Skip to main content

Thank you for visiting nature.com. You are using a browser version with limited support for CSS. To obtain the best experience, we recommend you use a more up to date browser (or turn off compatibility mode in Internet Explorer). In the meantime, to ensure continued support, we are displaying the site without styles and JavaScript.

Ten principles of heterochromatin formation and function

Key Points

  • Protein domains that bind ('read') histones bearing specific post-translational modifications are frequently physically coupled to enzymes that catalyse the addition ('writer') or removal ('eraser') of histone modifications.

  • Transcription of heterochromatin produces noncoding RNAs that provide recruitment platforms for chromatin-modifying enzymes.

  • The processes that initiate heterochromatin establishment are separable from those that mediate its maintenance. Once initiated, heterochromatin can engulf neighbouring chromatin, but spreading is limited by multiple mechanisms.

  • Reader–writer coupling suggests that heterochromatin can direct its persistence through replication and cell division independently of nucleic acid cues. Experimental tests suggest that heterochromatin heritability is strongly countered by opposing activities.

  • Heterochromatin suppresses chromosome rearrangements by directing specific avenues of repair within repetitive DNA. Heterochromatin also promotes accurate chromosome segregation.

  • Domains of heterochromatin limit the repertoire of expressed genes in differentiated cells and inhibit their reprogramming to pluripotent cells. A variety of human diseases are affected by the alterations in the ability to form, or the distribution of, heterochromatin.

Abstract

Heterochromatin is a key architectural feature of eukaryotic chromosomes, which endows particular genomic domains with specific functional properties. The capacity of heterochromatin to restrain the activity of mobile elements, isolate DNA repair in repetitive regions and ensure accurate chromosome segregation is crucial for maintaining genomic stability. Nucleosomes at heterochromatin regions display histone post-translational modifications that contribute to developmental regulation by restricting lineage-specific gene expression. The mechanisms of heterochromatin establishment and of heterochromatin maintenance are separable and involve the ability of sequence-specific factors bound to nascent transcripts to recruit chromatin-modifying enzymes. Heterochromatin can spread along the chromatin from nucleation sites. The propensity of heterochromatin to promote its own spreading and inheritance is counteracted by inhibitory factors. Because of its importance for chromosome function, heterochromatin has key roles in the pathogenesis of various human diseases. In this Review, we discuss conserved principles of heterochromatin formation and function using selected examples from studies of a range of eukaryotes, from yeast to human, with an emphasis on insights obtained from unicellular model organisms.

Your institute does not have access to this article

Relevant articles

Open Access articles citing this article.

Access options

Buy article

Get time limited or full article access on ReadCube.

$32.00

All prices are NET prices.

Figure 1: Core heterochromatin components and mechanisms.
Figure 2: Determining whether a factor is required for the establishment, but not maintenance, of heterochromatin.
Figure 3: The regulation of heterochromatin spreading.
Figure 4: Reader–writer coupling allows the maintenance of repressive chromatin modifications through DNA replication and their transmission through cell division.
Figure 5: Heterochromatin functions in mammalian cells.

References

  1. Zhou, C. Y., Johnson, S. L., Gamarra, N. I. & Narlikar, G. J. Mechanisms of ATP-dependent chromatin remodeling motots. Annu. Rev. Biophys. 45, 153–181 (2016).

    CAS  PubMed  Google Scholar 

  2. Rea, S. et al. Regulation of chromatin structure by site-specific histone H3 methyltransferases. Nature 406, 593–599 (2000).

    CAS  PubMed  Google Scholar 

  3. Tschiersch, B. et al. The protein encoded by the Drosophila position-effect variegation suppressor gene Su(var)3-9 combines domains of antagonistic regulators of homeotic gene complexes. EMBO J. 13, 3822 (1994).

    CAS  PubMed  PubMed Central  Google Scholar 

  4. Eissenberg, J. C. et al. Mutation in a heterochromatin-specific chromosomal protein is associated with suppression of position-effect variegation in Drosophila melanogaster. Proc. Natl Acad. Sci. USA 87, 9923–9927 (1990).

    CAS  PubMed  PubMed Central  Google Scholar 

  5. 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 410, 116–120 (2001).

    CAS  PubMed  Google Scholar 

  6. Bannister, A. J. et al. Selective recognition of methylated lysine 9 on histone H3 by the HP1 chromo domain. Nature 410, 120–124 (2001).

    CAS  PubMed  Google Scholar 

  7. Lorentz, A., Ostermann, K., Fleck, O. & Schmidt, H. Switching gene swi6, involved in repression of silent mating-type loci in fission yeast, encodes a homologue of chromatin-associated proteins from Drosophila and mammals. Gene 143, 139–143 (1994).

    CAS  PubMed  Google Scholar 

  8. Allshire, R. C., Nimmo, E. R., Ekwall, K., Javerzat, J. P. & Cranston, G. Mutations derepressing silent centromeric domains in fission yeast disrupt chromosome segregation. Genes Dev. 9, 218–233 (1995).

    CAS  PubMed  Google Scholar 

  9. Thon, G. & Verhein-Hansen, J. Four chromo-domain proteins of Schizosaccharomyces pombe differentially repress transcription at various chromosomal locations. Genetics 155, 551–568 (2000).

    CAS  PubMed  PubMed Central  Google Scholar 

  10. Klar, A. J. & Bonaduce, M. J. swi6, a gene required for mating-type switching, prohibits meiotic recombination in the mat2-mat3 “cold spot” of fission yeast. Genetics 129, 1033–1042 (1991).

    CAS  PubMed  PubMed Central  Google Scholar 

  11. Lorentz, A., Heim, L. & Schmidt, H. The switching gene swi6 affects recombination and gene expression in the mating-type region of Schizosaccharomyces pombe. Mol. Gen. Genet. 233, 436–442 (1992).

    CAS  PubMed  Google Scholar 

  12. Ekwall, K. & Ruusala, T. Mutations in rik1, clr2, clr3 and clr4 genes asymmetrically derepress the silent mating-type loci in fission yeast. Genetics 136, 53–64 (1994).

    CAS  PubMed  PubMed Central  Google Scholar 

  13. Thon, G., Cohen, A. & Klar, A. J. Three additional linkage groups that repress transcription and meiotic recombination in the mating-type region of Schizosaccharomyces pombe. Genetics 138, 29–38 (1994).

    CAS  PubMed  PubMed Central  Google Scholar 

  14. Tamaru, H. & Selker, E. U. A histone H3 methyltransferase controls DNA methylation in Neurospora crassa. Nature 414, 277–283 (2001).

    CAS  PubMed  Google Scholar 

  15. Jackson, J. P., Lindroth, A. M., Cao, X. & Jacobsen, S. E. Control of CpNpG DNA methylation by the KRYPTONITE histone H3 methyltransferase. Nature 416, 556–560 (2002).

    CAS  PubMed  Google Scholar 

  16. Lehnertz, B. et al. Suv39h-mediated histone H3 lysine 9 methylation directs DNA methylation to major satellite repeats at pericentric heterochromatin. Curr. Biol. 13, 1192–1200 (2003).

    CAS  PubMed  Google Scholar 

  17. Hashimshony, T., Zhang, J., Keshet, I., Bustin, M. & Cedar, H. The role of DNA methylation in setting up chromatin structure during development. Nat. Genet. 34, 187–192 (2003).

    CAS  PubMed  Google Scholar 

  18. Kueng, S., Oppikofer, M. & Gasser, S. M. SIR proteins and the assembly of silent chromatin in budding yeast. Ann. Rev. Genet. 47, 275–306 (2013).

    CAS  PubMed  Google Scholar 

  19. Rusche, L. N., Kirchmaier, A. L. & Rine, J. The establishment, inheritance, and function of silenced chromatin in Saccharomyces cerevisiae. Ann. Rev. Biochem. 72, 481–516 (2003).

    CAS  PubMed  Google Scholar 

  20. Armache, K. J., Garlick, J. D., Canzio, D., Narlikar, G. J. & Kingston, R. E. Structural basis of silencing: Sir3 BAH domain in complex with a nucleosome at 3.0 A resolution. Science 334, 977–982 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  21. Hanson, S. J. & Wolfe, K. H. An evolutionary perspective on yeast mating-type switching. Genetics 206, 9–32 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  22. Ekwall, K. et al. Mutations in the fission yeast silencing factors clr4+ and rik1+ disrupt the localisation of the chromo domain protein Swi6p and impair centromere function. J. Cell Sci. 109, 2637–2648 (1996).

    CAS  PubMed  Google Scholar 

  23. Maison, C. et al. Higher-order structure in pericentric heterochromatin involves a distinct pattern of histone modification and an RNA component. Nat. Genet. 30, 329–334 (2002).

    PubMed  Google Scholar 

  24. Sadaie, M., Iida, T., Urano, T. & Nakayama, J. A chromodomain protein, Chp1, is required for the establishment of heterochromatin in fission yeast. EMBO J. 23, 3825–3835 (2004).

    CAS  PubMed  PubMed Central  Google Scholar 

  25. Brasher, S. V. et al. The structure of mouse HP1 suggests a unique mode of single peptide recognition by the shadow chromo domain dimer. EMBO J. 19, 1587–1597 (2000).

    CAS  PubMed  PubMed Central  Google Scholar 

  26. Cowieson, N. P., Partridge, J. F., Allshire, R. C. & McLaughlin, P. J. Dimerisation of a chromo shadow domain and distinctions from the chromodomain as revealed by structural analysis. Curr. Biol. 10, 517–525 (2000).

    CAS  PubMed  Google Scholar 

  27. Motamedi, M. R. et al. HP1 proteins form distinct complexes and mediate heterochromatic gene silencing by nonoverlapping mechanisms. Mol. Cell 32, 778–790 (2008).

    CAS  PubMed  PubMed Central  Google Scholar 

  28. Fischer, T. et al. Diverse roles of HP1 proteins in heterochromatin assembly and functions in fission yeast. Proc. Natl Acad. Sci. USA 106, 8998–9003 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  29. Garcia, J. F., Dumesic, P. A., Hartley, P. D., El-Samad, H. & Madhani, H. D. Combinatorial, site-specific requirement for heterochromatic silencing factors in the elimination of nucleosome-free regions. Genes Dev. 24, 1758–1771 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  30. Creamer, K. M. et al. The Mi-2 homolog Mit1 actively positions nucleosomes within heterochromatin to suppress transcription. Mol. Cell. Biol. 34, 2046–2061 (2014).

    PubMed  PubMed Central  Google Scholar 

  31. Canzio, D. et al. A conformational switch in HP1 releases auto-inhibition to drive heterochromatin assembly. Nature 496, 377–381 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  32. Cao, R. et al. Role of histone H3 lysine 27 methylation in polycomb-group silencing. Science 298, 1039–1043 (2002).

    CAS  PubMed  Google Scholar 

  33. Müller, J. et al. Histone methyltransferase activity of a Drosophila polycomb group repressor complex. Cell 111, 197–208 (2002).

    PubMed  Google Scholar 

  34. Czermin, B. et al. Drosophila enhancer of Zeste/ESC complexes have a histone H3 methyltransferase activity that marks chromosomal Polycomb sites. Cell 111, 185–196 (2002).

    CAS  PubMed  Google Scholar 

  35. Kuzmichev, A., Nishioka, K., Erdjument-Bromage, H., Tempst, P. & Reinberg, D. Histone methyltransferase activity associated with a human multiprotein complex containing the Enhancer of Zeste protein. Genes Dev. 16, 2893–2905 (2002).

    CAS  PubMed  PubMed Central  Google Scholar 

  36. Fischle, W. et al. Molecular basis for the discrimination of repressive methyl-lysine marks in histone H3 by Polycomb and HP1 chromodomains. Genes Dev. 17, 1870–1881 (2003).

    CAS  PubMed  PubMed Central  Google Scholar 

  37. Margueron, R. et al. Role of the polycomb protein EED in the propagation of repressive histone marks. Nature 461, 762–767 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  38. Volpe, T. A. et al. Regulation of heterochromatic silencing and histone H3 lysine-9 methylation by RNAi. Science 297, 1833–1837 (2002).

    CAS  PubMed  Google Scholar 

  39. Kloc, A., Zaratiegui, M., Nora, E. & Martienssen, R. RNA interference guides histone modification during the S phase of chromosomal replication. Curr. Biol. 18, 490–495 (2008).

    CAS  PubMed  PubMed Central  Google Scholar 

  40. Chen, E. S. et al. Cell cycle control of centromeric repeat transcription and heterochromatin assembly. Nature 451, 734–737 (2008).

    CAS  PubMed  Google Scholar 

  41. Lu, J. & Gilbert, D. M. Proliferation-dependent and cell cycle regulated transcription of mouse pericentric heterochromatin. J. Cell Biol. 179, 411–421 (2007).

    CAS  PubMed  PubMed Central  Google Scholar 

  42. Reinhart, B. & Bartel, D. P. Small RNAs correspond to centromere heterochromatic repeats. Science 13, 1831 (2002).

    Google Scholar 

  43. Motamedi, M. R. et al. Two RNAi complexes, RITS and RDRC, physically interact and localize to noncoding centromeric RNAs. Cell 119, 789–802 (2004).

    CAS  PubMed  Google Scholar 

  44. Bayne, E. H. et al. Stc1: a critical link between RNAi and chromatin modification required for heterochromatin integrity. Cell 140, 666–677 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  45. Zhang, K., Mosch, K., Fischle, W. & Grewal, S. I. Roles of the Clr4 methyltransferase complex in nucleation, spreading and maintenance of heterochromatin. Nat. Struct. Mol. Biol. 15, 381–388 (2008).

    CAS  PubMed  Google Scholar 

  46. Verdel, A. et al. RNAi-mediated targeting of heterochromatin by the RITS complex. Science 303, 672–676 (2004).

    CAS  PubMed  PubMed Central  Google Scholar 

  47. Buhler, M., Verdel, A. & Moazed, D. Tethering RITS to a nascent transcript initiates RNAi- and heterochromatin-dependent gene silencing. Cell 125, 873–886 (2006).

    CAS  PubMed  Google Scholar 

  48. Gerace, E. L., Halic, M. & Moazed, D. The methyltransferase activity of Clr4Suv39h triggers RNAi independently of histone H3K9 methylation. Mol. Cell 39, 360–372 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  49. Jain, R., Iglesias, N. & Moazed, D. Distinct functions of argonaute slicer in siRNA maturation and heterochromatin formation. Mol. Cell 63, 191–205 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  50. Colmenares, S. U., Buker, S. M., Buhler, M., Dlakic, M. & Moazed, D. Coupling of double-stranded RNA synthesis and siRNA generation in fission yeast RNAi. Mol. Cell 27, 449–461 (2007).

    CAS  PubMed  Google Scholar 

  51. Kato, H. et al. RNA polymerase II is required for RNAi-dependent heterochromatin assembly. Science 309, 467–469 (2005).

    CAS  PubMed  Google Scholar 

  52. Djupedal, I. et al. RNA Pol II subunit Rpb7 promotes centromeric transcription and RNAi-directed chromatin silencing. Genes Dev. 19, 2301–2306 (2005).

    CAS  PubMed  PubMed Central  Google Scholar 

  53. Hong, E. J., Villen, J., Gerace, E. L., Gygi, S. P. & Moazed, D. A cullin E3 ubiquitin ligase complex associates with Rik1 and the Clr4 histone H3-K9 methyltransferase and is required for RNAi-mediated heterochromatin formation. RNA Biol. 2, 106–111 (2005).

    CAS  PubMed  Google Scholar 

  54. Horn, P. J., Bastie, J. N. & Peterson, C. L. A. Rik1-associated, cullin-dependent E3 ubiquitin ligase is essential for heterochromatin formation. Genes Dev. 19, 1705–1714 (2005).

    CAS  PubMed  PubMed Central  Google Scholar 

  55. Jia, S., Kobayashi, R. & Grewal, S. I. Ubiquitin ligase component Cul4 associates with Clr4 histone methyltransferase to assemble heterochromatin. Nat. Cell Biol. 7, 1007–1013 (2005).

    CAS  PubMed  Google Scholar 

  56. Sugiyama, T., Cam, H., Verdel, A., Moazed, D. & Grewal, S. I. RNA-dependent RNA polymerase is an essential component of a self-enforcing loop coupling heterochromatin assembly to siRNA production. Proc. Natl Acad. Sci. USA 102, 152–157 (2005).

    CAS  PubMed  Google Scholar 

  57. Partridge, J. F., Borgstrøm, B. & Allshire, R. Distinct protein interaction domains and protein spreading in a complex centromere. Genes Dev. 14, 783–791 (2000).

    CAS  PubMed  PubMed Central  Google Scholar 

  58. Cam, H. P. et al. Comprehensive analysis of heterochromatin- and RNAi-mediated epigenetic control of the fission yeast genome. Nat. Genet. 37, 809–819 (2005).

    CAS  PubMed  Google Scholar 

  59. Rougemaille, M. et al. Ers1 links HP1 to RNAi. Proc. Natl Acad. Sci. USA 109, 11258–11263 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  60. Hayashi, A. et al. Heterochromatin protein 1 homologue Swi6 acts in concert with Ers1 to regulate RNAi-directed heterochromatin assembly. Proc. Natl Acad. Sci. USA 109, 6159–6164 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  61. Rougemaille, M., Shankar, S., Braun, S., Rowley, M. & Madhani, H. D. Ers1, a rapidly diverging protein essential for RNA interference-dependent heterochromatic silencing in Schizosaccharomyces pombe. J. Biol. Chem. 283, 25770–25773 (2008).

    CAS  PubMed  PubMed Central  Google Scholar 

  62. Wierzbicki, A. T., Ream, T. S., Haag, J. R. & Pikaard, C. S. RNA polymerase V transcription guides ARGONAUTE4 to chromatin. Nat. Genet. 41, 630–634 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  63. Zhong, X. et al. Molecular mechanism of action of plant DRM de novo DNA methyltransferases. Cell 157, 1050–1060 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  64. Liu, Z. W. et al. The SET domain proteins SUVH2 and SUVH9 are required for Pol V occupancy at RNA-directed DNA methylation loci. PLoS Genet. 10, e1003948 (2014).

    PubMed  PubMed Central  Google Scholar 

  65. Herr, A. J., Jensen, M. B., Dalmay, T. & Baulcombe, D. C. RNA polymerase IV directs silencing of endogenous DNA. Science 308, 118–120 (2005).

    CAS  PubMed  Google Scholar 

  66. Blevins, T. et al. Identification of Pol IV and RDR2-dependent precursors of 24 nt siRNAs guiding de novo DNA methylation in Arabidopsis. eLife 4, e09591 (2015).

    PubMed  PubMed Central  Google Scholar 

  67. Zhai, J. et al. A one precursor one siRNA model for Pol IV-dependent siRNA biogenesis. Cell 163, 445–455 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  68. Zhang, H. et al. DTF1 is a core component of RNA-directed DNA methylation and may assist in the recruitment of Pol IV. Proc. Natl Acad. Sci. USA 110, 8290–8295 (2013). References 67 and 68 show that short double-stranded RNA precursors generated by Pol IV and RNA-dependent polymerase 2 produce a single siRNA duplex through the activity of the Dicer Dcl3.

    CAS  PubMed  PubMed Central  Google Scholar 

  69. Law, J. A. et al. Polymerase IV occupancy at RNA-directed DNA methylation sites requires SHH1. Nature 498, 385–389 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  70. Reyes-Turcu, F. E., Zhang, K., Zofall, M., Chen, E. & Grewal, S. I. Defects in RNA quality control factors reveal RNAi-independent nucleation of heterochromatin. Nat. Struct. Mol. Biol. 18, 1132–1138 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  71. Wittmann, S. et al. The conserved protein Seb1 drives transcription termination by binding RNA polymerase II and nascent RNA. Nat. Commun. 8, 14861 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  72. Lemay, J. F. et al. The Nrd1-like protein Seb1 coordinates cotranscriptional 3′ end processing and polyadenylation site selection. Genes Dev. 30, 1558–1572 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  73. Sugiyama, T. et al. SHREC, an effector complex for heterochromatic transcriptional silencing. Cell 128, 491–504 (2007).

    CAS  PubMed  Google Scholar 

  74. Marina, D. B., Shankar, S., Natarajan, P., Finn, K. J. & Madhani, H. D. A conserved ncRNA-binding protein recruits silencing factors to heterochromatin through an RNAi-independent mechanism. Genes Dev. 27, 1851–1856 (2013). This article shows that the conserved RNA-binding protein Seb1, an orthologue of S. cerevisiae Nrd1, is an essential mediator of RNAi-independent heterochromatin assembly at fission yeast pericentromeric repeats.

    CAS  PubMed  PubMed Central  Google Scholar 

  75. Shirai, A. et al. Impact of nucleic acid and methylated H3K9 binding activities of Suv39h1 on its heterochromatin assembly. eLife 6, e25317 (2017).

    PubMed  PubMed Central  Google Scholar 

  76. Johnson, W. L. et al. RNA-dependent stabilization of SUV39H1 at constitutive heterochromatin. eLife 6, e25299 (2017).

    PubMed  PubMed Central  Google Scholar 

  77. Velazquez Camacho, O. et al. Major satellite repeat RNA stabilize heterochromatin retention of Suv39h enzymes by RNA-nucleosome association and RNA:DNA hybrid formation. eLife 6, e25293 (2017). References 75–77 show that the nucleic acid binding activities of the chromodomain of SUV39 enzymes stabilize their association with heterochromatin.

  78. Chu, C. et al. Systematic discovery of Xist RNA binding proteins. Cell 161, 404–416 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  79. Minajigi, A. et al. A comprehensive Xist interactome reveals cohesin repulsion and an RNA-directed chromosome conformation. Science 349, aab2276 (2015).

    Google Scholar 

  80. Monfort, A. et al. Identification of Spen as a crucial factor for Xist function through forward genetic screening in haploid embryonic stem cells. Cell Rep. 12, 554–561 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  81. Moindrot, B. et al. A Pooled shRNA screen identifies Rbm15, Spen, and Wtap as factors required for Xist RNA-mediated silencing. Cell Rep. 12, 562–572 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  82. McHugh, C. A. et al. The Xist lncRNA interacts directly with SHARP to silence transcription through HDAC3. Nature 521, 232–236 (2015). References 80–82 identify the RNA binding protein SPEN (SHARP) as crucial for the establishment of X inactivation in mice.

    CAS  PubMed  PubMed Central  Google Scholar 

  83. Mira-Bontenbal, H. & Gribnau, J. New Xist-interacting proteins in X-chromosome inactivation. Curr. Biol. 26, R338–R342 (2016).

    CAS  PubMed  Google Scholar 

  84. Folco, H. D., Pidoux, A. L., Urano, T. & Allshire, R. C. Heterochromatin and RNAi are required to establish CENP-A chromatin at centromeres. Science 319, 94–97 (2008).

    CAS  PubMed  PubMed Central  Google Scholar 

  85. Buscaino, A. et al. Distinct roles for Sir2 and RNAi in centromeric heterochromatin nucleation, spreading and maintenance. EMBO J. 32, 1250–1264 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  86. Ekwall, K., Olsson, T., Turner, B. M., Cranston, G. & Allshire, R. C. Transient inhibition of histone deacetylation alters the structural and functional imprint at fission yeast centromeres. Cell 91, 1021–1032 (1997).

    CAS  PubMed  Google Scholar 

  87. Hall, I. M. et al. Establishment and maintenance of a heterochromatin domain. Science 297, 2232–2237 (2002).

    CAS  PubMed  Google Scholar 

  88. Djupedal, I. et al. Analysis of small RNA in fission yeast; centromeric siRNAs are potentially generated through a structured RNA. EMBO J. 28, 3832–3844 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  89. Halic, M. & Moazed, D. Dicer-independent primal RNAs trigger RNAi and heterochromatin formation. Cell 140, 504–516 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  90. Simmer, F. et al. Hairpin RNA induces secondary small interfering RNA synthesis and silencing in trans in fission yeast. EMBO Rep. 11, 112–118 (2010).

    CAS  PubMed  PubMed Central  Google Scholar 

  91. Iida, T., Nakayama, J. & Moazed, D. siRNA-mediated heterochromatin establishment requires HP1 and is associated with antisense transcription. Mol. Cell 31, 178–189 (2008).

    CAS  PubMed  PubMed Central  Google Scholar 

  92. Sadeghi, L., Prasad, P., Ekwall, K., Cohen, A. & Svensson, J. P. The Paf1 complex factors Leo1 and Paf1 promote local histone turnover to modulate chromatin states in fission yeast. EMBO Rep. 16, 1673–1687 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  93. Kowalik, K. M. et al. The Paf1 complex represses small-RNA-mediated epigenetic gene silencing. Nature 520, 248–252 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  94. Verrier, L. et al. Global regulation of heterochromatin spreading by Leo1. Open Biol. 5, 150045 (2015). References 92–94 show that the Paf1 complex, which is a Pol II elongation factor, inhibits heterochromatin assembly.

    PubMed  PubMed Central  Google Scholar 

  95. Yu, R., Jih, G., Iglesias, N. & Moazed, D. Determinants of heterochromatic siRNA biogenesis and function. Mol. Cell 53, 262–276 (2014).

    CAS  PubMed  Google Scholar 

  96. Wang, J. et al. The proper connection between shelterin components is required for telomeric heterochromatin assembly. Genes Dev. 30, 827–839 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  97. Kanoh, J., Sadaie, M., Urano, T. & Ishikawa, F. Telomere binding protein Taz1 establishes Swi6 heterochromatin independently of RNAi at telomeres. Curr. Biol. 15, 1808–1819 (2005).

    CAS  PubMed  Google Scholar 

  98. Hansen, K. R., Ibarra, P. T. & Thon, G. Evolutionary-conserved telomere-linked helicase genes of fission yeast are repressed by silencing factors, RNAi components and the telomere-binding protein Taz1. Nucleic Acids Res. 34, 78–88 (2006).

    CAS  PubMed  PubMed Central  Google Scholar 

  99. Weick, E. M. & Miska, E. A. piRNAs: from biogenesis to function. Development 141, 3458–3471 (2014).

    CAS  PubMed  Google Scholar 

  100. Das, P. P. et al. Piwi and piRNAs act upstream of an endogenous siRNA pathway to suppress Tc3 transposon mobility in the Caenorhabditis elegans germline. Mol. Cell 31, 79–90 (2008).

    CAS  PubMed  PubMed Central  Google Scholar 

  101. Gu, T. & Elgin, S. C. Maternal depletion of Piwi, a component of the RNAi system, impacts heterochromatin formation in Drosophila. PLoS Genet. 9, e1003780 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  102. Blevins, T. et al. A two-step process for epigenetic inheritance in Arabidopsis. Mol. Cell 54, 30–42 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  103. Wutz, A. & Jaenisch, R. A shift from reversible to irreversible X inactivation is triggered during ES cell differentiation. Mol. Cell 5, 695–705 (2000).

    CAS  PubMed  Google Scholar 

  104. Csankovszki, G., Nagy, A. & Jaenisch, R. Synergism of Xist RNA, DNA methylation, and histone hypoacetylation in maintaining X chromosome inactivation. J. Cell Biol. 153, 773–784 (2001).

    CAS  PubMed  PubMed Central  Google Scholar 

  105. Elgin, S. C. & Reuter, G. Position-effect variegation, heterochromatin formation, and gene silencing in Drosophila. Cold Spring Harb. Perspect. Biol. 5, a017780 (2013).

    PubMed  PubMed Central  Google Scholar 

  106. Spofford, J. B. Parental control of position-effect variegation: I. Parental heterochromatin and expression of the white locus in compound-X Drosophila melanogaster. Proc. Natl Acad. Sci. USA 45, 1003–1007 (1959).

    CAS  PubMed  PubMed Central  Google Scholar 

  107. Tartof, K. D., Hobbs, C. & Jones, M. A structural basis for variegating position effects. Cell 37, 869–878 (1984).

    CAS  PubMed  Google Scholar 

  108. Talbert, P. B. & Henikoff, S. A reexamination of spreading of position-effect variegation in the white-roughest region of Drosophila melanogaster. Genetics 154, 259–272 (2000).

    CAS  PubMed  PubMed Central  Google Scholar 

  109. Hecht, A., Strahl-Bolsinger, S. & Grunstein, M. Spreading of transcriptional repressor SIR3 from telomeric heterochromatin. Nature 383, 92–96 (1996).

    CAS  PubMed  Google Scholar 

  110. Hecht, A., Laroche, T., Strahl-Bolsinger, S., Gasser, S. M. & Grunstein, M. Histone H3 and H4 N-termini interact with SIR3 and SIR4 proteins: a molecular model for the formation of heterochromatin in yeast. Cell 80, 583–592 (1995).

    CAS  PubMed  Google Scholar 

  111. Renauld, H. et al. Silent domains are assembled continuously from the telomere and are defined by promoter distance and strength, and by SIR3 dosage. Genes Dev. 7, 1133–1145 (1993).

    CAS  PubMed  Google Scholar 

  112. Al-Sady, B., Madhani, H. D. & Narlikar, G. J. Division of labor between the chromodomains of HP1 and Suv39 methylase enables coordination of heterochromatin spread. Mol. Cell 51, 80–91 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  113. Yamada, T., Fischle, W., Sugiyama, T., Allis, C. D. & Grewal, S. I. The nucleation and maintenance of heterochromatin by a histone deacetylase in fission yeast. Mol. Cell 20, 173–185 (2005).

    CAS  PubMed  Google Scholar 

  114. Obersriebnig, M. J., Pallesen, E. M., Sneppen, K., Trusina, A. & Thon, G. Nucleation and spreading of a heterochromatic domain in fission yeast. Nat. Commun. 7, 11518 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  115. Erdel, F. & Greene, E. C. Generalized nucleation and looping model for epigenetic memory of histone modifications. Proc. Natl Acad. Sci. USA 113, E4180–E4189 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  116. Larson, A. G. et al. Liquid droplet formation by HP1α suggests a role for phase separation in heterochromatin. Nature 547, 236–240 (2017). The paper demonstrates that human HP1 α can undergo phase separation in vitro upon phosphorylation and that this correlates with its ability to form foci in vivo.

    CAS  PubMed  PubMed Central  Google Scholar 

  117. Strom, A. R. et al. Phase separation drives heterochromatin domain formation. Nature 547, 241–245 (2017). The article shows that D. melanogaster HP1a can undergo phase separation in vitro and that heterochromatic foci in fly and human cells have the properties of liquid droplets.

    CAS  PubMed  PubMed Central  Google Scholar 

  118. Simon, M. D. et al. High-resolution Xist binding maps reveal two-step spreading during X-chromosome inactivation. Nature 504, 465–469 (2013). High-resolution RNA mapping identifies the phases of XIST assembly during X inactivation, revealing initial binding to gene-rich regions before appearance in gene-poor regions.

    CAS  PubMed  PubMed Central  Google Scholar 

  119. Engreitz, J. M. et al. The Xist lncRNA exploits three-dimensional genome architecture to spread across the X chromosome. Science 341, 1237973 (2013). The article examines X inactivation in the context of long-range chromatin interactions and concludes that XIST first spreads from the X chromosome inactivation centre to regions in close 3D proximity to the initiating locus.

    PubMed  PubMed Central  Google Scholar 

  120. White, W. M., Willard, H. F., Van Dyke, D. L. & Wolff, D. J. The spreading of X inactivation into autosomal material of an x;autosome translocation: evidence for a difference between autosomal and X-chromosomal DNA. Am. J. Hum. Genet. 63, 20–28 (1998).

    CAS  PubMed  PubMed Central  Google Scholar 

  121. Popova, B. C., Tada, T., Takagi, N., Brockdorff, N. & Nesterova, T. B. Attenuated spread of X-inactivation in an X;autosome translocation. Proc. Natl Acad. Sci. USA 103, 7706–7711 (2006).

    CAS  PubMed  PubMed Central  Google Scholar 

  122. Bala Tannan, N. et al. DNA methylation profiling in X;autosome translocations supports a role for L1 repeats in the spread of X chromosome inactivation. Hum. Mol. Genet. 23, 1224–1236 (2014).

    CAS  PubMed  Google Scholar 

  123. Wutz, A., Rasmussen, T. P. & Jaenisch, R. Chromosomal silencing & localization are mediated by different domains of Xist RNA. Nat. Genet. 30, 167–174 (2002).

    CAS  PubMed  Google Scholar 

  124. Lee, J. T. & Jaenisch, R. Long-range cis effects of ectopic X-inactivation centres on a mouse autosome. Nature 386, 275–279 (1997).

    CAS  PubMed  Google Scholar 

  125. Herzing, L. B., Romer, J. T., Horn, J. M. & Ashworth, A. Xist has properties of the X-chromosome inactivation centre. Nature 386, 272–275 (1997).

    CAS  PubMed  Google Scholar 

  126. da Rocha, S. T. & Heard, E. Novel players in X inactivation: insights into Xist-mediated gene silencing and chromosome conformation. Nat. Struct. Mol. Biol. 24, 197–204 (2017).

    CAS  PubMed  Google Scholar 

  127. Jiang, J. et al. Translating dosage compensation to trisomy 21. Nature 500, 296–300 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  128. Raab, J. R. et al. Human tRNA genes function as chromatin insulators. EMBO J. 31, 330–350 (2012).

    CAS  PubMed  Google Scholar 

  129. Donze, D., Adams, C. R., Rine, J. & Kamakaka, R. T. The boundaries of the silenced HMR domain in Saccharomyces cerevisiae. Genes Dev. 13, 698–708 (1999).

    CAS  PubMed  PubMed Central  Google Scholar 

  130. Scott, K. C., Merrett, S. L. & Willard, H. F. A heterochromatin barrier partitions the fission yeast centromere into discrete chromatin domains. Curr. Biol. 16, 119–129 (2006).

    CAS  PubMed  Google Scholar 

  131. Noma, K., Cam, H. P., Maraia, R. J. & Grewal, S. I. A role for TFIIIC transcription factor complex in genome organization. Cell 125, 859–872 (2006).

    CAS  PubMed  Google Scholar 

  132. Coveney, J. & Woodland, H. R. The DNase I sensitivity of Xenopus laevis genes transcribed by RNA polymerase III. Nature 298, 578–580 (1982).

    CAS  PubMed  Google Scholar 

  133. DeLotto, R. & Schedl, P. Internal promoter elements of transfer RNA genes are preferentially exposed in chromatin. J. Mol. Biol. 179, 607–628 (1984).

    CAS  PubMed  Google Scholar 

  134. Takahashi, K. et al. A low copy number central sequence with strict symmetry and unusual chromatin structure in fission yeast centromere. Mol. Biol. Cell 3, 819–835 (1992).

    CAS  PubMed  PubMed Central  Google Scholar 

  135. Aygun, O., Mehta, S. & Grewal, S. I. HDAC-mediated suppression of histone turnover promotes epigenetic stability of heterochromatin. Nat. Struct. Mol. Biol. 20, 547–554 (2013).

    PubMed  PubMed Central  Google Scholar 

  136. Hartley, P. D. & Madhani, H. D. Mechanisms that specify promoter nucleosome location and identity. Cell 137, 445–458 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  137. Raisner, R. M. et al. Histone variant H2A.Z marks the 5′ ends of both active and inactive genes in euchromatin. Cell 123, 233–248 (2005).

    CAS  PubMed  PubMed Central  Google Scholar 

  138. Meneghini, M. D., Wu, M. & Madhani, H. D. Conserved histone variant H2A.Z protects euchromatin from the ectopic spread of silent heterochromatin. Cell 112, 725–736 (2003).

    CAS  PubMed  Google Scholar 

  139. Venkatasubrahmanyam, S., Hwang, W. W., Meneghini, M. D., Tong, A. H. & Madhani, H. D. Genome-wide, as opposed to local, antisilencing is mediated redundantly by the euchromatic factors Set1 and H2A.Z. Proc. Natl Acad. Sci. USA 104, 16609–16614 (2007).

    CAS  PubMed  PubMed Central  Google Scholar 

  140. Tompa, R. & Madhani, H. D. Histone H3 lysine 36 methylation antagonizes silencing in Saccharomyces cerevisiae independently of the Rpd3S histone deacetylase complex. Genetics 175, 585–593 (2007).

    CAS  PubMed  PubMed Central  Google Scholar 

  141. Santos-Rosa, H., Bannister, A. J., Dehe, P. M., Geli, V. & Kouzarides, T. Methylation of H3 lysine 4 at euchromatin promotes Sir3p association with heterochromatin. J. Biol. Chem. 279, 47506–47512 (2004).

    CAS  PubMed  Google Scholar 

  142. van Leeuwen, F., Gafken, P. R. & Gottschling, D. E. Dot1p modulates silencing in yeast by methylation of the nucleosome core. Cell 109, 745–756 (2002).

    CAS  PubMed  Google Scholar 

  143. Verzijlbergen, K. F., Faber, A. W., Stulemeijer, I. J. & van Leeuwen, F. Multiple histone modifications in euchromatin promote heterochromatin formation by redundant mechanisms in Saccharomyces cerevisiae. BMC Mol. Biol. 10, 76 (2009).

    PubMed  PubMed Central  Google Scholar 

  144. Li, X. et al. Chromatin boundaries require functional collaboration between the hSET1 and NURF complexes. Blood 118, 1386–1394 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  145. Ayoub, N. et al. A novel jmjC domain protein modulates heterochromatization in fission yeast. Mol. Cell. Biol. 23, 4356–4370 (2003).

    CAS  PubMed  PubMed Central  Google Scholar 

  146. Trewick, S. C., McLaughlin, P. J. & Allshire, R. C. Methylation: lost in hydroxylation? EMBO Rep. 6, 315–320 (2005).

    CAS  PubMed  PubMed Central  Google Scholar 

  147. Zofall, M. & Grewal, S. I. Swi6/HP1 recruits a JmjC domain protein to facilitate transcription of heterochromatic repeats. Mol. Cell 22, 681–692 (2006).

    CAS  PubMed  Google Scholar 

  148. Trewick, S. C., Minc, E., Antonelli, R., Urano, T. & Allshire, R. C. The JmjC domain protein Epe1 prevents unregulated assembly and disassembly of heterochromatin. EMBO J. 26, 4670–4682 (2007).

    CAS  PubMed  PubMed Central  Google Scholar 

  149. Braun, S. et al. The Cul4-DdbCdt2 ubiquitin ligase inhibits invasion of a boundary-associated antisilencing factor into heterochromatin. Cell 144, 41–54 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  150. Garcia, J. F., Al-Sady, B. & Madhani, H. D. Intrinsic toxicity of unchecked heterochromatin spread is suppressed by redundant chromatin boundary functions in Schizosacchromyces pombe. G3 5, 1453–1461 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  151. Wang, J., Reddy, B. D. & Jia, S. Rapid epigenetic adaptation to uncontrolled heterochromatin spreading. eLife 4, e06179 (2015). Increased H3K9me-dependent heterochromatin formation in fission yeast cells lacking factors that counteract its assembly can be suppressed by spontaneous heterochromatin-mediated silencing of genes encoding components of the Clr4 histone H3K9 methyltransferase complex.

    PubMed Central  Google Scholar 

  152. Lee, N. N. et al. Mtr4-like protein coordinates nuclear RNA processing for heterochromatin assembly and for telomere maintenance. Cell 155, 1061–1074 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  153. Zofall, M. et al. RNA elimination machinery targeting meiotic mRNAs promotes facultative heterochromatin formation. Science 335, 96–100 (2012).

    CAS  PubMed  Google Scholar 

  154. Yamanaka, S. et al. RNAi triggered by specialized machinery silences developmental genes and retrotransposons. Nature 493, 557–560 (2013).

    CAS  PubMed  Google Scholar 

  155. Joh, R. I. et al. Survival in quiescence requires the euchromatic deployment of Clr4/SUV39H by Argonaute-associated small RNAs. Mol. Cell 64, 1088–1101 (2016). References 152–155 report the presence of regulated heterochromatin islands outside of the main heterochromatin domains at centromeres, telomeres and the mating-type loci in fission yeast.

    CAS  PubMed  PubMed Central  Google Scholar 

  156. Dumesic, P. A. et al. Product binding enforces the genomic specificity of a yeast polycomb repressive complex. Cell 160, 204–218 (2015). Reports the first yeast Polycomb system in C. neoformans and reveals that tethering of its PRC2-like complex to sites of previous action at subtelomeric regions prevents it from erroneously modifying H3K9me-marked centromeric heterochromatin.

    CAS  PubMed  Google Scholar 

  157. Alabert, C. & Groth, A. Chromatin replication and epigenome maintenance. Nat. Rev. Mol. Cell. Biol. 13, 153–167 (2012).

    CAS  PubMed  Google Scholar 

  158. Jones, P. A. & Liang, G. Rethinking how DNA methylation patterns are maintained. Nat. Rev. Genet. 10, 805–811 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  159. Freitag, M., Hickey, P. C., Khlafallah, T. K., Read, N. D. & Selker, E. U. HP1 is essential for DNA methylation in Neurospora. Mol. Cell 13, 427–434 (2004).

    CAS  PubMed  Google Scholar 

  160. Du, J., Johnson, L. M., Jacobsen, S. E. & Patel, D. J. DNA methylation pathways and their crosstalk with histone methylation. Nat. Rev. Mol. Cell. Biol. 16, 519–532 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  161. Wang, X. & Moazed, D. DNA sequence-dependent epigenetic inheritance of gene silencing and histone H3K9 methylation. Science 356, 88–91 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  162. Kagansky, A. et al. Synthetic heterochromatin bypasses RNAi and centromeric repeats to establish functional centromeres. Science 324, 1716–1719 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  163. Audergon, P. N. et al. Epigenetics. Restricted epigenetic inheritance of H3K9 methylation. Science 348, 132–135 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  164. Ragunathan, K., Jih, G. & Moazed, D. Epigenetic inheritance uncoupled from sequence-specific recruitment. Science 348, 1258699 (2015). References 163 and 164 demonstrate that transient tethering of the Clr4 H3K9 methyltransferase to a genomic site in fission yeast results in the formation of heritable heterochromatin and gene silencing, provided that a histone demethylase, Epe1, is removed from cells.

    PubMed  Google Scholar 

  165. Bintu, L. et al. Dynamics of epigenetic regulation at the single-cell level. Science 351, 720–724 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  166. Amabile, A. et al. Inheritable silencing of endogenous genes by hit-and-run targeted epigenetic editing. Cell 167, 219–232.e14 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  167. Hathaway, N. A. et al. Dynamics and memory of heterochromatin in living cells. Cell 149, 1447–1460 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  168. Berry, S., Hartley, M., Olsson, T. S., Dean, C. & Howard, M. Local chromatin environment of a Polycomb target gene instructs its own epigenetic inheritance. eLife 4, e07205 (2015).

    PubMed Central  Google Scholar 

  169. Laprell, F., Finkl, K. & Muller, J. Propagation of Polycomb-repressed chromatin requires sequence-specific recruitment to DNA. Science 356, 85–88 (2017).

    CAS  PubMed  Google Scholar 

  170. Coleman, R. T. & Struhl, G. Causal role for inheritance of H3K27me3 in maintaining the OFF state of a Drosophila HOX gene. Science http://dx.doi.org/10.1126/science.aai8236 (2017). References 169 and 170 show that binding sites for DNA-binding proteins are required for the heritability of H3K27me-marked silent domains in D. melanogaster.

  171. Grewal, S. I. & Klar, A. J. Chromosomal inheritance of epigenetic states in fission yeast during mitosis and meiosis. Cell 86, 95–101 (1996).

    CAS  PubMed  Google Scholar 

  172. Jia, S., Noma, K. & Grewal, S. I. RNAi-independent heterochromatin nucleation by the stress-activated ATF/CREB family proteins. Science 304, 1971–1976 (2004).

    CAS  PubMed  Google Scholar 

  173. Taneja, N. et al. SNF2 family protein Fft3 suppresses nucleosome turnover to promote epigenetic inheritance and proper replication. Mol. Cell 66, 50–62.e6 (2017).

    CAS  PubMed  PubMed Central  Google Scholar 

  174. Steglich, B. et al. The Fun30 chromatin remodeler Fft3 controls nuclear organization and chromatin structure of insulators and subtelomeres in fission yeast. PLoS Genet. 11, e1005101 (2015).

    PubMed  PubMed Central  Google Scholar 

  175. Stralfors, A., Walfridsson, J., Bhuiyan, H. & Ekwall, K. The FUN30 chromatin remodeler, Fft3, protects centromeric and subtelomeric domains from euchromatin formation. PLOS Genet. 7, e1001334 (2011).

    PubMed  PubMed Central  Google Scholar 

  176. Mari-Ordonez, A. et al. Reconstructing de novo silencing of an active plant retrotransposon. Nat. Genet. 45, 1029–1039 (2013).

    CAS  PubMed  Google Scholar 

  177. Lanciano, S. et al. Sequencing the extrachromosomal circular mobilome reveals retrotransposon activity in plants. PLOS Genet. 13, e1006630 (2017).

    PubMed  PubMed Central  Google Scholar 

  178. Hickey, D. A. Selfish DNA: a sexually-transmitted nuclear parasite. Genetics 101, 519–531 (1982).

    CAS  PubMed  PubMed Central  Google Scholar 

  179. Zeller, P. et al. Histone H3K9 methylation is dispensable for Caenorhabditis elegans development but suppresses RNA:DNA hybrid-associated repeat instability. Nat. Genet. 48, 1385–1395 (2016). This article reveals that C. elegans mutants lacking H3K9 methylation have increased levels of R-loops and consequent genetic instability.

    CAS  PubMed  Google Scholar 

  180. Klattenhoff, C. et al. The Drosophila HP1 homolog Rhino is required for transposon silencing and piRNA production by dual-strand clusters. Cell 138, 1137–1149 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  181. Sienski, G., Donertas, D. & Brennecke, J. Transcriptional silencing of transposons by Piwi and maelstrom and its impact on chromatin state and gene expression. Cell 151, 964–980 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  182. Brennecke, J. et al. Discrete small RNA-generating loci as master regulators of transposon activity in Drosophila. Cell 128, 1089–1103 (2007).

    CAS  PubMed  Google Scholar 

  183. Aravin, A. A. et al. A piRNA pathway primed by individual transposons is linked to de novo DNA methylation in mice. Mol. Cell 31, 785–799 (2008).

    CAS  PubMed  PubMed Central  Google Scholar 

  184. Kojima-Kita, K. et al. MIWI2 as an effector of DNA methylation and gene silencing in embryonic male germ cells. Cell Rep. 16, 2819–2828 (2016).

    CAS  PubMed  Google Scholar 

  185. Kuramochi-Miyagawa, S. et al. DNA methylation of retrotransposon genes is regulated by Piwi family members MILI and MIWI2 in murine fetal testes. Genes Dev. 22, 908–917 (2008).

    CAS  PubMed  PubMed Central  Google Scholar 

  186. Peng, J. C. & Karpen, G. H. H3K9 methylation and RNA interference regulate nucleolar organization and repeated DNA stability. Nat. Cell Biol. 9, 25–35 (2007).

    CAS  PubMed  Google Scholar 

  187. Chiolo, I. et al. Double-strand breaks in heterochromatin move outside of a dynamic HP1a domain to complete recombinational repair. Cell 144, 732–744 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  188. Jakob, B. et al. DNA double-strand breaks in heterochromatin elicit fast repair protein recruitment, histone H2AX phosphorylation and relocation to euchromatin. Nucleic Acids Res. 39, 6489–6499 (2011).

    CAS  PubMed  PubMed Central  Google Scholar 

  189. Ryu, T. et al. Heterochromatic breaks move to the nuclear periphery to continue recombinational repair. Nat. Cell Biol. 17, 1401–1411 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  190. Tsouroula, K. et al. Temporal and spatial uncoupling of DNA double strand break repair pathways within mammalian heterochromatin. Mol. Cell 63, 293–305 (2016).

    CAS  PubMed  Google Scholar 

  191. Janssen, A. et al. A single double-strand break system reveals repair dynamics and mechanisms in heterochromatin and euchromatin. Genes Dev. 30, 1645–1657 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  192. McKinley, K. L. & Cheeseman, I. M. The molecular basis for centromere identity and function. Nat. Rev. Mol. Cell. Biol. 17, 16–29 (2016).

    CAS  PubMed  Google Scholar 

  193. Sullivan, L. L., Maloney, K. A., Towers, A. J., Gregory, S. G. & Sullivan, B. A. Human centromere repositioning within euchromatin after partial chromosome deletion. Chromosome Res. 24, 451–466 (2016).

    CAS  PubMed  PubMed Central  Google Scholar 

  194. Sato, H., Masuda, F., Takayama, Y., Takahashi, K. & Saitoh, S. Epigenetic inactivation and subsequent heterochromatinization of a centromere stabilize dicentric chromosomes. Curr. Biol. 22, 658–667 (2012).

    CAS  PubMed  Google Scholar 

  195. Nakano, M. et al. Inactivation of a human kinetochore by specific targeting of chromatin modifiers. Dev. Cell 14, 507–522 (2008).

    CAS  PubMed  PubMed Central  Google Scholar 

  196. Cardinale, S. et al. Hierarchical inactivation of a synthetic human kinetochore by a chromatin modifier. Mol. Biol. Cell 20, 4194–4204 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  197. Uhlmann, F. SMC complexes: from DNA to chromosomes. Nat. Rev. Mol. Cell. Biol. 17, 399–412 (2016).

    CAS  PubMed  Google Scholar 

  198. Bernard, P. et al. Requirement of heterochromatin for cohesion at centromeres. Science 294, 2539–2542 (2001).

    CAS  PubMed  Google Scholar 

  199. Nonaka, N. et al. Recruitment of cohesin to heterochromatic regions by Swi6/HP1 in fission yeast. Nat. Cell Biol. 4, 89–93 (2002).

    CAS  PubMed  Google Scholar 

  200. Pidoux, A. L., Uzawa, S., Perry, P. E., Cande, W. Z. & Allshire, R. C. Live analysis of lagging chromosomes during anaphase and their effect on spindle elongation rate in fission yeast. J. Cell Sci. 113, 4177–4191 (2000).

    CAS  PubMed  Google Scholar 

  201. Gregan, J. et al. The kinetochore proteins Pcs1 and Mde4 and heterochromatin are required to prevent merotelic orientation. Curr. Biol. 17, 1190–1200 (2007).

    CAS  PubMed  PubMed Central  Google Scholar 

  202. Ekwall, K. et al. The chromodomain protein Swi6: a key component at fission yeast centromeres. Science 269, 1429–1431 (1995).

    CAS  PubMed  Google Scholar 

  203. Tanno, Y. et al. The inner centromere-shugoshin network prevents chromosomal instability. Science 349, 1237–1240 (2015).

    CAS  PubMed  Google Scholar 

  204. Klar, A. J., Ishikawa, K. & Moore, S. A. Unique DNA recombination mechanism of the mating/cell-type switching of fission yeasts: a review. Microbiol. Spectr. 2, http://dx.doi.org/10.1128/microbiolspec.MDNA3-0003-2014 (2014).

  205. Jia, S., Yamada, T. & Grewal, S. I. Heterochromatin regulates cell type-specific long-range chromatin interactions essential for directed recombination. Cell 119, 469–480 (2004).

    CAS  PubMed  Google Scholar 

  206. Soufi, A., Donahue, G. & Zaret, K. S. Facilitators and impediments of the pluripotency reprogramming factors' initial engagement with the genome. Cell 151, 994–1004 (2012). This paper shows that megabase-sized heterochromatin domains in somatic cells impede the binding of pluripotency transcription factors to their targets.

    CAS  PubMed  PubMed Central  Google Scholar 

  207. Becker, J. S., Nicetto, D. & Zaret, K. S. H3K9me3-dependent heterochromatin: barrier to cell fate changes. Trends Genet. 32, 29–41 (2016).

    CAS  PubMed  Google Scholar 

  208. Chen, J. et al. H3K9 methylation is a barrier during somatic cell reprogramming into iPSCs. Nat. Genet. 45, 34–42 (2013).

    CAS  PubMed  Google Scholar 

  209. Sridharan, R. et al. Proteomic and genomic approaches reveal critical functions of H3K9 methylation and heterochromatin protein-1γ in reprogramming to pluripotency. Nat. Cell Biol. 15, 872–882 (2013).

    CAS  PubMed  PubMed Central  Google Scholar 

  210. Cheloufi, S. et al. The histone chaperone CAF-1 safeguards somatic cell identity. Nature 528, 218–224 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  211. Matoba, S. et al. Embryonic development following somatic cell nuclear transfer impeded by persisting histone methylation. Cell 159, 884–895 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  212. Castro-Diaz, N. et al. Evolutionally dynamic L1 regulation in embryonic stem cells. Genes Dev. 28, 1397–1409 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  213. Jacobs, F. M. J. et al. An evolutionary arms race between KRAB zinc-finger genes ZNF91/93 and SVA/L1 retrotransposons. Nature 516, 242–245 (2014).

    CAS  PubMed  PubMed Central  Google Scholar 

  214. Wolf, D. & Goff, S. P. Embryonic stem cells use ZFP809 to silence retroviral DNAs. Nature 458, 1201–1204 (2009).

    CAS  PubMed  PubMed Central  Google Scholar 

  215. Imbeault, M., Helleboid, P.-Y. & Trono, D. KRAB zinc-finger proteins contribute to the evolution of gene regulatory networks. Nature 543, 550–554 (2017). This paper shows that transposable elements in tetrapods are recognized and silenced by KRAB-ZFP proteins that coevolve with the elements in an ongoing arms race.

    CAS  PubMed  Google Scholar 

  216. Timms, R. T., Tchasovnikarova, I. A. & Lehner, P. J. Position-effect variegation revisited: HUSHing up heterochromatin in human cells. Bioessays 38, 333–343 (2016).

    CAS  PubMed  Google Scholar 

  217. Tchasovnikarova, I. A. et al. Epigenetic silencing by the HUSH complex mediates position-effect variegation in human cells. Science 348, 1481–1485 (2015). A genetic screen in haploid cells for factors that silence an integrated retroviral reporter identifies a protein complex containing the H3K9 methyltransferase SETDB1 and the H32K9me-binding MPP8 chromodomain protein.

    CAS  PubMed  PubMed Central  Google Scholar 

  218. Wolf, G. et al. The KRAB zinc finger protein ZFP809 is required to initiate epigenetic silencing of endogenous retroviruses. Genes Dev. 29, 538–554 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  219. Dalgaard, K. et al. Trim28 haploinsufficiency triggers bi-stable epigenetic obesity. Cell 164, 353–364 (2016). Haploinsufficiency of a component of the KRAB–KAP1 H3K9me-recruiting complex is shown to result in epigenetic variability in obesity in mice.

    CAS  PubMed  PubMed Central  Google Scholar 

  220. Zhang, W. et al. A Werner syndrome stem cell model unveils heterochromatin alterations as a driver of human aging. Science 348, 1160–1163 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  221. Janke, R., Dodson, A. E. & Rine, J. Metabolism and epigenetics. Annu. Rev. Cell Dev. Biol. 31, 473–496 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  222. Sharma, U. & Rando, O. J. Metabolic inputs into the epigenome. Cell Metab. 25, 544–558 (2017).

    CAS  PubMed  Google Scholar 

  223. Lu, C. et al. IDH mutation impairs histone demethylation and results in a block to cell differentiation. Nature 483, 474–478 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  224. Xiao, M. et al. Inhibition of α-KG-dependent histone and DNA demethylases by fumarate and succinate that are accumulated in mutations of FH and SDH tumor suppressors. Genes Dev. 26, 1326–1338 (2012).

    CAS  PubMed  PubMed Central  Google Scholar 

  225. Carey, B. W., Finley, L. W. S., Cross, J. R., Allis, C. D. & Thompson, C. B. Intracellular α-ketoglutarate maintains the pluripotency of embryonic stem cells. Nature 518, 413–416 (2015).

    CAS  PubMed  Google Scholar 

  226. Pan, M. et al. Regional glutamine deficiency in tumours promotes dedifferentiation through inhibition of histone demethylation. Nat. Cell Biol. 18, 1090–1101 (2016). References 223–226 show how imbalances in metabolite levels generated by the tricarboxylic acid cycle because of mutation, oversupply or undersupply of nutrients result in altered cell fate and tumorigenesis.

    CAS  PubMed  PubMed Central  Google Scholar 

  227. Janke, R., Iavarone, A. T. & Rine, J. Oncometabolite D-2-hydroxyglutarate enhances gene silencing through inhibition of specific H3K36 histone demethylases. eLife 6, e22451 (2017).

    PubMed  PubMed Central  Google Scholar 

  228. Passarge, E. Emil Heitz and the concept of heterochromatin: longitudinal chromosome differentiation was recognized fifty years ago. Am. J. Hum. Genet. 31, 106 (1979).

    CAS  PubMed  PubMed Central  Google Scholar 

  229. Muller, H. J. Types of visible variations induced by X-rays in Drosophila. J. Genet. 22, 299–334 (1930).

    Google Scholar 

  230. Schultz, J. Variegation in Drosophila and the inert chromosome regions. Proc. Natl Acad. Sci. USA 22, 27–33 (1936).

    CAS  PubMed  PubMed Central  Google Scholar 

  231. Gowen, J. & Gay, E. Chromosome constitution and behavior in eversporting and mottling in Drosophila melanogaster. Genetics 19, 189 (1934).

    CAS  PubMed  PubMed Central  Google Scholar 

  232. Dimitri, P. & Pisano, C. Position effect variegation in Drosophila melanogaster: relationship between suppression effect and the amount of Y chromosome. Genetics 122, 793–800 (1989).

    CAS  PubMed  PubMed Central  Google Scholar 

  233. Spradling, A. C. & Karpen, G. H. Sixty years of mystery. Genetics 126, 779–784 (1990).

    CAS  PubMed  PubMed Central  Google Scholar 

  234. Henikoff, S. Position-effect variegation after 60 years. Trends Genet. 6, 422–426 (1990).

    CAS  PubMed  Google Scholar 

  235. Reute, G. & Spierer, P. Position effect variegation and chromatin proteins. BioEssays 14, 605–612 (1992).

    Google Scholar 

  236. Britten, R. J. & Kohne, D. E. Repeated Sequences in DNA. Science 161, 529–540 (1968).

    CAS  PubMed  Google Scholar 

  237. Kit, S. Equilibrium sedimentation in density gradients of DNA preparations from animal tissues. J. Mol. Biol. 3, 711–716 (1961).

    CAS  PubMed  Google Scholar 

  238. Yasmineh, W. G. & Yunis, J. J. Localization of mouse satellite DNA in constitutive heterochromatin. Exp. Cell Res. 59, 69–75 (1970).

    CAS  PubMed  Google Scholar 

  239. Flamm, W. G., Bond, H. E., Burr, H. E. & Bond, S. B. Satellite DNA isolated from mouse liver; some physical and metabolic properties. Biochim. Biophys. Acta 123, 652–654 (1966).

    CAS  PubMed  Google Scholar 

  240. Flamm, W. G., McCallum, M. & Walker, P. M. The isolation of complementary strands from a mouse DNA fraction. Proc. Natl Acad. Sci. USA 57, 1729–1734 (1967).

    CAS  PubMed  PubMed Central  Google Scholar 

  241. Filipski, J., Thiery, J.-P. & Bernardi, G. An analysis of the bovine genome by Cs2SO4—Ag+ density gradient centrifugation. J. Mol. Biol. 80, 177–197 (1973).

    CAS  PubMed  Google Scholar 

  242. Southern, E. M. Base sequence and evolution of guinea-pig α-satellite DNA. Nature 227, 794–798 (1970).

    CAS  PubMed  Google Scholar 

  243. Fry, K. et al. Nucleotide sequence of HS-β satellite DNA from kangaroo rat Dipodomys ordii. Proc. Natl Acad. Sci. USA 70, 2642 (1973).

    CAS  PubMed  PubMed Central  Google Scholar 

  244. Jones, K. W. Chromosomal and nuclear location of mouse satellite DNA in individual cells. Nature 225, 912–915 (1970).

    CAS  PubMed  Google Scholar 

  245. Pardue, M. L. & Gall, J. G. Chromosomal localization of mouse satellite DNA. Science 168, 1356–1358 (1970).

    CAS  PubMed  Google Scholar 

  246. Rae, P. M. M. & Franke, W. W. The interphase distribution of satellite DNA-containing heterochromatin in mouse nuclei. Chromosoma 39, 443–456 (1972).

    CAS  PubMed  Google Scholar 

  247. Flamm, W. G., Walker, P. M. & McCallum, M. Some properties of the single strands isolated from the DNA of the nuclear satellite of the mouse (Mus musculus). J. Mol. Biol. 40, 423–443 (1969).

    CAS  PubMed  Google Scholar 

  248. Yunis, J. J. & Yasmineh, W. G. Satellite DNA in constitutive heterochromatin of the guinea pig. Science 168, 263–265 (1970).

    CAS  PubMed  Google Scholar 

  249. Lima-de-Faria, A. & Jaworska, H. Late DNA Synthesis in heterochromatin. Nature 217, 138–142 (1968).

    CAS  PubMed  Google Scholar 

  250. Gall, J., Cohen, E. & Polan, M. Repetitive DNA sequences in Drosophila. Chromosoma 33, 319–344 (1971).

    CAS  PubMed  Google Scholar 

  251. Deans, C. & Maggert, K. A. What do you mean, “epigenetic”? Genetics 199, 887–896 (2015).

    CAS  PubMed  PubMed Central  Google Scholar 

  252. Bird, A. Perceptions of epigenetics. Nature 447, 396–398 (2007).

    CAS  PubMed  Google Scholar 

  253. Castel, S. E. & Martienssen, R. A. RNA interference in the nucleus: roles for small RNAs in transcription, epigenetics and beyond. Nat. Rev. Mol. Cell. Biol. 14, 100–112 (2013).

    CAS  Google Scholar 

Download references

Acknowledgements

R.C.A. is a Wellcome Principal Research Fellow; his research is supported by the UK Wellcome Trust (200885) and core funding of the UK Wellcome Centre for Cell Biology (203149). Research in the laboratory of H.D.M. is supported by grants from the US National Institutes of Health. H.D.M. is a Chan-Zuckerberg BioHub investigator. The authors apologize to colleagues whose work could not be cited because of length restrictions. The authors dedicate this piece to the memory of A. Klar, whose pioneering studies of cell-type specification and gene silencing in Saccharomyces cerevisiae and Schizosaccharomyces pombe paved the way for many advances.

Author information

Authors and Affiliations

Authors

Contributions

R.C.A. and H.D.M. each researched data for the article, made substantial contributions to the discussion of content, wrote the manuscript and reviewed and edited it before submission.

Corresponding authors

Correspondence to Robin C. Allshire or Hiten D. Madhani.

Ethics declarations

Competing interests

The authors declare no competing financial interests.

PowerPoint slides

Glossary

Post-translational modifications

(PTMs). Chemical groups (such as methyl or acetyl) on amino acid side chains that are enzymatically added by 'writer', removed by 'eraser' and recognized by 'reader' protein modules.

Satellite repeats

Short repetitive sequences that exhibit a distinct satellite peak on buoyant density gradients owing to their skewed base composition.

Constitutive heterochromatin

In most eukaryotes, heterochromatin that is consistently formed throughout the cell cycle and in many cell types, for example, centrome-reassociated heterochromatin.

Facultative heterochromatin

Locus-specific and cell-type-specific heterochromatin, for example, the inactive X chromosome in mammals.

Chromoshadow domain

(CSD). Dimerization domain in heterochromatin protein 1-related proteins that forms a peptide-binding groove at the dimer interface that can recruit additional heterochromatin proteins.

Argonaute

Proteins with PAZ and Piwi domains that are loaded with small RNAs, which target them and their associated proteins to long RNAs that bear homology to the small RNA.

Pericentromeric heterochromatin

Large blocks of heterochromatin formed on the tandem repeats that surround the centromere–kinetochore region.

X chromosome inactivation

Mechanism of dosage compensation in female mammals in which one of the two X chromosomes is inactivated by the formation of facultative heterochromatin.

X-inactive specific transcript

(XIST). Long noncoding RNA that designates the X chromosome from which it is expressed for X chromosome inactivation.

Piwi-associated RNAs

(piRNAs). Small RNAs associated with Piwi members of the Argonaute protein superfamily, which promotes repression of transposable elements in animal gonads.

R-loops

Nascent RNA that remains associated with its DNA template through hybridization, thereby dislodging the opposite, nontemplate DNA strand.

Heterochromatin islands

Extensive domains of heterochromatin on chromosome arms, which are distinct from the main centromeric and telomeric heterochromatin domains.

Reprogramming-resistant regions

Large lineage-specific chromosomal regions that are assembled into heterochromatin and thus resist binding by reprogramming factors.

Endogenous retroelements

Mobile elements that replicate through reverse transcription followed by genomic integration. The term also includes degenerate, immobile elements.

Rights and permissions

Reprints and Permissions

About this article

Verify currency and authenticity via CrossMark

Cite this article

Allshire, R., Madhani, H. Ten principles of heterochromatin formation and function. Nat Rev Mol Cell Biol 19, 229–244 (2018). https://doi.org/10.1038/nrm.2017.119

Download citation

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1038/nrm.2017.119

Further reading

Search

Quick links

Nature Briefing

Sign up for the Nature Briefing newsletter — what matters in science, free to your inbox daily.

Get the most important science stories of the day, free in your inbox. Sign up for Nature Briefing