya A. Siomi H. Siomi M.C. Saito K. DmGTSF1 is necessary for Piwi-piRISC-mediated transcriptional transposon silencing in the Drosophila ovary Genes Dev. 2013 27 1656 1661 10.1101/gad.221515.113 23913921 PMC3744724 · DOI
  114. [124]Rangan P. Malone C.D. Navarro C. Newbold S.P. Hayes P.S. Sachidanandam R. Hannon G.J. Lehmann R. piRNA Production Requires Heterochromatin Formation in Drosophila Curr. Biol. 2011 21 1373 1379 10.1016/j.cub.2011.06.057 21820311 PMC3205116 · DOI
  115. [125]Osumi K. Sato K. Murano K. Siomi H. Siomi M.C. Essential roles of Windei and nuclear monoubiquitination of Eggless/SETDB1 in transposon silencing EMBO Rep. 2019 20 e48296 10.15252/embr.201948296 31576653 PMC6893296 · DOI
  116. [126]Andreev V.I. Yu C. Wang J. Schnabl J. Tirian L. Gehre M. Handler D. Duchek P. Novatchkova M. Baumgartner L. Panoramix SUMOylation on chromatin connects the piRNA pathway to the cellular heterochromatin machinery Nat. Struct. Mol. Biol. 2022 29 130 142 10.1038/s41594-022-00721-x 35173350 PMC11749891 · DOI
  117. [127]Klenov M.S. Lavrov S.A. Korbut A.P. Stolyarenko A.D. Yakushev E.Y. Reuter M. Pillai R.S. Gvozdev V.A. Impact of nuclear Piwi elimination on chromatin state in Drosophila melanogaster ovaries Nucleic Acids Res. 2014 42 6208 6218 10.1093/nar/gku268 24782529 PMC4041442 · DOI
  118. [128]Lepesant J.M.J. Iampietro C. Galeota E. Augé B. Aguirrenbengoa M. Mercé C. Chaubet C. Rocher V. Haenlin M. Waltzer L. A dual role of dLsd1 in oogenesis: Regulating developmental genes and repressing transposons Nucleic Acids Res. 2019 48 1206 1224 10.1093/nar/gkz1142 PMC7026653 31799607 · DOI
  119. [129]Yang F. Quan Z. Huang H. He M. Liu X. Cai T. Xi R. Ovaries absent links dLsd1 to HP1a for local H3K4 demethylation required for heterochromatic gene silencing eLife 2019 8 e40806 10.7554/eLife.40806 30648969 PMC6335052 · DOI
  120. [130]Mugat B. Nicot S. Varela-Chavez C. Jourdan C. Sato K. Basyuk E. Juge F. Siomi M.C. Pelisson A. Chambeyron S. The Mi-2 nucleosome remodeler and the Rpd3 histone deacetylase are involved in piRNA-guided heterochromatin formation Nat. Commun. 2020 11 2818 10.1038/s41467-020-16635-5 32499524 PMC7272611 · DOI
  121. [131]Zhao K. Cheng S. Miao N. Xu P. Lu X. Zhang Y. Wang M. Ouyang X. Yuan X. Liu W. A Pandas complex adapted for piRNA-guided transcriptional silencing and heterochromatin formation Nat. Cell Biol. 2019 21 1261 1272 10.1038/s41556-019-0396-0 31570835 · DOI
  122. [132]Fabry M.H. Ciabrelli F. Munafo M. Eastwood E.L. Kneuss E. Falciatori I. Falconio F.A. Hannon G.J. Czech B. piRNA-guided co-transcriptional silencing coopts nuclear export factors Elife 2019 8 e47999 10.7554/eLife.47999 31219034 PMC6677536 · DOI
  123. [133]Murano K. Iwasaki Y.W. Ishizu H. Mashiko A. Shibuya A. Kondo S. Adachi S. Suzuki S. Saito K. Natsume T. Nuclear RNA export factor variant initiates piRNA-guided co-transcriptional silencing EMBO J. 2019 38 e102870 10.15252/embj.2019102870 31368590 PMC6717896 · DOI
  124. [134]Batki J. Schnabl J. Wang J. Handler D. Andreev V.I. Stieger C.E. Novatchkova M. Lampersberger L. Kauneckaite K. Xie W. The nascent RNA binding complex SFiNX licenses piRNA-guided heterochromatin formation Nat. Struct. Mol. Biol. 2019 26 720 731 10.1038/s41594-019-0270-6 31384064 PMC6828549 · DOI
  125. [135]Eastwood E.L. Jara K.A. Bornelov S. Munafo M. Frantzis V. Kneuss E. Barbar E.J. Czech B. Hannon G.J. Dimerisation of the PICTS complex via LC8/Cut-up drives co-transcriptional transposon silencing in Drosophila Elife 2021 10 e65557 10.7554/eLife.65557 33538693 PMC7861614 · DOI
  126. [136]Schopp T. Zoch A. Berrens R.V. Auchynnikava T. Kabayama Y. Vasiliauskaite L. Rappsilber J. Allshire R.C. O’Carroll D. TEX15 is an essential executor of MIWI2-directed transposon DNA methylation and silencing Nat. Commun. 2020 11 3739 10.1038/s41467-020-17372-5 32719317 PMC7385494 · DOI
  127. [137]Zoch A. Auchynnikava T. Berrens R.V. Kabayama Y. Schopp T. Heep M. Vasiliauskaite L. Perez-Rico Y.A. Cook A.G. Shkumatava A. SPOCD1 is an essential executor of piRNA-directed de novo DNA methylation Nature 2020 584 635 639 10.1038/s41586-020-2557-5 32674113 PMC7612247 · DOI
  128. [138]Klattenhoff C. Xi H. Li C. Lee S. Xu J. Khurana J.S. Zhang F. Schultz N. Koppetsch B.S. Nowosielska A. The Drosophila HP1 Homolog Rhino Is Required for Transposon Silencing and piRNA Production by Dual-Strand Clusters Cell 2009 138 1137 1149 10.1016/j.cell.2009.07.014 19732946 PMC2770713 · DOI
  129. [139]Mohn F. Sienski G. Handler D. Brennecke J. The Rhino-Deadlock-Cutoff Complex Licenses Noncanonical Transcription of Dual-Strand piRNA Clusters in Drosophila Cell 2014 157 1364 1379 10.1016/j.cell.2014.04.031 24906153 · DOI
  130. [140]Zhang Z. Wang J. Schultz N. Zhang F. Parhad S.S. Tu S. Vreven T. Zamore P.D. Weng Z. Theurkauf W.E. The HP1 Homolog Rhino Anchors a Nuclear Complex that Suppresses piRNA Precursor Splicing Cell 2014 157 1353 1363 10.1016/j.cell.2014.04.030 24906152 PMC4167631 · DOI
  131. [141]ElMaghraby M.F. Andersen P.R. Pühringer F. Hohmann U. Meixner K. Lendl T. Tirian L. Brennecke J. A Heterochromatin-Specific RNA Export Pathway Facilitates piRNA Production Cell 2019 178 964 979.e20 10.1016/j.cell.2019.07.007 31398345 · DOI
  132. [142]Kneuss E. Munafò M. Eastwood E.L. Deumer U.-S. Preall J.B. Hannon G.J. Czech B. Specialization of the Drosophila nuclear export family protein Nxf3 for piRNA precursor export Genes Dev. 2019 33 1208 1220 10.1101/gad.328690.119 31416967 PMC6719614 · DOI
  133. [143]Tzeng T.-Y. Lee C.-H. Chan L.-W. Shen C.-K.J. Epigenetic regulation of the Drosophila chromosome 4 by the histone H3K9 methyltransferase dSETDB1 Proc. Natl. Acad. Sci. USA 2007 104 12691 12696 10.1073/pnas.0705534104 17652514 PMC1937528 · DOI
  134. [144]He J. Fu X. Zhang M. He F. Li W. Abdul M. Zhou J. Sun L. Chang C. Li Y. Transposable elements are regulated by context-specific patterns of chromatin marks in mouse embryonic stem cells Nat. Commun. 2019 10 1 13 10.1038/s41467-018-08006-y 30604769 PMC6318327 · DOI
  135. [145]van Mierlo G. Dirks R.A.M. De Clerck L. Brinkman A.B. Huth M. Kloet S.L. Saksouk N. Kroeze L.I. Willems S. Farlik M. Integrative Proteomic Profiling Reveals PRC2-Dependent Epigenetic Crosstalk Maintains Ground-State Pluripotency Cell Stem Cell 2019 24 123 137.e8 10.1016/j.stem.2018.10.017 30472157 · DOI
  136. [146]Miller S.A. Damle M. Kim J. Kingston R.E. Full methylation of H3K27 by PRC2 is dispensable for initial embryoid body formation but required to maintain differentiated cell identity Development 2021 148 10.1242/dev.196329 PMC8077505 33688077 · DOI
  137. [147]Jain P. Di Croce L. Mutations and deletions of PRC2 in prostate cancer BioEssays 2016 38 446 454 10.1002/bies.201500162 27000413 · DOI
  138. [148]Deleris A. Stroud H. Bernatavichute Y. Johnson E. Klein G. Schubert D. Jacobsen S.E. Loss of the DNA Methyltransferase MET1 Induces H3K9 Hypermethylation at PcG Target Genes and Redistribution of H3K27 Trimethylation to Transposons in Arabidopsis thaliana PLoS Genet. 2012 8 e1003062 10.1371/journal.pgen.1003062 23209430 PMC3510029 · DOI
  139. [149]Déléris A. Berger F. Duharcourt S. Role of Polycomb in the control of transposable elements Trends Genet. 2021 37 882 889 10.1016/j.tig.2021.06.003 34210514 · DOI
  140. [150]Frapporti A. Pina C.M. Arnaiz O. Holoch D. Kawaguchi T. Humbert A. Eleftheriou E. Lombard B. Loew D. Sperling L. The Polycomb protein Ezl1 mediates H3K9 and H3K27 methylation to repress transposable elements in Paramecium Nat. Commun. 2019 10 1 15 10.1038/s41467-019-10648-5 31221974 PMC6586856 · DOI
  141. [151]Miró-Pina C. Charmant O. Kawaguchi T. Holoch D. Michaud A. Cohen I. Humbert A. Jaszczyszyn Y. Chevreux G. Del Maestro L. Paramecium Polycomb repressive complex 2 physically interacts with the small RNA-binding PIWI protein to repress transposable elements Dev. Cell 2022 57 1037 1052.e8 10.1016/j.devcel.2022.03.014 35429435 · DOI
  142. [152]Leeb M. Pasini D. Novatchkova M. Jaritz M. Helin K. Wutz A. Polycomb complexes act redundantly to repress genomic repeats and genes Genes Dev. 2010 24 265 276 10.1101/gad.544410 20123906 PMC2811828 · DOI
  143. [153]Ozturk N. Dansranjavin T. Gies S. Calay D. Shiplu S. Creppe C. Hendrickx J. Schagdarsurengin U. H4K20me3 marks distal intergenic and repetitive regions in human mature spermatozoa Development 2021 148 10.1242/dev.196477 34345914 · DOI
  144. [154]Kurup J.T. Han Z. Jin W. Kidder B.L. H4K20me3 methyltransferase SUV420H2 shapes the chromatin landscape of pluripotent embryonic stem cells Development 2020 10.1242/dev.188516 PMC7725612 33144397 · DOI
  145. [155]Schotta G. Sengupta R. Kubicek S. Malin S. Kauer M. Callén E. Celeste A. Pagani M. Opravil S. De La Rosa-Velazquez I.A. A chromatin-wide transition to H4K20 monomethylation impairs genome integrity and programmed DNA rearrangements in the mouse Genes Dev. 2008 22 2048 2061 10.1101/gad.476008 18676810 PMC2492754 · DOI
  146. [156]Ren W. Fan H. Grimm S.A. Kim J.J. Li L. Guo Y. Petell C.J. Tan X.-F. Zhang Z.-M. Coan J.P. DNMT1 reads heterochromatic H4K20me3 to reinforce LINE-1 DNA methylation Nat. Commun. 2021 12 1 16 10.1038/s41467-021-22665-4 33941775 PMC8093215 · DOI
  147. [157]Schotta G. Lachner M. Sarma K. Ebert A. Sengupta R. Reuter G. Reinberg D. Jenuwein T. A silencing pathway to induce H3-K9 and H4-K20 trimethylation at constitutive heterochromatin Genes Dev. 2004 18 1251 1262 10.1101/gad.300704 15145825 PMC420351 · DOI
  148. [158]Kourmouli N. Jeppesen P. Mahadevhaiah S. Burgoyne P. Wu R. Gilbert D.M. Bongiorni S. Prantera G. Fanti L. Pimpinelli S. Heterochromatin and tri-methylated lysine 20 of histone H4 in animals J. Cell Sci. 2004 117 Pt 12 2491 2501 10.1242/jcs.01238 15128874 · DOI
  149. [159]van Kruijsbergen I. Hontelez S. Elurbe D.M. van Heeringen S.J. Huynen M.A. Veenstra G.J.C. Heterochromatic histone modifications at transposons in Xenopus tropicalis embryos Dev. Biol. 2017 426 460 471 10.1016/j.ydbio.2016.08.031 27639284 PMC5350053 · DOI
  150. [160]Girardot M. Hirasawa R. Kacem S. Fritsch L. Pontis J. Kota S.K. Filipponi D. Fabbrizio E. Sardet C. Lohmann F. PRMT5-mediated histone H4 arginine-3 symmetrical dimethylation marks chromatin at G + C-rich regions of the mouse genome Nucleic Acids Res. 2014 42 235 248 10.1093/nar/gkt884 24097435 PMC3874197 · DOI
  151. [161]Kim S. Günesdogan U. Zylicz J.J. Hackett J.A. Cougot D. Bao S. Lee C. Dietmann S. Allen G.E. Sengupta R. PRMT5 Protects Genomic Integrity during Global DNA Demethylation in Primordial Germ Cells and Preimplantation Embryos Mol. Cell 2014 56 564 579 10.1016/j.molcel.2014.10.003 25457166 PMC4250265 · DOI
  152. [162]Celen A.B. Sahin U. Sumoylation on its 25th anniversary: Mechanisms, pathology, and emerging concepts FEBS J. 2020 287 3110 3140 10.1111/febs.15319 32255256 · DOI
  153. [163]Ryu H.-Y. Hochstrasser M. Histone sumoylation and chromatin dynamics Nucleic Acids Res. 2021 49 6043 6052 10.1093/nar/gkab280 33885816 PMC8216275 · DOI
  154. [164]Maison C. Bailly D. Quivy J.-P. Almouzni G. The methyltransferase Suv39h1 links the SUMO pathway to HP1α marking at pericentric heterochromatin Nat. Commun. 2016 7 12224 10.1038/ncomms12224 27426629 PMC4960310 · DOI
  155. [165]Maison C. Bailly D. Roche D. de Oca R.M. Probst A.V. Vassias I. Dingli F. Lombard B. Loew D. Quivy J.-P. SUMOylation promotes de novo targeting of HP1α to pericentric heterochromatin Nat. Genet. 2011 43 220 227 10.1038/ng.765 21317888 · DOI
  156. [166]Shin J.A. Choi E.S. Kim H.S. Ho J.C. Watts F.Z. Park S.D. Jang Y.K. SUMO Modification Is Involved in the Maintenance of Heterochromatin Stability in Fission Yeast Mol. Cell 2005 19 817 828 10.1016/j.molcel.2005.08.021 16168376 · DOI
  157. [167]Stielow B. Sapetschnig A. Wink C. Krüger I. Suske G. SUMO-modified Sp3 represses transcription by provoking local heterochromatic gene silencing EMBO Rep. 2008 9 899 906 10.1038/embor.2008.127 18617891 PMC2529347 · DOI
  158. [168]Thompson P.J. Dulberg V. Moon K.-M. Foster L.J. Chen C. Karimi M.M. Lorincz M.C. hnRNP K Coordinates Transcriptional Silencing by SETDB1 in Embryonic Stem Cells PLoS Genet. 2015 11 e1004933 10.1371/journal.pgen.1004933 25611934 PMC4303303 · DOI
  159. [169]Uchimura Y. Ichimura T. Uwada J. Tachibana T. Sugahara S. Nakao M. Saitoh H. Involvement of SUMO Modification in MBD1- and MCAF1-mediated Heterochromatin Formation J. Biol. Chem. 2006 281 23180 23190 10.1074/jbc.M602280200 16757475 · DOI
  160. [170]Psakhye I. Jentsch S. Protein Group Modification and Synergy in the SUMO Pathway as Exemplified in DNA Repair Cell 2012 151 807 820 10.1016/j.cell.2012.10.021 23122649 · DOI · Paper page
  161. [171]Efroni S. Duttagupta R. Cheng J. Dehghani H. Hoeppner D.J. Dash C. Bazett-Jones D.P. Le Grice S. McKay R.D. Buetow K.H. Global Transcription in Pluripotent Embryonic Stem Cells Cell Stem Cell 2008 2 437 447 10.1016/j.stem.2008.03.021 18462694 PMC2435228 · DOI
  162. [172]Jachowicz J. Bing X. Pontabry J. Bošković A. Rando O.J. Torres-Padilla M.-E. LINE-1 activation after fertilization regulates global chromatin accessibility in the early mouse embryo Nat. Genet. 2017 49 1502 1510 10.1038/ng.3945 28846101 · DOI
  163. [173]Baillie J.K. Barnett M.W. Upton K.R. Gerhardt D.J. Richmond T.A. De Sapio F. Brennan P.M. Rizzu P. Smith S. Fell M. Somatic retrotransposition alters the genetic landscape of the human brain Nature 2011 479 534 537 10.1038/nature10531 22037309 PMC3224101 · DOI · Paper page
  164. [174]Perrat P.N. DasGupta S. Wang J. Theurkauf W. Weng Z. Rosbash M. Waddell S. Transposition-Driven Genomic Heterogeneity in the Drosophila Brain Science 2013 340 91 95 10.1126/science.1231965 23559253 PMC3887341 · DOI
  165. [175]Tam O.H. Ostrow L. Hammell M.G. Diseases of the nERVous system: Retrotransposon activity in neurodegenerative disease Mob. DNA 2019 10 1 14 10.1186/s13100-019-0176-1 31372185 PMC6659213 · DOI
  166. [176]Jang H.S. Shah N. Du A. Dailey Z.Z. Pehrsson E. Godoy P.M. Zhang D. Li D. Xing X. Kim S. Transposable elements drive widespread expression of oncogenes in human cancers Nat. Genet. 2019 51 611 617 10.1038/s41588-019-0373-3 30926969 PMC6443099 · DOI
  167. [177]Chuong E. Elde N.C. Feschotte E.B.C.N.C.E.C. Regulatory activities of transposable elements: From conflicts to benefits Nat. Rev. Genet. 2016 18 71 86 10.1038/nrg.2016.139 27867194 PMC5498291 · DOI
  168. [178]Pehrsson E.C. Choudhary M.N.K. Sundaram V. Wang T. The epigenomic landscape of transposable elements across normal human development and anatomy Nat. Commun. 2019 10 1 16 10.1038/s41467-019-13555-x 31822674 PMC6904449 · DOI
  169. [179]Fadloun A. Le Gras S. Jost B. Ziegler-Birling C. Takahashi H. Gorab E. Carninci P. Torres-Padilla M.-E. Chromatin signatures and retrotransposon profiling in mouse embryos reveal regulation of LINE-1 by RNA Nat. Struct. Mol. Biol. 2013 20 332 338 10.1038/nsmb.2495 23353788 · DOI
  170. [180]Sze C.C. Shilatifard A. MLL3/MLL4/COMPASS Family on Epigenetic Regulation of Enhancer Function and Cancer Cold Spring Harb. Perspect. Med. 2016 6 a026427 10.1101/cshperspect.a026427 27638352 PMC5088509 · DOI · Paper page
  171. [181]Macfarlan T.S. Gifford W.D. Agarwal S. Driscoll S. Lettieri K. Wang J. Andrews S.E. Franco L. Rosenfeld M.G. Ren B. Endogenous retroviruses and neighboring genes are coordinately repressed by LSD1/KDM1A Genes Dev. 2011 25 594 607 10.1101/gad.2008511 21357675 PMC3059833 · DOI
  172. [182]Ancelin K. Syx L. Borensztein M. Ranisavljevic N. Vassilev I. Briseno-Roa L. Liu T. Metzger E. Servant N. Barillot E. Maternal LSD1/KDM1A is an essential regulator of chromatin and transcription landscapes during zygotic genome activation eLife 2016 5 e08851 10.7554/eLife.08851 26836306 PMC4829419 · DOI
  173. [183]Dai Q. Shen Y. Wang Y. Wang X. Francisco J.C. Luo Z. Lin C. Striking a balance: Regulation of transposable elements by Zfp281 and Mll2 in mouse embryonic stem cells Nucleic Acids Res. 2017 45 12301 12310 10.1093/nar/gkx841 29036642 PMC5716208 · DOI
  174. [184]Chaouch A. Berlandi J. Chen C.C. Frey F. Badini S. Harutyunyan A.S. Chen X. Krug B. Hébert S. Jeibmann A. Histone H3.3 K27M and K36M mutations de-repress transposable elements through perturbation of antagonistic chromatin marks Mol. Cell 2021 81 4876 4890.e7 10.1016/j.molcel.2021.10.008 34739871 PMC9990445 · DOI
  175. [185]Ahmad K. Henikoff S. Histone H3 variants specify modes of chromatin assembly Proc. Natl. Acad. Sci. USA 2002 99 16477 16484 10.1073/pnas.172403699 12177448 PMC139911 · DOI
  176. [186]Elsässer S.J. Noh K.-M. Diaz N. Allis C.D. Banaszynski L.A. Histone H3.3 is required for endogenous retroviral element silencing in embryonic stem cells Nature 2015 522 240 244 10.1038/nature14345 25938714 PMC4509593 · DOI
  177. [187]Zhou J. Wang X. He K. Charron J.-B.F. Elling A.A. Deng X.W. Genome-wide profiling of histone H3 lysine 9 acetylation and dimethylation in Arabidopsis reveals correlation between multiple histone marks and gene expression Plant Mol. Biol. 2010 72 585 595 10.1007/s11103-009-9594-7 20054610 · DOI
  178. [188]Yang J. Yuan L. Yen M.R. Zheng F. Ji R. Peng T. Gu D. Yang S. Cui Y. Chen P.Y. SWI3B and HDA6 interact and are required for transposon silencing in Arabidopsis Plant. J. 2020 102 809 822 10.1111/tpj.14666 31883159 · DOI
  179. [189]Liu X. Yu C.-W. Duan J. Luo M. Wang K. Tian G. Cui Y. Wu K. HDA6 Directly Interacts with DNA Methyltransferase MET1 and Maintains Transposable Element Silencing in Arabidopsis Plant Physiol. 2011 158 119 129 10.1104/pp.111.184275 21994348 PMC3252112 · DOI
  180. [190]Lennartsson A. Arner E. Fagiolini M. Saxena A. Andersson R. Takahashi H. Noro Y. Sng J. Sandelin A. Hensch T.K. Remodeling of retrotransposon elements during epigenetic induction of adult visual cortical plasticity by HDAC inhibitors Epigenet. Chromatin 2015 8 1 15 10.1186/s13072-015-0043-3 PMC4678690 26673794 · DOI
  181. [191]Szabo Q. Bantignies F. Cavalli G. Principles of genome folding into topologically associating domains Sci. Adv. 2019 5 eaaw1668 10.1126/sciadv.aaw1668 30989119 PMC6457944 · DOI
  182. [192]Rowley M.J. Corces V.G. Organizational principles of 3D genome architecture Nat. Rev. Genet. 2018 19 789 800 10.1038/s41576-018-0060-8 30367165 PMC6312108 · DOI · Paper page
  183. [193]Iwasaki Y.W. Sriswasdi S. Kinugasa Y. Adachi J. Horikoshi Y. Shibuya A. Iwasaki W. Tashiro S. Tomonaga T. Siomi H. Piwi-piRNA complexes induce stepwise changes in nuclear architecture at target loci EMBO J. 2021 40 e108345 10.15252/embj.2021108345 34337769 PMC8441340 · DOI
  184. [194]Choudhary M.N. Friedman R.Z. Wang J.T. Jang H.S. Zhuo X. Wang T. Co-opted transposons help perpetuate conserved higher-order chromosomal structures Genome Biol. 2020 21 16 10.1186/s13059-019-1916-8 31973766 PMC6979391 · DOI
  185. [195]Dominissini D. Moshitch-Moshkovitz S. Schwartz S. Salmon-Divon M. Ungar L. Osenberg S. Cesarkas K. Jacob-Hirsch J. Amariglio N. Kupiec M. Topology of the human and mouse m6A RNA methylomes revealed by m6A-seq Nature 2012 485 201 206 10.1038/nature11112 22575960 · DOI · Paper page
  186. [196]Meyer K.D. Saletore Y. Zumbo P. Elemento O. Mason C.E. Jaffrey S.R. Comprehensive Analysis of mRNA Methylation Reveals Enrichment in 3′ UTRs and near Stop Codons Cell 2012 149 1635 1646 10.1016/j.cell.2012.05.003 22608085 PMC3383396 · DOI · Paper page
  187. [197]Liu J. Dou X. Chen C. Chen C. Liu C. Xu M.M. Zhao S. Shen B. Gao Y. Han D. N6 -methyladenosine of chromosome-associated regulatory RNA regulates chromatin state and transcription Science 2020 367 580 586 10.1126/science.aay6018 31949099 PMC7213019 · DOI · Paper page
  188. [198]Shi H. Wei J. He C. Where, When, and How: Context-Dependent Functions of RNA Methylation Writers, Readers, and Erasers Mol. Cell 2019 74 640 650 10.1016/j.molcel.2019.04.025 31100245 PMC6527355 · DOI
  189. [199]Bokar J.A. Shambaugh M.E. Polayes D. Matera A.G. Rottman F.M. Purification and cDNA cloning of the AdoMet-binding subunit of the human mRNA (N6-adenosine)-methyltransferase RNA 1997 3 1233 1247 9409616 PMC1369564
  190. [200]Liu J. Yue Y. Han D. Wang X. Fu Y. Zhang L. Jia G. Yu M. Lu Z. Deng X. A METTL3–METTL14 complex mediates mammalian nuclear RNA N6-adenosine methylation Nat. Chem. Biol. 2013 10 93 95 10.1038/nchembio.1432 24316715 PMC3911877 · DOI · Paper page
  191. [201]Pendleton K.E. Chen B. Liu K. Hunter O.V. Xie Y. Tu B.P. Conrad N.K. The U6 snRNA m 6 A Methyltransferase METTL16 Regulates SAM Synthetase Intron Retention Cell 2017 169 824 835.e14 10.1016/j.cell.2017.05.003 28525753 PMC5502809 · DOI
  192. [202]Ma H. Wang X. Cai J. Dai Q. Natchiar S.K. Lv R. Chen K. Lu Z. Chen H. Shi Y.G. N6-Methyladenosine methyltransferase ZCCHC4 mediates ribosomal RNA methylation Nat. Chem. Biol. 2018 15 88 94 10.1038/s41589-018-0184-3 30531910 PMC6463480 · DOI
  193. [203]Fu Y. Jia G. Pang X. Wang R.N. Wang X. Li C.J. Smemo S. Dai Q. Bailey K.A. Nobrega M.A. FTO-mediated formation of N6-hydroxymethyladenosine and N6-formyladenosine in mammalian RNA Nat. Commun. 2013 4 1 8 10.1038/ncomms2822 PMC3658177 23653210 · DOI
  194. [204]Jia G. Fu Y. Zhao X. Dai Q. Zheng G. Yang Y. Yi C. Lindahl T. Pan T. Yang Y.-G. N6-Methyladenosine in nuclear RNA is a major substrate of the obesity-associated FTO Nat. Chem. Biol. 2011 7 885 887 Erratum in Nat. Chem. Biol. 2012, 8, 1008 10.1038/nchembio.687 22002720 PMC3218240 · DOI · Paper page
  195. [205]Zheng G. Dahl J.A. Niu Y. Fedorcsak P. Huang C.-M. Li C.J. Vågbø C.B. Shi Y. Wang W.-L. Song S.-H. ALKBH5 Is a Mammalian RNA Demethylase that Impacts RNA Metabolism and Mouse Fertility Mol. Cell 2013 49 18 29 10.1016/j.molcel.2012.10.015 23177736 PMC3646334 · DOI · Paper page
  196. [206]Jang K.H. Heras C.R. Lee G. m(6)A in the Signal Transduction Network Mol. Cells 2022 45 435 443 10.14348/molcells.2022.0017 35748227 PMC9260138 · DOI
  197. [207]Xu W. Li J. He C. Wen J. Ma H. Rong B. Diao J. Wang L. Wang J. Wu F. METTL3 regulates heterochromatin in mouse embryonic stem cells Nature 2021 591 317 321 10.1038/s41586-021-03210-1 33505026 · DOI
  198. [208]Chelmicki T. Roger E. Teissandier A. Dura M. Bonneville L. Rucli S. Dossin F. Fouassier C. Lameiras S. Bourc’His D. m6A RNA methylation regulates the fate of endogenous retroviruses Nature 2021 591 312 316 10.1038/s41586-020-03135-1 33442060 · DOI
  199. [209]Liu J. Gao M. He J. Wu K. Lin S. Jin L. Chen Y. Liu H. Shi J. Wang X. The RNA m6A reader YTHDC1 silences retrotransposons and guards ES cell identity Nature 2021 591 322 326 10.1038/s41586-021-03313-9 33658714 · DOI
  200. [210]Chen C. Liu W. Guo J. Liu Y. Liu X. Liu J. Dou X. Le R. Huang Y. Li C. Correction to: Nuclear m6A reader YTHDC1 regulates the scaffold function of LINE1 RNA in mouse ESCs and early embryos Protein Cell 2021 13 470 471 10.1007/s13238-021-00853-8 34432224 PMC9095788 · DOI

200 of 209 shown

Cited by

Sorted by citations

Authors
Di Stefano, L.
Affiliations
Molecular, Cellular and Developmental Biology Department (MCD), Centre de Biologie Intégrative (CBI), University of Toulouse, CNRS, UPS, 31062 Toulouse, France
ORCID
Di Stefano, Luisa
Venue
Cells
Publisher
MDPI AG
Published
2022-08-11
Volume
11
Issue
16
Pages
2501
ISSN
2073-4409 (ISSN-L)
DOI
10.3390/cells11162501
PMC
PMC9406493
OpenAlex
W4291000053
Cited by
18
References
11
Citations by year
2026: 7 · 2025: 7 · 2024: 3 · 2023: 1
FWCI
0.25
Type
journal article
Language
en
Open access
Licence
Locations
  • Cells (publishedVersion, cc-by)
  • PubMed Central (publishedVersion, cc-by)
  • PubMed (publishedVersion)
  • HAL (submittedVersion, cc-by)
  • DOAJ (DOAJ: Directory of Open Access Journals) (submittedVersion, cc-by-sa)
Funders
  • French National Research Agency (ANR-20-CE12-0015-01)
  • CNRS (ANR-20-CE12-0015-01)
Topics
  • Life Sciences › Agricultural and Biological Sciences › Plant Science › Chromosomal and Genetic Variations
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Genomics and Chromatin Dynamics
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Molecular Biology › Epigenetics and DNA Methylation
Keywords
transposable elements, transposon silencing, chromatin, histone modifications, chromatin proteins, epigenetic regulation, Drosophila, mammals, genomic instability
MeSH terms
Animals, Chromatin, DNA Transposable Elements, Drosophila, Mammals, Histone Code

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