Abstract
Insulators prevent promiscuous gene regulation by restricting the action of enhancers and silencers. Recent studies have revealed a number of similarities between insulators and promoters, including binding of specific transcription factors, chromatin-modification signatures and localization to specific subnuclear positions. We propose that enhancer-blockers and silencing barrier-insulators might have evolved as specialized derivatives of promoters and that the two types of element use related mechanisms to mediate their distinct functions. These insights can help to reconcile different models of insulator action.
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References
Verdel, A. & Moazed, D. RNAi-directed assembly of heterochromatin in fission yeast. FEBS Lett. 579, 5872–5878 (2005).
Pirrotta, V. & Gross, D. S. Epigenetic silencing mechanisms in budding yeast and fruit fly: different paths, same destinations. Mol. Cell 18, 395–398 (2005).
Cairns, B. R. The logic of chromatin architecture and remodelling at promoters. Nature 461, 193–198 (2009).
Blackwood, E. M. & Kadonaga, J. T. Going the distance: a current view of enhancer action. Science 281, 61–63 (1998).
Juven-Gershon, T. & Kadonaga, J. T. Regulation of gene expression via the core promoter and the basal transcriptional machinery. Dev. Biol. 339, 225–229 (2010).
West, A. G. & Fraser, P. Remote control of gene transcription. Hum. Mol. Genet. 14, R101–R111 (2005).
Stamatoyannopoulos, G. Control of globin gene expression during development and erythroid differentiation. Exp. Hematol. 33, 259–271 (2005).
Feinberg, A. P. Phenotypic plasticity and the epigenetics of human disease. Nature 447, 433–440 (2007).
Valenzuela, L. & Kamakaka, R. T. Chromatin insulators. Annu. Rev. Genet. 40, 107–138 (2006).
Gaszner, M. & Felsenfeld, G. Insulators: exploiting transcriptional and epigenetic mechanisms. Nature Rev. Genet. 7, 703–713 (2006).
Roseman, R. R., Pirrotta, V. & Geyer, P. K. The su(Hw) protein insulates expression of the Drosophila melanogaster white gene from chromosomal position-effects. EMBO J. 12, 435–442 (1993).
Majumder, P. et al. Diverse transcription influences can be insulated by the Drosophila SF1 chromatin boundary. Nucleic Acids Res. 37, 4227–4233 (2009).
Chung, J. H., Whiteley, M. & Felsenfeld, G. A 5′ element of the chicken β-globin domain serves as an insulator in human erythroid cells and protects against position effect in Drosophila. Cell 74, 505–514 (1993).
Lunyak, V. V. et al. Developmentally regulated activation of a SINE B2 repeat as a domain boundary in organogenesis. Science 317, 248–251 (2007).
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).
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).
Valenzuela, L., Dhillon, N. & Kamakaka, R. T. Transcription independent insulation at TFIIIC-dependent insulators. Genetics 183, 131–148 (2009).
Simms, T. A. et al. TFIIIC binding sites function as both heterochromatin barriers and chromatin insulators in Saccharomyces cerevisiae. Eukaryot. Cell 7, 2078–2086 (2008).
Recillas-Targa, F. et al. Position-effect protection and enhancer blocking by the chicken β-globin insulator are separable activities. Proc. Natl Acad. Sci. USA 99, 6883–6888 (2002).
Yusufzai, T. M., Tagami, H., Nakatani, Y. & Felsenfeld, G. CTCF tethers an insulator to subnuclear sites, suggesting shared insulator mechanisms across species. Mol. Cell 13, 291–298 (2004).
West, A. G., Huang, S., Gaszner, M., Litt, M. D. & Felsenfeld, G. Recruitment of histone modifications by USF proteins at a vertebrate barrier element. Mol. Cell 16, 453–463 (2004).
Huang, S., Li, X., Yusufzai, T. M., Qiu, Y. & Felsenfeld, G. USF1 recruits histone modification complexes and is critical for maintenance of a chromatin barrier. Mol. Cell. Biol. 27, 7991–8002 (2007).
Dickson, J. et al. VEZF1 elements mediate protection from DNA methylation. PLoS Genet. 6, e1000804 (2010).
Filippova, G. N. et al. Boundaries between chromosomal domains of X inactivation and escape bind CTCF and lack CpG methylation during early development. Dev. Cell 8, 31–42 (2005).
Ottaviani, A. et al. The D4Z4 macrosatellite repeat acts as a CTCF and A-type lamins-dependent insulator in facio-scapulo-humeral dystrophy. PLoS Genet. 5, e1000394 (2009).
Cuddapah, S. et al. Global analysis of the insulator binding protein CTCF in chromatin barrier regions reveals demarcation of active and repressive domains. Genome Res. 19, 24–32 (2009).
Guelen, L. et al. Domain organization of human chromosomes revealed by mapping of nuclear lamina interactions. Nature 453, 948–951 (2008).
Wendt, K. S. & Peters, J. M. How cohesin and CTCF cooperate in regulating gene expression. Chromosome Res. 17, 201–214 (2009).
Dubey, R. N. & Gartenberg, M. R. A tDNA establishes cohesion of a neighboring silent chromatin domain. Genes Dev. 21, 2150–2160 (2007).
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).
Akhtar, A. & Gasser, S. M. The nuclear envelope and transcriptional control. Nature Rev. Genet. 8, 507–517 (2007).
Vassetzky, Y. et al. Chromosome conformation capture (from 3C to 5C) and its ChIP-based modification. Methods Mol. Biol. 567, 171–188 (2009).
Oki, M. & Kamakaka, R. T. Barrier function at HMR. Mol. Cell 19, 707–716 (2005).
Ishihara, K., Oshimura, M. & Nakao, M. CTCF-dependent chromatin insulator is linked to epigenetic remodeling. Mol. Cell 23, 733–742 (2006).
Dhillon, N. et al. DNA polymerase e, acetylases and remodellers cooperate to form a specialized chromatin structure at a tRNA insulator. EMBO J. 28, 2583–2600 (2009).
Geyer, P. K. The role of insulator elements in defining domains of gene expression. Curr. Opin. Genet. Dev. 7, 242–248 (1997).
Gerasimova, T. I. & Corces, V. G. Chromatin insulators and boundaries: effects on transcription and nuclear organization. Annu. Rev. Genet. 35, 193–208 (2001).
Chopra, V. S., Cande, J., Hong, J. W. & Levine, M. Stalled Hox promoters as chromosomal boundaries. Genes Dev. 23, 1505–1509 (2009).
Soshnev, A. A., Li, X., Wehling, M. D. & Geyer, P. K. Context differences reveal insulator and activator functions of a Su(Hw) binding region. PLoS Genet. 4, e1000159 (2008).
Jiang, N., Emberly, E., Cuvier, O. & Hart, C. M. Genome-wide mapping of boundary element-associated factor (BEAF) binding sites in Drosophila melanogaster links BEAF to transcription. Mol. Cell. Biol. 29, 3556–3568 (2009).
Bushey, A. M., Ramos, E. & Corces, V. G. Three subclasses of a Drosophila insulator show distinct and cell type-specific genomic distributions. Genes Dev. 23, 1338–1350 (2009).
Smith, S. T. et al. Genome wide ChIP–chip analyses reveal important roles for CTCF in Drosophila genome organization. Dev. Biol. 328, 518–528 (2009).
Bartkuhn, M. et al. Active promoters and insulators are marked by the centrosomal protein 190. EMBO J. 28, 877–888 (2009).
Negre, N. et al. A comprehensive map of insulator elements for the Drosophila genome. PLoS Genet. 6, e1000814 (2010).
Heintzman, N. D. et al. Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nature Genet. 39, 311–318 (2007).
Kim, T. H. et al. Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome. Cell 128, 1231–1245 (2007).
Xie, X. et al. Systematic discovery of regulatory motifs in conserved regions of the human genome, including thousands of CTCF insulator sites. Proc. Natl Acad. Sci. USA 104, 7145–7150 (2007).
Zlatanova, J. & Caiafa, P. CTCF and its protein partners: divide and rule? J. Cell Sci. 122, 1275–1284 (2009).
Boyle, A. P. et al. High-resolution mapping and characterization of open chromatin across the genome. Cell 132, 311–322 (2008).
Jin, C. et al. H3.3/H2A.Z. double variant-containing nucleosomes mark 'nucleosome-free regions' of active promoters and other regulatory regions. Nature Genet. 41, 941–945 (2009).
Fu, Y., Sinha, M., Peterson, C. L. & Weng, Z. The insulator binding protein CTCF positions 20 nucleosomes around its binding sites across the human genome. PLoS Genet. 4, e1000138 (2008).
Li, M., Belozerov, V. E. & Cai, H. N. Modulation of chromatin boundary activities by nucleosome-remodeling activities in Drosophila melanogaster. Mol. Cell. Biol. 30, 1067–1076 (2009).
Gerasimova, T. I., Byrd, K. & Corces, V. G. A chromatin insulator determines the nuclear localization of DNA. Mol. Cell 6, 1025–1035 (2000).
Capelson, M. & Corces, V. G. The ubiquitin ligase dTopors directs the nuclear organization of a chromatin insulator. Mol. Cell 20, 105–116 (2005).
Golovnin, A. et al. 'Insulator bodies' are aggregates of proteins but not of insulators. EMBO Rep. 9, 440–445 (2008).
Byrd, K. & Corces, V. G. Visualization of chromatin domains created by the gypsy insulator of Drosophila. J. Cell Biol. 162, 565–574 (2003).
Maeda, R. K. & Karch, F. Making connections: boundaries and insulators in Drosophila. Curr. Opin. Genet. Dev. 17, 394–399 (2007).
Kuhn, E. J. & Geyer, P. K. Genomic insulators: connecting properties to mechanism. Curr. Opin. Cell Biol. 15, 259–265 (2003).
Nolis, I. K. et al. Transcription factors mediate long-range enhancer–promoter interactions. Proc. Natl Acad. Sci. USA 106, 20222–20227 (2009).
Bartolomei, M. S. Genomic imprinting: employing and avoiding epigenetic processes. Genes Dev. 23, 2124–2133 (2009).
Mishiro, T. et al. Architectural roles of multiple chromatin insulators at the human apolipoprotein gene cluster. EMBO J. 28, 1234–1245 (2009).
Dorsett, D. Cohesin, gene expression and development: lessons from Drosophila. Chromosome Res. 17, 185–200 (2009).
Petrykowska, H. M., Vockley, C. M. & Elnitski, L. Detection and characterization of silencers and enhancer-blockers in the greater CFTR locus. Genome Res. 18, 1238–1246 (2008).
Acknowledgements
We would like to thank B. Cairns, O. Rando, M. Bulger, D. Clark, G. Hartzog, M. Oki, K. Noma, S. Henikoff, P. Geyer and G. Felsenfeld for comments on an early draft of this Review. We would also like to thank members of the Ro laboratory for comments and criticisms. We apologize for the selective citations, which are a consequence of space limitations. This work was supported by grants from the US National Institutes of Health to R.T.K. (GM078068) and J.R.R (T32-GM008646), and by grant 2008-16 from the GREAT Training Program of the University of California System-wide Biotechnology Research and Education Program to J.R.R.
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Raab, J., Kamakaka, R. Insulators and promoters: closer than we think. Nat Rev Genet 11, 439–446 (2010). https://doi.org/10.1038/nrg2765
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DOI: https://doi.org/10.1038/nrg2765
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