Structural polymorphism at LCR and its role in beta-globin gene regulation

Biochimie

Volumn 92, Issue 9, 2010, Pages 1199-1206

  Kukreti, Shrikant ^a   Kaur, Harpreet ^b   Kaushik, Mahima ^a   Bansal, Aparna ^a   Saxena, Sarika ^a   Kaushik, Shikha ^a   Kukreti, Ritushree ^b  

^a UNIVERSITY OF DELHI   (India)

^b CSIR INSTITUTE OF GENOMICS AND INTEGRATIVE BIOLOGY   (India)

Author keywords

Globin gene LCR; A B transition; Hypersensitive sites (HSs); Regulatory elements; Structural polymorphism

Indexed keywords

BETA GLOBULIN; DEOXYRIBONUCLEASE I; DNA;

CHROMATIN; CONTROLLED STUDY; DNA SEQUENCE; DNA STRUCTURE; EXON; GENE EXPRESSION; GENE LOCUS; GENE MUTATION; GENOME; INTRON; REGULATOR GENE; REVIEW; SINGLE NUCLEOTIDE POLYMORPHISM;

ANIMALS; BETA-GLOBINS; CHROMATIN; GENE EXPRESSION REGULATION; HUMANS; LOCUS CONTROL REGION;

EUKARYOTA;

EID: 77955842752     PISSN: 03009084     EISSN: 61831638     Source Type: Journal    
DOI: 10.1016/j.biochi.2010.04.020     Document Type: Review

References (52)

1. Sinden R.R. DNA Structure and Function 1994, Academic Press, New York.
2. Thein S.L., Joy Ho P. Gene regulation and deregulation: a β globin perspective. Blood Rev. 2000, 14:78-93.
3. Li Q., Peterson K.R., Fang X., Stamatoyannopoulos G. Locus control regions. Blood 2002, 100:3077-3086.
4. Susanna H., Kellie Mcqueen J., Kenneth Peterson R. Chromatin structure and control of β-like globin gene switching. Exp. Biol. Med. 2002, 22:683-700.
5. Wijgerde M., Grosveld F., Fraser P. Transcription complex stability and chromatin dynamics in vivo. Nature 1995, 377:209-213.
6. Kaushik M., Kukreti R., Grover D., et al. Hairpin-duplex equilibrium reflected in the A → B transition in an undecamer quasi-palindrome present in the locus control region of the human β-globin gene cluster. Nucleic Acids Res. 2003, 31:6904-6915.
7. Kaushik M., Kukreti S. Structural polymorphism exhibited by a quasi-palindrome present in the locus control region (LCR) of the human β-globin gene cluster. Nucleic Acids Res. 2006, 34:3511-3522.
8. Liu D.P., et al. Cluster specific regulation pattern of upstream regulatory elements in human α- and β-globin gene clusters. Exp. Cell Res. 2008, 314:115-122.
9. Liu D.P., et al. Gene order in human α-globin locus is required for their temporal specific expressions. Genes Cells 2006, 11:123-131.
10. Smith Z.E., Higgs D.R. The pattern of replication at a human telomeric region (16p13.3): its relationship to chromosome structure and gene expression. Hum. Mol. Genet. 1999, 8:1373-1386.
11. Higgs D.R., Sharpe J.A., Wood W.G. Understanding alpha globin gene expression: a step towards effective gene therapy. Semin. Hematol. 1998, 35:93-104.
12. Samakoglu S., Philipsen S., Grosveld F., Lüleci G., Bagci H. Nucleotide changes in the gamma-globin promoter and the (AT)x(N)y(AT)z polymorphic sequence of beta LCRHS-2 region associated with altered levels of HbF. Eur. J. Hum. Genet. 1999, 7:345-356.
13. Orkin S.H. Regulation of globin gene expression in erythroid cells. Eur. J. Biochem. 1995, 23:271-281.
14. Navas P.A., Peterson K.R., Li Q., McArthur M., Stamatoyannopoulos G. The 5'HS4 core element of the human β-globin locus control region is required for high-level globin gene expression in definitive but not in primitive erythropoiesis. J. Mol. Biol. 2001, 312:17-26.
15. Ryan T.M., Behringer R.R., Martin N.C., Townes T.M., Palmiter R.D., Brinster R.L. A single erythroid-specific DNase I super-hypersensitive site activates high levels of human β-globin gene expression in transgenic mice. Genes Dev. 1989, 3:314-323.
16. Peterson K.R., Clegg C.H., Navas P.A., Norton E.J., Kimbrough T.G., Stamatoyannopoulos G. Effect of deletion of 5'HS3 or 5'HS2 of the human β-globin locus control region on the developmental regulation of globin gene expression in β-globin locus yeast artificial chromosome transgenic mice. Proc. Natl. Acad. Sci. U. S. A. 1996, 93:6605-6609.
17. Caterina J.J., Ryan T.M., Pawlik K.M., Palmiter R.D., Brinster R.L., Behringer R.R., Townes T.M. Human β-globin locus control region: analysis of the 5'DNase I hypersensitive site HS2 in transgenic mice. Proc. Natl. Acad. Sci. U. S. A. 1991, 88:1626-1630.
18. Fang X., Yin W., Xiang P., Han H., Stamatoyannopoulos G., Li Q. The higher structure of chromatin in the LCR of the β-globin locus changes during development. J. Mol. Biol. 2009, 394:197-208.
19. Wada-Kiyama Y., Kiyama R. Periodicity of DNA bend sites in human epsilon- globin gene region possibility of sequence-directed nucleosome phasing. J. Biol. Chem. 1994, 269:22238-22244.
20. Felsenfeld G. Chromatin as an essential part of the transcriptional mechanism. Nature (London) 1992, 355:219-224.
21. Tuan D., Kong S., Hu K. Transcription of the hypersensitive site HS2 enhancer in erythroid cells. Proc. Natl. Acad. Sci. U. S. A. 1992, 89:11219-11223.
22. Blom van Assendelft G., Hanscombe O., Grosveld F., Greaves D.R. The β-globin dominant control region activates homologous and heterologous promoters in a tissue-specific manner. Cell 1989, 56:969-977.
23. Ney P.A., Sorrentino B.P., McDonagh K.T., Nienhuis A.W. Tandem AP-1-binding sites within the human β-globin dominant control region function as an inducible enhancer in erythroid cells. Genes Dev. 1990, 4:993-1006.
24. Talbot D., Grosveld F. The 5'HS2 of the globin locus control region enhances transcription through the interaction of a multimeric complex binding at two functionally distinct NF-E2 binding sites. EMBO J. 1991, 10:1391-1398.
25. Molete M.J., Petrykowska H., Eric Bouhassira E., Yong-Qing F., Webb M., Ross Hardison C. Sequences flanking hypersensitive sites of the β-globin locus control region are required for synergistic enhancement. Mol. Cell. Biol. 2001, 21:2969-2980.
26. Bungert J., Tanimoto K., Patel S., Liu Q., Fear M., Engel J.D. Hypersensitive site 2 specifies a unique function within the human beta-globin locus control region to stimulate globin gene transcription. Mol. Cell. Biol. 1999, 19:3062-3072.
27. Forrester W.C., Epner E., Driscoll M.C., et al. 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, 4:1637-1649.
28. Gribnau J., de Boer E., Trimborn T., et al. Chromatin interaction mechanism of transcriptional control in vivo. EMBO J. 1998, 17:6020-6027.
29. Grosveld F. Activation by locus control regions?. Curr. Opin. Genet. Dev. 1999, 9:152-157.
30. Milot E., Strouboulis J., Trimborn T., et al. Heterochromatin effects on the frequency and duration of LCR-mediated gene transcription. Cell 1996, 87:105-114.
31. Blackwood E.M., Kadonaga J.T. Going the distance: a current view of enhancer action. Science 1998, 281:61-63.
32. Bulger M., Groudline M. Looping versus linking: toward a model for long-distance gene activation. Genes Dev. 1999, 13:2465-2477.
33. Engel J.D., Tanimoto K. Looping, linking, and chromatin activity: new insights into beta-globin locus regulation. Cell 2000, 100:499-502.
34. Zhang W., Kadam S., Emerson B.M., Bieker J.J. Site specific acetylation by p300 or CREB binding protein regulates erythroid Kruppel-like factor transcriptional activity via its interaction with the SWI-SNF complex. Mol. Cell. Biol. 2001, 21:2413-2422.
35. Bender M.A., Bulger M., Close J., Groudine M. Beta-globin gene switching and DNase I sensitivity of the endogenous beta-globin locus in mice do not require the locus control region. Mol. Cell 2000, 5:387-393.
36. Fang X., Xiang P., Yin W., Stamatoyannopoulos G., Li Q. Cooperativeness of the higher chromatin structure of the beta-globin locus revealed by the deletion mutations of DNase I hypersensitive site 3 of the LCR. J. Mol. Biol. 2007, 365:31-37.
37. Bungert J., Dave U., Lim K.C., Kienw K.H., Shavit J.A., Liu Q., Engel J.D. Synergistic regulation of human β-globin gene switching by locus control region elements HS3 and HS4. Genes Dev. 1995, 9:3083-3096.
38. Li Q., Barkess G., Qian H. Chromatin looping and the probability of transcription. Trends Genet. 2006, 22:197-202.
39. Li X., Hu X., Patel B., Zhou Z., Liang S., Ybarra R., Qiu Y., Felsenfeld G., Bungert J., Huang S. H4R3 methylation facilitates {β}-globin transcription by regulating histone acetyltransferase binding and H3 acetylation. Blood 2010, 115:2028-2037.
40. Kukreti R., Rao C.B., Das S.K., et al. Study of the single nucleotide polymorphism (SNP) at the palindromic sequence of hypersensitive site (HS) 4 of the human beta-globin locus control region (LCR) in Indian population. Am. J. Hematol. 2002, 69:77-79.
41. Ulrich M.J., Gray T.J., Ley T.J. An intramolecular DNA triplex is disrupted by point mutations associated with hereditary persistence of fetal hemoglobin. J. Biol. Chem. 1992, 267:18649-18658.
42. Lathem G.J., Forgacs E., Beard W.A., et al. Vertical- scanning mutagenesis of a critical tryptophan in the " minor groove binding track" of HIV-1 reverse transcriptase. Major groove DNA adducts identify specific protein interaction in the minor groove. J. Biol. Chem. 2000, 275:15025-15033.
43. Boulikas T. Homeodomain protein binding sites, inverted repeats, and nuclear matrix attachment regions along the human beta-globin gene complex. J. Cell Biochem. 1993, 52:23-36.
44. John Bissler J. DNA inverted repeats and human disease. Front. Biosci. 1998, 3:408-418.
45. Pearson C.E., Sinden R.R. Alternative structures in duplex DNA formed within the trinucleotide repeats of the myotonic dystrophy and fragile-X loci. Biochemistry 1996, 35:5041-5053.
46. Pearson C.E., Sinden R.R. Trinucleotide repeat DNA structures: dynamic mutations from dynamic DNA. Curr. Opin. Struct. Biol. 1998, 3:321-330.
47. Ng H.L., Kopka M.L., Dickerson R.E. The structure of a stable intermediate in the A ↔ B DNA helix transition. Proc. Natl. Acad. Sci. U. S. A. 2000, 97:2035-2039.
48. Liang S., Moghimi B., Yang T.P., Strouboulis J., Bungert J. Locus control region mediated regulation of adult β-globin gene expression. J. Cell Biochem. 2008, 105:9-16.
49. Levings P.P., Bungert J. The human β-globin locus control region. Eur. J. Biochem. 2002, 269:1589-1599.
50. Tang Y., Liu D.-P., Liang C.-C. Further understanding of the β-globin locus regulation at the molecular level: looping or linking models?. Genes Cells 2002, 7:889-900.
51. Oner C., Dimovski A.J., Ataly C., Gurgery A., Gu Y.C., Huisman T.H., Lanclos K.D. Sequence variations in the 5' hypersensitive site-2 of the locus control region of beta s chromosomes are associated with different levels of fetal globin in hemoglobin S homozygotes. Blood 1992, 7:813-819.
52. Waring M. Facilitating structural transition in DNA. Proc. Natl. Acad. Sci. U. S. A. 2000, 97:11685-11687.