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. 2004 May;167(1):411–421. doi: 10.1534/genetics.167.1.411

The epigenetic stability of the locus control region-deficient IgH locus in mouse hybridoma cells is a clonally varying, heritable feature.

Diana Ronai 1, Maribel Berru 1, Marc J Shulman 1
PMCID: PMC1470874  PMID: 15166165

Abstract

Cis-acting elements such as enhancers and locus control regions (LCRs) prevent silencing of gene expression. We have shown previously that targeted deletion of an LCR in the immunoglobulin heavy-chain (IgH) locus creates conditions in which the immunoglobulin micro heavy chain gene can exist in either of two epigenetically inherited states, one in which micro expression is positive and one in which micro expression is negative, and that the positive and negative states are maintained by a cis-acting mechanism. As described here, the stability of these states, i.e., the propensity of a cell to switch from one state to the other, varied among subclones and was an inherited, clonal feature. A similar variation in stability was seen for IgH loci that both lacked and retained the matrix attachment regions associated with the LCR. Our analysis of cell hybrids formed by fusing cells in which the micro expression had different stabilities indicated that stability was also determined by a cis-acting feature of the IgH locus. Our results thus show that a single-copy gene in the same chromosomal location and in the presence of the same transcription factors can exist in many different states of expression.

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Selected References

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  1. Aparicio O. M., Gottschling D. E. Overcoming telomeric silencing: a trans-activator competes to establish gene expression in a cell cycle-dependent way. Genes Dev. 1994 May 15;8(10):1133–1146. doi: 10.1101/gad.8.10.1133. [DOI] [PubMed] [Google Scholar]
  2. Arulampalam V., Eckhardt L., Pettersson S. The enhancer shift: a model to explain the developmental control of IgH gene expression in B-lineage cells. Immunol Today. 1997 Nov;18(11):549–554. doi: 10.1016/s0167-5699(97)01154-7. [DOI] [PubMed] [Google Scholar]
  3. Baar J., Shulman M. J. The Ig heavy chain switch region is a hotspot for insertion of transfected DNA. J Immunol. 1995 Aug 15;155(4):1911–1920. [PubMed] [Google Scholar]
  4. Becskei A., Serrano L. Engineering stability in gene networks by autoregulation. Nature. 2000 Jun 1;405(6786):590–593. doi: 10.1038/35014651. [DOI] [PubMed] [Google Scholar]
  5. Bell A. C., Felsenfeld G. Methylation of a CTCF-dependent boundary controls imprinted expression of the Igf2 gene. Nature. 2000 May 25;405(6785):482–485. doi: 10.1038/35013100. [DOI] [PubMed] [Google Scholar]
  6. Cameron E. E., Bachman K. E., Myöhänen S., Herman J. G., Baylin S. B. Synergy of demethylation and histone deacetylase inhibition in the re-expression of genes silenced in cancer. Nat Genet. 1999 Jan;21(1):103–107. doi: 10.1038/5047. [DOI] [PubMed] [Google Scholar]
  7. Chess A., Simon I., Cedar H., Axel R. Allelic inactivation regulates olfactory receptor gene expression. Cell. 1994 Sep 9;78(5):823–834. doi: 10.1016/s0092-8674(94)90562-2. [DOI] [PubMed] [Google Scholar]
  8. Czerkinsky C. C., Nilsson L. A., Nygren H., Ouchterlony O., Tarkowski A. A solid-phase enzyme-linked immunospot (ELISPOT) assay for enumeration of specific antibody-secreting cells. J Immunol Methods. 1983 Dec 16;65(1-2):109–121. doi: 10.1016/0022-1759(83)90308-3. [DOI] [PubMed] [Google Scholar]
  9. Eden S., Cedar H. Role of DNA methylation in the regulation of transcription. Curr Opin Genet Dev. 1994 Apr;4(2):255–259. doi: 10.1016/s0959-437x(05)80052-8. [DOI] [PubMed] [Google Scholar]
  10. Ellmeier Wilfried, Sunshine Mary Jean, Maschek Romana, Littman Dan R. Combined deletion of CD8 locus cis-regulatory elements affects initiation but not maintenance of CD8 expression. Immunity. 2002 May;16(5):623–634. doi: 10.1016/s1074-7613(02)00309-6. [DOI] [PubMed] [Google Scholar]
  11. Fernández L. A., Winkler M., Grosschedl R. Matrix attachment region-dependent function of the immunoglobulin mu enhancer involves histone acetylation at a distance without changes in enhancer occupancy. Mol Cell Biol. 2001 Jan;21(1):196–208. doi: 10.1128/MCB.21.1.196-208.2001. [DOI] [PMC free article] [PubMed] [Google Scholar]
  12. Fiering S., Whitelaw E., Martin D. I. To be or not to be active: the stochastic nature of enhancer action. Bioessays. 2000 Apr;22(4):381–387. doi: 10.1002/(SICI)1521-1878(200004)22:4<381::AID-BIES8>3.0.CO;2-E. [DOI] [PubMed] [Google Scholar]
  13. Forrester W. C., Fernández L. A., Grosschedl R. Nuclear matrix attachment regions antagonize methylation-dependent repression of long-range enhancer-promoter interactions. Genes Dev. 1999 Nov 15;13(22):3003–3014. doi: 10.1101/gad.13.22.3003. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Forrester W. C., van Genderen C., Jenuwein T., Grosschedl R. Dependence of enhancer-mediated transcription of the immunoglobulin mu gene on nuclear matrix attachment regions. Science. 1994 Aug 26;265(5176):1221–1225. doi: 10.1126/science.8066460. [DOI] [PubMed] [Google Scholar]
  15. Francastel C., Walters M. C., Groudine M., Martin D. I. A functional enhancer suppresses silencing of a transgene and prevents its localization close to centrometric heterochromatin. Cell. 1999 Oct 29;99(3):259–269. doi: 10.1016/s0092-8674(00)81657-8. [DOI] [PubMed] [Google Scholar]
  16. Garefalaki Anna, Coles Mark, Hirschberg Sandra, Mavria Georgia, Norton Trisha, Hostert Arnd, Kioussis Dimitris. Variegated expression of CD8 alpha resulting from in situ deletion of regulatory sequences. Immunity. 2002 May;16(5):635–647. doi: 10.1016/s1074-7613(02)00308-4. [DOI] [PubMed] [Google Scholar]
  17. Gram H., Zenke G., Geisse S., Kleuser B., Bürki K. High-level expression of a human immunoglobulin gamma 1 transgene depends on switch region sequences. Eur J Immunol. 1992 May;22(5):1185–1191. doi: 10.1002/eji.1830220512. [DOI] [PubMed] [Google Scholar]
  18. Hark A. T., Schoenherr C. J., Katz D. J., Ingram R. S., Levorse J. M., Tilghman S. M. CTCF mediates methylation-sensitive enhancer-blocking activity at the H19/Igf2 locus. Nature. 2000 May 25;405(6785):486–489. doi: 10.1038/35013106. [DOI] [PubMed] [Google Scholar]
  19. Held W., Roland J., Raulet D. H. Allelic exclusion of Ly49-family genes encoding class I MHC-specific receptors on NK cells. Nature. 1995 Jul 27;376(6538):355–358. doi: 10.1038/376355a0. [DOI] [PubMed] [Google Scholar]
  20. Hu-Li J., Pannetier C., Guo L., Löhning M., Gu H., Watson C., Assenmacher M., Radbruch A., Paul W. E. Regulation of expression of IL-4 alleles: analysis using a chimeric GFP/IL-4 gene. Immunity. 2001 Jan;14(1):1–11. doi: 10.1016/s1074-7613(01)00084-x. [DOI] [PubMed] [Google Scholar]
  21. Kirillov A., Kistler B., Mostoslavsky R., Cedar H., Wirth T., Bergman Y. A role for nuclear NF-kappaB in B-cell-specific demethylation of the Igkappa locus. Nat Genet. 1996 Aug;13(4):435–441. doi: 10.1038/ng0895-435. [DOI] [PubMed] [Google Scholar]
  22. Lorincz Matthew C., Schübeler Dirk, Hutchinson Shauna R., Dickerson David R., Groudine Mark. DNA methylation density influences the stability of an epigenetic imprint and Dnmt3a/b-independent de novo methylation. Mol Cell Biol. 2002 Nov;22(21):7572–7580. doi: 10.1128/MCB.22.21.7572-7580.2002. [DOI] [PMC free article] [PubMed] [Google Scholar]
  23. Lundgren M., Chow C. M., Sabbattini P., Georgiou A., Minaee S., Dillon N. Transcription factor dosage affects changes in higher order chromatin structure associated with activation of a heterochromatic gene. Cell. 2000 Nov 22;103(5):733–743. doi: 10.1016/s0092-8674(00)00177-x. [DOI] [PubMed] [Google Scholar]
  24. Magis W., Fiering S., Groudine M., Martin D. I. An upstream activator of transcription coordinately increases the level and epigenetic stability of gene expression. Proc Natl Acad Sci U S A. 1996 Nov 26;93(24):13914–13918. doi: 10.1073/pnas.93.24.13914. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. McMorrow T., van den Wijngaard A., Wollenschlaeger A., van de Corput M., Monkhorst K., Trimborn T., Fraser P., van Lohuizen M., Jenuwein T., Djabali M. Activation of the beta globin locus by transcription factors and chromatin modifiers. EMBO J. 2000 Sep 15;19(18):4986–4996. doi: 10.1093/emboj/19.18.4986. [DOI] [PMC free article] [PubMed] [Google Scholar]
  26. Morgan H. D., Sutherland H. G., Martin D. I., Whitelaw E. Epigenetic inheritance at the agouti locus in the mouse. Nat Genet. 1999 Nov;23(3):314–318. doi: 10.1038/15490. [DOI] [PubMed] [Google Scholar]
  27. Nan X., Ng H. H., Johnson C. A., Laherty C. D., Turner B. M., Eisenman R. N., Bird A. Transcriptional repression by the methyl-CpG-binding protein MeCP2 involves a histone deacetylase complex. Nature. 1998 May 28;393(6683):386–389. doi: 10.1038/30764. [DOI] [PubMed] [Google Scholar]
  28. Oancea A. E., Tsui F. W., Shulman M. J. Targeted removal of the mu switch region from mouse hybridoma cells. A test of its role in gene expression in the endogenous IgH locus. J Immunol. 1995 Dec 15;155(12):5678–5683. [PubMed] [Google Scholar]
  29. Rassoulzadegan Minoo, Magliano Marc, Cuzin François. Transvection effects involving DNA methylation during meiosis in the mouse. EMBO J. 2002 Feb 1;21(3):440–450. doi: 10.1093/emboj/21.3.440. [DOI] [PMC free article] [PubMed] [Google Scholar]
  30. Robertson K. D., Ait-Si-Ali S., Yokochi T., Wade P. A., Jones P. L., Wolffe A. P. DNMT1 forms a complex with Rb, E2F1 and HDAC1 and represses transcription from E2F-responsive promoters. Nat Genet. 2000 Jul;25(3):338–342. doi: 10.1038/77124. [DOI] [PubMed] [Google Scholar]
  31. Ronai Diana, Berru Maribel, Shulman Marc J. Positive and negative transcriptional states of a variegating immunoglobulin heavy chain (IgH) locus are maintained by a cis-acting epigenetic mechanism. J Immunol. 2002 Dec 15;169(12):6919–6927. doi: 10.4049/jimmunol.169.12.6919. [DOI] [PubMed] [Google Scholar]
  32. Rose J. A., Yates P. A., Simpson J., Tischfield J. A., Stambrook P. J., Turker M. S. Biallelic methylation and silencing of mouse Aprt in normal kidney cells. Cancer Res. 2000 Jul 1;60(13):3404–3408. [PubMed] [Google Scholar]
  33. Sun W., Xiong J., Shulman M. J. Production of mouse V/human C chimeric kappa genes by homologous recombination in hybridoma cells. Analysis of vector design and recombinant gene expression. J Immunol. 1994 Jan 15;152(2):695–704. [PubMed] [Google Scholar]
  34. Tanamachi D. M., Hanke T., Takizawa H., Jamieson A. M., Raulet D. R. Expression of natural killer receptor alleles at different Ly49 loci occurs independently and is regulated by major histocompatibility complex class I molecules. J Exp Med. 2001 Feb 5;193(3):307–315. doi: 10.1084/jem.193.3.307. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Vance Russell E., Jamieson Amanda M., Cado Dragana, Raulet David H. Implications of CD94 deficiency and monoallelic NKG2A expression for natural killer cell development and repertoire formation. Proc Natl Acad Sci U S A. 2002 Jan 8;99(2):868–873. doi: 10.1073/pnas.022500599. [DOI] [PMC free article] [PubMed] [Google Scholar]
  36. Wade P. A., Gegonne A., Jones P. L., Ballestar E., Aubry F., Wolffe A. P. Mi-2 complex couples DNA methylation to chromatin remodelling and histone deacetylation. Nat Genet. 1999 Sep;23(1):62–66. doi: 10.1038/12664. [DOI] [PubMed] [Google Scholar]
  37. Wiersma E. J., Ronai D., Berru M., Tsui F. W., Shulman M. J. Role of the intronic elements in the endogenous immunoglobulin heavy chain locus. Either the matrix attachment regions or the core enhancer is sufficient to maintain expression. J Biol Chem. 1999 Feb 19;274(8):4858–4862. doi: 10.1074/jbc.274.8.4858. [DOI] [PubMed] [Google Scholar]
  38. Yates Phillip A., Burman Robert, Simpson James, Ponomoreva Olga N., Thayer Mathew J., Turker Mitchell S. Silencing of mouse Aprt is a gradual process in differentiated cells. Mol Cell Biol. 2003 Jul;23(13):4461–4470. doi: 10.1128/MCB.23.13.4461-4470.2003. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. Yeivin A., Razin A. Gene methylation patterns and expression. EXS. 1993;64:523–568. doi: 10.1007/978-3-0348-9118-9_24. [DOI] [PubMed] [Google Scholar]
  40. de Krom Mariken, van de Corput Mariette, von Lindern Marieke, Grosveld Frank, Strouboulis John. Stochastic patterns in globin gene expression are established prior to transcriptional activation and are clonally inherited. Mol Cell. 2002 Jun;9(6):1319–1326. doi: 10.1016/s1097-2765(02)00558-0. [DOI] [PubMed] [Google Scholar]

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