Abstract
A large fraction of genes in the mammalian genome is repressed in every cell throughout development. Here, we propose that this long-term silencing is carried out by distinct molecular mechanisms that operate in a global manner and, once established, can be maintained autonomously through DNA replication. Both individually and in combination these mechanisms bring about repression, mainly by lowering gene accessibility through closed chromatin structures.
This is a preview of subscription content, access via your institution
Access options
Subscribe to this journal
Receive 12 print issues and online access
$189.00 per year
only $15.75 per issue
Buy this article
- Purchase on Springer Link
- Instant access to full article PDF
Prices may be subject to local taxes which are calculated during checkout
Similar content being viewed by others
References
Palmieri, S. L., Peter, W., Hess, H. & Scholer, H. R. Oct-4 transcription factor is differentially expressed in the mouse embryo during establishment of the first two extraembryonic cell lineages involved in implantation. Dev. Biol. 166, 259–267 (1994).
Bird, A. P. Gene number, noise reduction and biological complexity. Trends Genet. 11, 94–100 (1995).
Matzke, M. A. & Birchler, J. A. RNAi-mediated pathways in the nucleus. Nature Rev. Genet. 6, 24–35 (2005).
Schoenherr, C. J., Paquette, A. J. & Anderson, D. J. Identification of potential target genes for the neuron-restrictive silencer factor. Proc. Natl Acad. Sci. USA 93, 9881–9886 (1996).
Chen, Z. F., Paquette, A. J. & Anderson, D. J. NRSF/REST is required in vivo for repression of multiple neuronal target genes during embryogenesis. Nature Genet. 20, 136–142 (1998).
Schoenherr, C. J. & Anderson, D. J. The neuron-restrictive silencer factor (NRSF): a coordinate repressor of multiple neuron-specific genes. Science 267, 1360–1363 (1995).
Lund, A. H. & van Lohuizen, M. Polycomb complexes and silencing mechanisms. Curr. Opin. Cell. Biol. 16, 239–246 (2004).
Kafri, T. et al. Developmental pattern of gene-specific DNA methylation in the mouse embryo and germline. Genes Dev. 6, 705–714 (1992).
Monk, M., Boubelik, M. & Lehnert, S. Temporal and regional changes in DNA methylation in the embryonic, extraembryonic and germ cell lineages during mouse embryo development. Development 99, 371–382 (1987).
Jahner, D. & Jaenisch, R. in DNA Methylation: Biochemistry and Biological Significance (eds Razin, A., Cedar, H. & Riggs, A. D.) 189–220 (Springer, New York, 1984).
Frank, D. et al. Demethylation of CpG islands in embryonic cells. Nature 351, 239–241 (1991).
Brandeis, M. et al. Sp1 elements protect a CpG island from de novo methylation. Nature 371, 435–438 (1994).
Siegfried, Z. et al. DNA methylation represses transcription in vivo. Nature Genet. 22, 203–206 (1999).
Macleod, D., Charlton, J., Mullins, J. & Bird, A. P. Sp1 sites in the mouse Aprt gene promoter are required to prevent methylation of the CpG island. Genes Dev. 8, 2282–2292 (1994).
Gruenbaum, Y., Cedar, H. & Razin, A. Substrate and sequence specificity of a eukaryotic DNA methylase. Nature 292, 620–622 (1982).
Hand, R. Eucaryotic DNA: Organization of the genome for replication. Cell 15, 317–325 (1978).
Goren, A. & Cedar, H. Replicating by the clock. Nature Rev. Mol. Cell Biol. 4, 25–32 (2003).
Goldman, M. A., Holmquist, G. P., Caston, L. A. & Nag, A. Replication timing of genes and middle repetitive sequences. Science 224, 686–692 (1984).
Lercher, M. J., Urrutia, A. O. & Hurst, L. D. Clustering of housekeeping genes provides a unified model of gene order in the human genome. Nature Genet. 31, 180–183 (2002).
Ma, C., Leu, T. H. & Hamlin, J. L. Multiple origins of replication in the dihydrofolate reductase amplicons of a methotrexate-resistant chinese hamster cell line. Mol. Cell. Biol. 10, 1338–1346 (1990).
Selig, S., Okumura, K., Ward, D. C. & Cedar, H. Delineation of DNA replication time zones by fluorescence in situ hybridization. EMBO J. 11, 1217–1225 (1992).
Simon, I. et al. Developmental regulation of DNA replication timing at the human β-globin locus. EMBO J. 20, 6150–6157 (2001).
Cimbora, D. M. et al. Long-distance control of origin choice and replication timing in the human β-globin locus are independent of the locus control region. Mol. Cell. Biol. 20, 5581–5591 (2000).
Huberman, J. A. & Riggs, A. D. Autoradiography of chromosomal DNA fibers from Chinese hamster cells. Proc. Natl Acad. Sci. USA 55, 599–606 (1966).
Gottesfeld, J. & Bloomer, L. S. Assembly of transcriptionally active 5S RNA gene chromatin in vitro. Cell 28, 781–791 (1982).
Weintraub, H. Assembly of an active chromatin structure during replication. Nucleic Acids Res. 7, 781–792 (1979).
Zhang, J., Feng, X., Hashimshony, T., Keshet, I. & Cedar, H. The establishment of transcriptional competence in early and late S-phase. Nature 420, 198–202 (2002).
Jenuwein, T. & Allis, C. D. Translating the histone code. Science 293, 1074–1080 (2001).
Moazed, D. Common themes in mechanisms of gene silencing. Mol. Cell 8, 489–498 (2001).
Nan, X. et al. Transcriptional repression by the methyl-CpG-binding protein MeCP2 involves a histone deacetylase complex. Nature 393, 386–389 (1998).
Jones, P. L. et al. Methylated DNA and MeCP2 recruit histone deacetylase to repress transcription. Nature Genet. 19, 187–191 (1998).
Lande-Diner, L. et al. Gene repression paradigms in animal cells. Cold Spring Harb. Symp. Quant. Biol. 69, 1–8 (2004).
Peters, A. H. et al. Histone H3 lysine 9 methylation is an epigenetic imprint of facultative heterochromatin. Nature Genet. 30, 77–80 (2002).
Rice, J. C. et al. Histone methyltransferases direct different degrees of methylation to define distinct chromatin domains. Mol. Cell 12, 1591–1598 (2003).
Rea, S. et al. Regulation of chromatin structure by site-specific histone H3 methyltransferases. Nature 406, 593–599 (2000).
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).
Bannister, A. J. et al. Selective recognition of methylated lysine 9 on histone H3 by the HP1 chromo domain. Nature 410, 120–124 (2001).
Sarraf, S. A. & Stancheva, I. Methyl-CpG binding protein MBD1 couples histone H3 methylation at lysine 9 by SETDB1 to DNA replication and chromatin assembly. Mol. Cell 15, 595–605 (2004).
Roopra, A., Qazi, R., Schoenike, B., Daley, T. J. & Morrison, J. F. Localized domains of g9a-mediated histone methylation are required for silencing of neuronal genes. Mol. Cell 14, 727–738 (2004).
Gribnau, J., Hochedlinger, K., Hata, K., Li, E. & Jaenisch, R. Asynchronous replication timing of imprinted loci is independent of DNA methylation, but consistent with differential subnuclear localization. Genes Dev. 17, 759–773 (2003).
Bird, A. P. CpG-rich islands and the function of DNA methylation. Nature 321, 209–213 (1986).
Bird, A. P., Taggart, M., Frommer, M., Miller, O. J. & Macleod, D. A fraction of the mouse genome that is derived from islands of nonmethylated CpG-rich DNA. Cell 40, 91–99 (1985).
Jackson-Grusby, L. et al. Loss of genomic methylation causes p53-dependent apoptosis and epigenetic deregulation. Nature Genet. 27, 31–39 (2001).
Gidekel, S. & Bergman, Y. A unique developmental pattern of Oct-3/4 DNA methylation is controlled by a cis-demodification element. J. Biol. Chem. 277, 34521–34530 (2002).
Heard, E. Recent advances in X-chromosome inactivation. Curr. Opin. Cell Biol. 16, 247–255 (2004).
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).
Gilbert, D. M. Replication timing and transcriptional control: beyond cause and effect. Curr. Opin. Cell Biol. 14, 377–383 (2002).
Mather, E. L. & Perry, R. P. Transcriptional regulation of immunoglobulin V genes. Nucleic Acids Res. 9, 6855–6867 (1981).
Cobb, B. S. et al. Targeting of Ikaros to pericentromeric heterochromatin by direct DNA binding. Genes Dev. 14, 2146–2160 (2000).
Huang, Y., Myers, S. J. & Dingledine, R. Transcriptional repression by REST: recruitment of Sin3A and histone deacetylase to neuronal genes. Nature Neurosci. 2, 867–872 (1999).
Fazzio, T. G. et al. Widespread collaboration of Isw2 and Sin3–Rpd3 chromatin remodeling complexes in transcriptional repression. Mol. Cell. Biol. 21, 6450–6460 (2001).
Coisy, M. et al. Cyclin A repression in quiescent cells is associated with chromatin remodeling of its promoter and requires Brahma/SNF2α. Mol. Cell 15, 43–56 (2004).
Crighton, D. et al. p53 represses RNA polymerase III transcription by targeting TBP and inhibiting promoter occupancy by TFIIIB. EMBO J. 22, 2810–2820 (2003).
Tate, P. H. & Bird, A. P. Effects of DNA methylation on DNA-binding proteins and gene expression. Curr. Opin. Genet. Dev. 3, 226–231 (1993).
Hashimshony, T., Zhang, J., Keshet, I., Bustin, M. & Cedar, H. The role of DNA methylation in setting up chromatin structure during development. Nature Genet. 34, 187–192 (2003).
Keshet, I., Lieman-Hurwitz, J. & Cedar, H. DNA methylation affects the formation of active chromatin. Cell 44, 535–543 (1986).
Axel, R., Cedar, H. & Felsenfeld, G. The synthesis of globin RNA from duck reticulocyte chromatin in vitro. Proc. Natl Acad. Sci. USA 70, 2029–2032 (1973).
Cedar, H. & Felsenfeld, G. Transcription of chromatin in vitro. J. Mol. Biol. 77, 237–254 (1973).
Weintraub, H. & Groudine, M. Chromosomal subunits in active genes have an altered conformation. Science 193, 848–856 (1976).
Gazit, B. & Cedar, H. Nuclease sensitivity of active chromatin. Nucleic Acids Res. 8, 5143–5155 (1980).
Oettinger, M. A., Schatz, D. G., Gorka, C. & Baltimore, D. RAG-1 and RAG-2, adjacent genes that synergistically activate V(D)J recombination. Science 248, 1517–1523 (1990).
Mohandas, T., Sparker, R. S. & Shapiro, L. J. Reactivation of an inactive human X chromosome: Evidence for X inactivation by DNA methylation. Science 211, 393–396 (1981).
Wareham, K. A., Lyon, M. F., Glenister, P. H. & Williams, E. D. Age related reactivation of an X-linked gene. Nature 327, 725–727 (1987).
Kaslow, D. C. & Migeon, B. R. DNA methylation stabilizes X chromosome inactivation in eutherians but not in marsupials: evidence for multistep maintenance of mammalian X dosage compensation. Proc. Natl Acad. Sci. USA. 84, 6210–6214 (1987).
Berger, S. L. & Felsenfeld, G. Chromatin goes global. Mol. Cell 8, 263–268 (2001).
Rajewsky, K. Clonal selection and learning in the antibody system. Nature 381, 751–758 (1996).
Bergman, Y. & Cedar, H. A step-wise epigenetic process controls immunoglobulin allelic exclusion. Nature Rev. Immunol. 4, 753–61 (2004).
Goldmit, M. & Bergman, Y. Monoallelic gene expression: A repertoire of recurrent themes. Immunol. Rev. 200, 197–214 (2004).
Kosak, S. T. et al. Subnuclear compartmentalization of immunoglobulin loci during lymphocyte development. Science 296, 158–162 (2002).
Singh, N., Bergman, Y., Cedar, H. & Chess, A. Biallelic germline transcription at the κ-immunoglobulin locus. J. Exp. Med. 197, 743–750 (2003).
Mostoslavsky, R. et al. Asynchronous replication and allelic exclusion in the immune system. Nature 414, 221–225 (2001).
Mostoslavsky, R. et al. κ-chain monoallelic demethylation and the establishment of allelic exclusion. Genes Dev. 12, 1801–1811 (1998).
Kwon, J., Morshead, K. B., Guyon, J. R., Kingston, R. E. & Oettinger, M. A. Histone acetylation and hSWI/SNF remodeling act in concert to stimulate V(D)J cleavage of nucleosomal DNA. Mol. Cell 6, 1037–1048 (2000).
Engler, P. et al. A strain-specific modifier on mouse chromosome 4 controls the methylation of independent transgene loci. Cell 65, 1–20 (1991).
Hsieh, C. L. & Lieber, M. R. CpG methylated minichromosomes become inaccessible for V(D)J recombination after undergoing replication. EMBO J. 11, 315–325 (1992).
Cherry, S. R., Beard, C., Jaenisch, R. & Baltimore, D. V(D)J recombination is not activated by demethylation of the κ-locus. Proc. Natl Acad. Sci. USA 97, 8467–8472 (2000).
Ji, Y., Zhang, J., Lee, A. I., Cedar, H. & Bergman, Y. A multistep mechanism for the activation of rearrangement in the immune system. Proc. Natl Acad. Sci. USA 100, 7557–7562 (2003).
Gilbert, D. M. Nuclear position leaves its mark on replication timing. J. Cell Biol. 152, F11–F15 (2001).
Li, F. et al. The replication timing program of the Chinese hamster β-globin locus is established coincident with its repositioning near peripheral heterochromatin in early G1 phase. J. Cell Biol. 154, 283–292 (2001).
Dhar, V., Skoultchi, A. I. & Schildkraut, C. L. Activation and repression of a β-globin gene in cell hybrids is accompanied by a shift in its temporal regulation. Mol. Cell. Biol. 9, 3524–3532 (1989).
Forrester, W. C., Thompson, C., Elder, J. T. & Groudine, M. A developmentally stable chromatin structure in the human β-globin gene cluster. Proc. Natl Acad. Sci. USA 83, 1359–1363 (1986).
Groudine, M., Kohwi-Shigematsu, T., Gelinas, R., Stamatoyannopoulos, G. & Papayannopoulou, T. Human fetal to adult hemoglobin switching: changes in chromatin structure of the β-globin gene locus. Proc. Natl Acad. Sci. USA 80, 7551–7555 (1983).
Busslinger, M., Hurst, J. & Flavell, R. A. DNA methylation and the regulation of the globin gene expression. Cell 34, 197–206 (1983).
Thiel, G., Lietz, M. & Hohl, M. How mammalian transcriptional repressors work. Eur. J. Biochem. 271, 2855–2862 (2004).
Brown, K. E. et al. Association of transcriptionally silent genes with Ikaros complexes at centromeric heterochromatin. Cell 91, 845–854 (1997).
Hahm, K. et al. Helios, a T cell-restricted Ikaros family member that quantitatively associates with Ikaros at centromeric heterochromatin. Genes Dev. 12, 782–796 (1998).
Lunyak, V. V. et al. Corepressor-dependent silencing of chromosomal regions encoding neuronal genes. Science 298, 1747–1752 (2002).
Francis, N. J., Kingston, R. E. & Woodcock, C. L. Chromatin compaction by a polycomb group protein complex. Science 306, 1574–1577 (2004).
Baumann, M., Mamais, A., McBlane, F., Xiao, H. & Boyes, J. Regulation of V(D)J recombination by nucleosome positioning at recombination signal sequences. EMBO J. 22, 5197–5207 (2003).
Smith, K. T., Coffee, B. & Reines, D. Occupancy and synergistic activation of the FMR1 promoter by Nrf-1 and Sp1 in vivo. Hum. Mol. Genet. 13, 1611–1621 (2004).
de Vries, B. B. et al. Variable FMR1 gene methylation of large expansions leads to variable phenotype in three males from one fragile X family. J. Med. Genet. 33, 1007–1010 (1996).
Rousseau, F., Robb, L. J., Rouillard, P. & Der Kaloustian, V. M. No mental retardation in a man with 40% abnormal methylation at the FMR-1 locus and transmission of sperm cell mutations as premutations. Hum. Mol. Genet. 3, 927–930 (2000).
Smeets, H. J. et al. Normal phenotype in two brothers with a full FMR1 mutation. Hum. Mol. Genet. 4, 2103–2108 (2000).
Bardoni, B. & Mandel, J. L. Advances in understanding of fragile X pathogenesis and FMRP function, and in identification of X linked mental retardation genes. Curr. Opin. Genet. Dev. 12, 284–293 (2002).
Bird, A. P. & Wolffe, A. P. Methylation-induced repression — belts, braces, and chromatin. Cell 99, 451–454 (1999).
Eden, S., Hashimshony, T., Keshet, I., Thorne, A. W. & Cedar, H. DNA methylation models histone acetylation. Nature 394, 842–843 (1998).
Razin, A. & Cedar, H. Distribution of 5-methylcytosine in chromatin. Proc. Natl Acad. Sci. USA 74, 2725–2728 (1977).
Gruenbaum, Y., Naveh-Many, T., Cedar, H. & Razin, A. Sequence specificity of methylation in higher plant DNA. Nature 292, 860–862 (1981).
Gruenbaum, Y., Stein, R., Cedar, H. & Razin, A. Methylation of CpG sequences in eukaryotic DNA. FEBS Lett. 123, 67–71 (1981).
Rountree, M. R., Bachman, K. E. & Baylin, S. B. DNMT1 binds HDAC2 and a new co-repressor, DMAP1, to form a complex at replication foci. Nature Genet. 25, 269–277 (2000).
Kerem, B. S., Goitein, R., Diamond, G., Cedar, H. & Marcus, M. Mapping of DNase I sensitive regions on mitotic chromosomes. Cell 38, 493–499 (1984).
Acknowledgements
We would like to acknowledge the support of the US National Institutes of Health, the Israel Science Foundation, the Israel Cancer Research Fund, the Belfer Foundation and the Rosetrees Trust.
Author information
Authors and Affiliations
Corresponding author
Glossary
- CpG ISLAND
-
A DNA region of >500 bp that has a high CpG density and is usually unmethylated. CpG islands are found upstream of many mammalian genes.
- GASTRULATION
-
A morphogenetic process in vertebrate embryogenesis during which the endoderm, mesoderm and ectoderm germ layers are formed.
- MORULA
-
A pre-implantation embryo that consists of a solid cluster of cells.
Rights and permissions
About this article
Cite this article
Lande-Diner, L., Cedar, H. Silence of the genes — mechanisms of long-term repression. Nat Rev Genet 6, 648–654 (2005). https://doi.org/10.1038/nrg1639
Published:
Issue Date:
DOI: https://doi.org/10.1038/nrg1639
This article is cited by
-
Crosstalk between DNA methylation and gene expression in colorectal cancer, a potential plasma biomarker for tracing this tumor
Scientific Reports (2020)
-
MeDIP-seq and nCpG analyses illuminate sexually dimorphic methylation of gonadal development genes with high historic methylation in turtle hatchlings with temperature-dependent sex determination
Epigenetics & Chromatin (2017)
-
Empirical comparison of reduced representation bisulfite sequencing and Infinium BeadChip reproducibility and coverage of DNA methylation in humans
npj Genomic Medicine (2017)
-
Clonal allelic predetermination of immunoglobulin-κ rearrangement
Nature (2012)
-
Chromosome-wide mapping of DNA methylation patterns in normal and malignant prostate cells reveals pervasive methylation of gene-associated and conserved intergenic sequences
BMC Genomics (2011)