Skip to main content
PMC home page
The EMBO Journal logoLink to The EMBO Journal
. 1995 Apr 18;14(8):1718–1726. doi: 10.1002/j.1460-2075.1995.tb07161.x

Contrasting effects of alpha and beta globin regulatory elements on chromatin structure may be related to their different chromosomal environments.

C F Craddock 1, P Vyas 1, J A Sharpe 1, H Ayyub 1, W G Wood 1, D R Higgs 1
PMCID: PMC398265  PMID: 7737123

Abstract

Expression of the human alpha and beta globin gene clusters is regulated by remote sequences, referred to as HS -40 and the beta-locus control region (beta-LCR) that lie 5-40 kb upstream of the genes they activate. Because of their common ancestry, similar organization and coordinate expression it has often been assumed that regulation of the globin gene clusters by HS -40 and the beta-LCR occurs via similar mechanisms. Using interspecific hybrids containing chromosomes with naturally occurring deletions of HS -40 we have shown that, in contrast to the beta-LCR, this element exerts no discernible effect on long-range chromatin structure and in addition does not influence formation of DNase I hypersensitive sites at the alpha globin promoters. These differences in the behaviour of HS -40 and the beta-LCR may reflect their contrasting influence on gene expression in transgenic mice and may result from the differing requirements of these elements in their radically different, natural chromosomal environments; the alpha cluster lying within a region of constitutively 'open' chromatin and the beta cluster in a segment of chromatin which opens in a tissue-specific manner. Differences in the hierarchical control of the alpha and beta globin clusters may exemplify more general differences in the regulation of eukaryotic genes which lie in similar open or closed chromosomal regions.

Full text

PDF
1718

Images in this article

1720Image
on p.1720
1721Image
on p.1721
1722Image
on p.1722
1723Image
on p.1723
1724Image
on p.1724
1724Image
on p.1724
1725Image
on p.1725

Selected References

These references are in PubMed. This may not be the complete list of references from this article.

  1. Andrews N. C., Erdjument-Bromage H., Davidson M. B., Tempst P., Orkin S. H. Erythroid transcription factor NF-E2 is a haematopoietic-specific basic-leucine zipper protein. Nature. 1993 Apr 22;362(6422):722–728. doi: 10.1038/362722a0. [DOI] [PubMed] [Google Scholar]
  2. Baron M. H., Maniatis T. Rapid reprogramming of globin gene expression in transient heterokaryons. Cell. 1986 Aug 15;46(4):591–602. doi: 10.1016/0092-8674(86)90885-8. [DOI] [PubMed] [Google Scholar]
  3. Baron M. H., Maniatis T. Regulated expression of human alpha- and beta-globin genes in transient heterokaryons. Mol Cell Biol. 1991 Mar;11(3):1239–1247. doi: 10.1128/mcb.11.3.1239. [DOI] [PMC free article] [PubMed] [Google Scholar]
  4. Beggs A. H., Migeon B. R. Chromatin loop structure of the human X chromosome: relevance to X inactivation and CpG clusters. Mol Cell Biol. 1989 Jun;9(6):2322–2331. doi: 10.1128/mcb.9.6.2322. [DOI] [PMC free article] [PubMed] [Google Scholar]
  5. Bernardi G., Olofsson B., Filipski J., Zerial M., Salinas J., Cuny G., Meunier-Rotival M., Rodier F. The mosaic genome of warm-blooded vertebrates. Science. 1985 May 24;228(4702):953–958. doi: 10.1126/science.4001930. [DOI] [PubMed] [Google Scholar]
  6. Bickmore W. A., Sumner A. T. Mammalian chromosome banding--an expression of genome organization. Trends Genet. 1989 May;5(5):144–148. doi: 10.1016/0168-9525(89)90055-3. [DOI] [PubMed] [Google Scholar]
  7. Bird A. P., Taggart M. H., Nicholls R. D., Higgs D. R. Non-methylated CpG-rich islands at the human alpha-globin locus: implications for evolution of the alpha-globin pseudogene. EMBO J. 1987 Apr;6(4):999–1004. doi: 10.1002/j.1460-2075.1987.tb04851.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  8. Buratowski S. The basics of basal transcription by RNA polymerase II. Cell. 1994 Apr 8;77(1):1–3. doi: 10.1016/0092-8674(94)90226-7. [DOI] [PubMed] [Google Scholar]
  9. Carson S., Wiles M. V. Far upstream regions of class II MHC Ea are necessary for position-independent, copy-dependent expression of Ea transgene. Nucleic Acids Res. 1993 May 11;21(9):2065–2072. doi: 10.1093/nar/21.9.2065. [DOI] [PMC free article] [PubMed] [Google Scholar]
  10. Charnay P., Treisman R., Mellon P., Chao M., Axel R., Maniatis T. Differences in human alpha- and beta-globin gene expression in mouse erythroleukemia cells: the role of intragenic sequences. Cell. 1984 Aug;38(1):251–263. doi: 10.1016/0092-8674(84)90547-6. [DOI] [PubMed] [Google Scholar]
  11. Chodosh L. A., Baldwin A. S., Carthew R. W., Sharp P. A. Human CCAAT-binding proteins have heterologous subunits. Cell. 1988 Apr 8;53(1):11–24. doi: 10.1016/0092-8674(88)90483-7. [DOI] [PubMed] [Google Scholar]
  12. Chomczynski P., Sacchi N. Single-step method of RNA isolation by acid guanidinium thiocyanate-phenol-chloroform extraction. Anal Biochem. 1987 Apr;162(1):156–159. doi: 10.1006/abio.1987.9999. [DOI] [PubMed] [Google Scholar]
  13. Church G. M., Gilbert W. Genomic sequencing. Proc Natl Acad Sci U S A. 1984 Apr;81(7):1991–1995. doi: 10.1073/pnas.81.7.1991. [DOI] [PMC free article] [PubMed] [Google Scholar]
  14. Craig J. M., Bickmore W. A. The distribution of CpG islands in mammalian chromosomes. Nat Genet. 1994 Jul;7(3):376–382. doi: 10.1038/ng0794-376. [DOI] [PubMed] [Google Scholar]
  15. Diaz P., Cado D., Winoto A. A locus control region in the T cell receptor alpha/delta locus. Immunity. 1994 Jun;1(3):207–217. doi: 10.1016/1074-7613(94)90099-x. [DOI] [PubMed] [Google Scholar]
  16. 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]
  17. Enoch T., Zinn K., Maniatis T. Activation of the human beta-interferon gene requires an interferon-inducible factor. Mol Cell Biol. 1986 Mar;6(3):801–810. doi: 10.1128/mcb.6.3.801. [DOI] [PMC free article] [PubMed] [Google Scholar]
  18. Evans T., Felsenfeld G., Reitman M. Control of globin gene transcription. Annu Rev Cell Biol. 1990;6:95–124. doi: 10.1146/annurev.cb.06.110190.000523. [DOI] [PubMed] [Google Scholar]
  19. Felsenfeld G. Chromatin as an essential part of the transcriptional mechanism. Nature. 1992 Jan 16;355(6357):219–224. doi: 10.1038/355219a0. [DOI] [PubMed] [Google Scholar]
  20. Fischel-Ghodsian N., Nicholls R. D., Higgs D. R. Unusual features of CpG-rich (HTF) islands in the human alpha globin complex: association with non-functional pseudogenes and presence within the 3' portion of the zeta gene. Nucleic Acids Res. 1987 Nov 25;15(22):9215–9225. doi: 10.1093/nar/15.22.9215. [DOI] [PMC free article] [PubMed] [Google Scholar]
  21. Flint J., Craddock C. F., Villegas A., Bentley D. P., Williams H. J., Galanello R., Cao A., Wood W. G., Ayyub H., Higgs D. R. Healing of broken human chromosomes by the addition of telomeric repeats. Am J Hum Genet. 1994 Sep;55(3):505–512. [PMC free article] [PubMed] [Google Scholar]
  22. Forrester W. C., Epner E., Driscoll M. C., Enver T., Brice M., Papayannopoulou T., Groudine M. A deletion of the human beta-globin locus activation region causes a major alteration in chromatin structure and replication across the entire beta-globin locus. Genes Dev. 1990 Oct;4(10):1637–1649. doi: 10.1101/gad.4.10.1637. [DOI] [PubMed] [Google Scholar]
  23. Garrard W. T. Histone H1 and the conformation of transcriptionally active chromatin. Bioessays. 1991 Feb;13(2):87–88. doi: 10.1002/bies.950130208. [DOI] [PubMed] [Google Scholar]
  24. Gourdon G., Sharpe J. A., Wells D., Wood W. G., Higgs D. R. Analysis of a 70 kb segment of DNA containing the human zeta and alpha-globin genes linked to their regulatory element (HS-40) in transgenic mice. Nucleic Acids Res. 1994 Oct 11;22(20):4139–4147. doi: 10.1093/nar/22.20.4139. [DOI] [PMC free article] [PubMed] [Google Scholar]
  25. Gross D. S., Garrard W. T. Nuclease hypersensitive sites in chromatin. Annu Rev Biochem. 1988;57:159–197. doi: 10.1146/annurev.bi.57.070188.001111. [DOI] [PubMed] [Google Scholar]
  26. Grosveld F., van Assendelft G. B., Greaves D. R., Kollias G. Position-independent, high-level expression of the human beta-globin gene in transgenic mice. Cell. 1987 Dec 24;51(6):975–985. doi: 10.1016/0092-8674(87)90584-8. [DOI] [PubMed] [Google Scholar]
  27. Hatton C. S., Wilkie A. O., Drysdale H. C., Wood W. G., Vickers M. A., Sharpe J., Ayyub H., Pretorius I. M., Buckle V. J., Higgs D. R. Alpha-thalassemia caused by a large (62 kb) deletion upstream of the human alpha globin gene cluster. Blood. 1990 Jul 1;76(1):221–227. [PubMed] [Google Scholar]
  28. Higgs D. R., Vickers M. A., Wilkie A. O., Pretorius I. M., Jarman A. P., Weatherall D. J. A review of the molecular genetics of the human alpha-globin gene cluster. Blood. 1989 Apr;73(5):1081–1104. [PubMed] [Google Scholar]
  29. Higgs D. R., Wood W. G., Jarman A. P., Sharpe J., Lida J., Pretorius I. M., Ayyub H. A major positive regulatory region located far upstream of the human alpha-globin gene locus. Genes Dev. 1990 Sep;4(9):1588–1601. doi: 10.1101/gad.4.9.1588. [DOI] [PubMed] [Google Scholar]
  30. Higgs D. R., Wood W. G. Understanding erythroid differentiation. Curr Biol. 1993 Aug 1;3(8):548–550. doi: 10.1016/0960-9822(93)90054-r. [DOI] [PubMed] [Google Scholar]
  31. Holmquist G. P. Chromosome bands, their chromatin flavors, and their functional features. Am J Hum Genet. 1992 Jul;51(1):17–37. [PMC free article] [PubMed] [Google Scholar]
  32. Jarman A. P., Higgs D. R. A new hypervariable marker for the human alpha-globin gene cluster. Am J Hum Genet. 1988 Sep;43(3):249–256. [PMC free article] [PubMed] [Google Scholar]
  33. Jarman A. P., Nicholls R. D., Weatherall D. J., Clegg J. B., Higgs D. R. Molecular characterisation of a hypervariable region downstream of the human alpha-globin gene cluster. EMBO J. 1986 Aug;5(8):1857–1863. doi: 10.1002/j.1460-2075.1986.tb04437.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  34. Jarman A. P., Wood W. G., Sharpe J. A., Gourdon G., Ayyub H., Higgs D. R. Characterization of the major regulatory element upstream of the human alpha-globin gene cluster. Mol Cell Biol. 1991 Sep;11(9):4679–4689. doi: 10.1128/mcb.11.9.4679. [DOI] [PMC free article] [PubMed] [Google Scholar]
  35. Jenuwein T., Forrester W. C., Qiu R. G., Grosschedl R. The immunoglobulin mu enhancer core establishes local factor access in nuclear chromatin independent of transcriptional stimulation. Genes Dev. 1993 Oct;7(10):2016–2032. doi: 10.1101/gad.7.10.2016. [DOI] [PubMed] [Google Scholar]
  36. Kioussis D., Vanin E., deLange T., Flavell R. A., Grosveld F. G. Beta-globin gene inactivation by DNA translocation in gamma beta-thalassaemia. Nature. 1983 Dec 15;306(5944):662–666. doi: 10.1038/306662a0. [DOI] [PubMed] [Google Scholar]
  37. Kornberg R. D., Lorch Y. Chromatin structure and transcription. Annu Rev Cell Biol. 1992;8:563–587. doi: 10.1146/annurev.cb.08.110192.003023. [DOI] [PubMed] [Google Scholar]
  38. Käs E., Poljak L., Adachi Y., Laemmli U. K. A model for chromatin opening: stimulation of topoisomerase II and restriction enzyme cleavage of chromatin by distamycin. EMBO J. 1993 Jan;12(1):115–126. doi: 10.1002/j.1460-2075.1993.tb05637.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  39. Lauer J., Shen C. K., Maniatis T. The chromosomal arrangement of human alpha-like globin genes: sequence homology and alpha-globin gene deletions. Cell. 1980 May;20(1):119–130. doi: 10.1016/0092-8674(80)90240-8. [DOI] [PubMed] [Google Scholar]
  40. Liebhaber S. A., Griese E. U., Weiss I., Cash F. E., Ayyub H., Higgs D. R., Horst J. Inactivation of human alpha-globin gene expression by a de novo deletion located upstream of the alpha-globin gene cluster. Proc Natl Acad Sci U S A. 1990 Dec;87(23):9431–9435. doi: 10.1073/pnas.87.23.9431. [DOI] [PMC free article] [PubMed] [Google Scholar]
  41. Nicholls R. D., Fischel-Ghodsian N., Higgs D. R. Recombination at the human alpha-globin gene cluster: sequence features and topological constraints. Cell. 1987 May 8;49(3):369–378. doi: 10.1016/0092-8674(87)90289-3. [DOI] [PubMed] [Google Scholar]
  42. Reitman M., Lee E., Westphal H., Felsenfeld G. An enhancer/locus control region is not sufficient to open chromatin. Mol Cell Biol. 1993 Jul;13(7):3990–3998. doi: 10.1128/mcb.13.7.3990. [DOI] [PMC free article] [PubMed] [Google Scholar]
  43. Shannon K. Genetic alterations in leukemia: events on a grand scale. Blood. 1992 Jul 1;80(1):1–2. [PubMed] [Google Scholar]
  44. Sharpe J. A., Chan-Thomas P. S., Lida J., Ayyub H., Wood W. G., Higgs D. R. Analysis of the human alpha globin upstream regulatory element (HS-40) in transgenic mice. EMBO J. 1992 Dec;11(12):4565–4572. doi: 10.1002/j.1460-2075.1992.tb05558.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
  45. Sharpe J. A., Summerhill R. J., Vyas P., Gourdon G., Higgs D. R., Wood W. G. Role of upstream DNase I hypersensitive sites in the regulation of human alpha globin gene expression. Blood. 1993 Sep 1;82(5):1666–1671. [PubMed] [Google Scholar]
  46. Sharpe J. A., Wells D. J., Whitelaw E., Vyas P., Higgs D. R., Wood W. G. Analysis of the human alpha-globin gene cluster in transgenic mice. Proc Natl Acad Sci U S A. 1993 Dec 1;90(23):11262–11266. doi: 10.1073/pnas.90.23.11262. [DOI] [PMC free article] [PubMed] [Google Scholar]
  47. Talbot D., Descombes P., Schibler U. The 5' flanking region of the rat LAP (C/EBP beta) gene can direct high-level, position-independent, copy number-dependent expression in multiple tissues in transgenic mice. Nucleic Acids Res. 1994 Mar 11;22(5):756–766. doi: 10.1093/nar/22.5.756. [DOI] [PMC free article] [PubMed] [Google Scholar]
  48. Tazi J., Bird A. Alternative chromatin structure at CpG islands. Cell. 1990 Mar 23;60(6):909–920. doi: 10.1016/0092-8674(90)90339-g. [DOI] [PubMed] [Google Scholar]
  49. Townes T. M., Behringer R. R. Human globin locus activation region (LAR): role in temporal control. Trends Genet. 1990 Jul;6(7):219–223. doi: 10.1016/0168-9525(90)90182-6. [DOI] [PubMed] [Google Scholar]
  50. Tsai S. F., Martin D. I., Zon L. I., D'Andrea A. D., Wong G. G., Orkin S. H. Cloning of cDNA for the major DNA-binding protein of the erythroid lineage through expression in mammalian cells. Nature. 1989 Jun 8;339(6224):446–451. doi: 10.1038/339446a0. [DOI] [PubMed] [Google Scholar]
  51. Vickers M. A., Higgs D. R. A novel deletion of the entire alpha-globin gene cluster in a British individual. Br J Haematol. 1989 Jul;72(3):471–473. doi: 10.1111/j.1365-2141.1989.tb07736.x. [DOI] [PubMed] [Google Scholar]
  52. Vickers M. A., Vyas P., Harris P. C., Simmons D. L., Higgs D. R. Structure of the human 3-methyladenine DNA glycosylase gene and localization close to the 16p telomere. Proc Natl Acad Sci U S A. 1993 Apr 15;90(8):3437–3441. doi: 10.1073/pnas.90.8.3437. [DOI] [PMC free article] [PubMed] [Google Scholar]
  53. Vyas P., Vickers M. A., Simmons D. L., Ayyub H., Craddock C. F., Higgs D. R. Cis-acting sequences regulating expression of the human alpha-globin cluster lie within constitutively open chromatin. Cell. 1992 May 29;69(5):781–793. doi: 10.1016/0092-8674(92)90290-s. [DOI] [PubMed] [Google Scholar]
  54. Wallrath L. L., Lu Q., Granok H., Elgin S. C. Architectural variations of inducible eukaryotic promoters: preset and remodeling chromatin structures. Bioessays. 1994 Mar;16(3):165–170. doi: 10.1002/bies.950160306. [DOI] [PubMed] [Google Scholar]
  55. Whitelaw E., Hogben P., Hanscombe O., Proudfoot N. J. Transcriptional promiscuity of the human alpha-globin gene. Mol Cell Biol. 1989 Jan;9(1):241–251. doi: 10.1128/mcb.9.1.241. [DOI] [PMC free article] [PubMed] [Google Scholar]
  56. Wilkie A. O., Lamb J., Harris P. C., Finney R. D., Higgs D. R. A truncated human chromosome 16 associated with alpha thalassaemia is stabilized by addition of telomeric repeat (TTAGGG)n. Nature. 1990 Aug 30;346(6287):868–871. doi: 10.1038/346868a0. [DOI] [PubMed] [Google Scholar]
  57. Workman J. L., Buchman A. R. Multiple functions of nucleosomes and regulatory factors in transcription. Trends Biochem Sci. 1993 Mar;18(3):90–95. doi: 10.1016/0968-0004(93)90160-o. [DOI] [PubMed] [Google Scholar]
  58. Yagi M., Gelinas R., Elder J. T., Peretz M., Papayannopoulou T., Stamatoyannopoulos G., Groudine M. Chromatin structure and developmental expression of the human alpha-globin cluster. Mol Cell Biol. 1986 Apr;6(4):1108–1116. doi: 10.1128/mcb.6.4.1108. [DOI] [PMC free article] [PubMed] [Google Scholar]
  59. Zhao K., Käs E., Gonzalez E., Laemmli U. K. SAR-dependent mobilization of histone H1 by HMG-I/Y in vitro: HMG-I/Y is enriched in H1-depleted chromatin. EMBO J. 1993 Aug;12(8):3237–3247. doi: 10.1002/j.1460-2075.1993.tb05993.x. [DOI] [PMC free article] [PubMed] [Google Scholar]

Articles from The EMBO Journal are provided here courtesy of Nature Publishing Group

RESOURCES