MARs of antigen receptor and co-receptor genes

Critical Reviews in Eukaryotic Gene Expression

Volumn 9, Issue 3-4, 1999, Pages 295-310

  Scheuermann, Richard H ^a   Garrard, William T ^b  

^a UNIVERSITY OF TEXAS SOUTHWESTERN MEDICAL CENTER   (United States)

^b UNIVERSITY OF TEXAS SOUTHWESTERN MEDICAL CENTER   (United States)

Author keywords

Chromatin remodeling; DNA methylation; Gene rearrangement; Histone acetylation; Immunoglobulin and T cell receptor genes; Nuclear matrix; SAR; Somatic hypermutation; Transcription

Indexed keywords

HISTONE; IMMUNOGLOBULIN; LYMPHOCYTE ANTIGEN RECEPTOR; NUCLEOLIN;

ACETYLATION; CELL NUCLEUS MATRIX; CHROMATIN; DNA METHYLATION; DNA SEQUENCE; ENHANCER REGION; GENE REARRANGEMENT; PRIORITY JOURNAL; REGULATORY MECHANISM; REVIEW; SOMATIC MUTATION; T LYMPHOCYTE RECEPTOR GENE; TRANSCRIPTION REGULATION;

EID: 0033373188     PISSN: 10454403     EISSN: None     Source Type: Journal    
DOI: 10.1615/CritRevEukarGeneExpr.v9.i3-4.140     Document Type: Review

References (62)

1. Andres V, Nadal-Ginard B, Mahdavi V (1992): Clox, a mammalian homeobox gene related to Drosophila cut, encodes DNA-binding regulatory proteins differentially expressed during development. Development 116:321-334.
2. Banan M, Rojas IC, Lee W-H, King HL, Harriss JV, Kobayashi R, Webb CF, Gottlieb PD (1997): Interaction of the nuclear matrix-associated region (MAR)-binding proteins, SATB1 and CDP/Cux, with a MAR element (L2a) in an upstream regulatory region of the mouse CD8a gene. J Biol Chem 272:18440-18452.
3. Berezney R, Wei X (1998): The new paradigm: integrating genomic function and nuclear architecture. [Review] [26 refs]. J Cell Biochem (Suppl) 31:30-31.
4. Blasquez VC, Hale MA, Trevorrow KW, Garrard WT (1992): Immunoglobulin kappa gene enhancers synergistically activate gene expression but independently determine chromatin structure. J Biol Chem 267:23888-23893.
5. Blasquez VC, Xu M, Moses SC, Garrard WT (1989): Immunoglobulin κ gene expression after stable integration. I. Role of the intronic MAR and enhancer in plasmacytoma cells. J Biol Chem 264:21183-21189.
6. Blochlinger K, Bodmer R, Jack JW, Jan LY, Jan YN (1988): Primary structure and expression of a product from cut, a locus involved in specifying sensory organ identity in Drosophila. Nature 333:629-635.
7. Bode J, Kohwi Y, Dickinson L, Joh T, Klehr D, Mielke C, Kohwi-Shigematsu T (1992): Biological significance of unwinding capability of nuclear matrix-associating DNAs. Science 255:195-197.
8. Bonnefoy E, Bandu MT, Doly J (1999): Specific binding of high-mobility-group I (HMGI) protein and histone H1 to the upstream AT-rich region of the murine beta interferon promoter: HMGI protein acts as a potential antirepressor of the promoter. Mol Cell Biol 19:2803-2816.
9. Brown KE, Guest SS, Smale ST, Hahm K, Merkenschlager M, Fisher AG (1997): Association of transcriptionally silent genes with Ikaros complexes at centromeric heterochromatin. Cell 91:845-854.
10. Chattopadhyay S, Whitehurst CE, Chen J (1998a): A nuclear matrix attachment region upstream of the T cell receptor β gene enhancer binds Cux/CDP and STAB1 and modulates enhancer-dependent reporter gene expression but not endogenous gene expression. J Biol Chem 273:29838-29846.
11. + thymocyte differentiation. J Immunol 160:1256-1267.
12. Cockerill PN (1990): Nuclear matrix attachment occurs in several regions of the IgH locus. Nucleic Acids Res 18:2643-2648.
13. Cockerill PN, Garrard WT (1986): Chromosomal loop anchorage of the kappa immunoglobulin gene occurs next to the enhancer in a region containing topoisomerase II sites. Cell 44:273-282.
14. Cockerill PN, Yuen MH, Garrard WT (1987): The enhancer of the immunoglobulin heavy chain locus is flanked by presumptive chromosomal loop anchorage element. J Biol Chem 262:5394-5397.
15. Cook PR (1999): The organization of replication and transcription. Science 284:1790-1795.
16. Cosma MP, Tanaka T, Nasmyth K (1999): Ordered recruitment of transcription and chromatin remodeling factors to a cell cycle-and developmentally regulated promoter. Cell 97:299-311.
17. Dickinson LA, Dickinson CD, Kohwi-Shigematsu T (1997): An atypical homeodomain in SATB1 promotes specific recognition of the key structural element in a matrix attachment region. J Biol Chem 272:11463-11470.
18. Dickinson LA, Joh T, Kohwi Y, Khowi-Shigematsu T (1992): A tissue specific MAR/SAR DNA-binding protein with unusual binding site recognition. Cell 70:631-645.
19. Dickinson LA, Khowi-Shigematsu T (1995): Nucleolin is a matrix attachment region DNA-binding protein that specifically recognizes a region with high base-unpairing potential. Mol Cell Biol 15:456-465.
20. Fishel BR, Sperry AO, Garrard WT (1993): Yeast calmodulin and a conserved nuclear protein participate in the in vivo binding of a matrix association region. Proc Natl Acad Sci USA 90:5623-5627.
21. Forrester WC, van Genderen C, Jenuwein T, Grosschedul R (1994): Dependence of enhancer-mediated transcription of the immunoglobulin μ gene of nuclear matrix attachment regions. Science 265:1221-1225.
22. Freeman LA, Garrard WT (1992): DNA supercoiling in chromatin structure and gene expression. Crit Rev Eukaryot Gene Expression 2:165-209.
23. Gasser SM, Laemmli UK (1986): Cohabitation of scaffold binding regions with upstream/enhancer elements of three developmentally regulated genes of D. melanogaster. Cell 46:521-530.
24. Goyenechea B, Klix N, Yelamos J, Williams GT, Riddell A, Neuberger MS, Milstein C (1997): Cells strongly expressing Ig(kappa) transgenes show clonal recruitment of hypermutation: a role for both MAR and the enhancers. EMBO J 16:3987-3994.
25. Hale MA, Garrard WT (1998): A targeted kappa immunoglobulin gene containing a deletion of the nuclear matrix association region exhibits spontaneous hyperrecombination in pre-B cells. Mol Immunol 35:609-620.
26. Harada R, Berube G, Tamplin OJ, Denis-Larose C, Nepveu A (1995): DNA-binding specificity of the cut repeats from the human cut-like protein. Mol Cell Biol 15: 129-140.
27. Herrscher RF, Kaplan MH, Lelsz DL, Das C, Scheuermann RH, Tucker PW (1995): The immunoglobulin heavy-chain matrix-associating regions are bound by Bright: a B cell-specific trans-activator that describes a new DNA-binding protein family. Genes Dev 9:3067-3082.
28. Jenuwein T, Forrester WC, Fernandez-Herrero LA, Laible G, Dull M, Grosschedl R (1997): Extension of chromatin accessibility by nuclear matrix attachment regions. Nature 385:269-272.
29. Kim J, Sif S, Jones B, Jackson A, Koipally J, Heller E, Winandy S, Viel A, Sawyer A, Ikeda T, Kingston R, Georgopoulos K (1999): Ikaros DNA-binding proteins direct formation of chromatin remodeling complexes in lymphocytes. Immunity 10:345-355.
30. Kirillov A, Kistler B, Mostoslavsky R, Cedar H, Wirth T, Bergman Y (1996): A role for nuclear NF-kappaB in B-cell-specific demethylation of the Igkappa locus. Nat Genet 13:435-441.
31. Kohwi-Shigematsu T, Maass K, Bode J (1997): A thymocyte factor SATB1 suppresses transcription of stably integrated matrix-attachment region-linked reporter genes. Biochemistry 36:12005-12010.
32. Li S, Moy L, Pittman N, Shue G, Aufiero B, Neufeld EJ, LeLeiko NS, Walsh MJ (1999): Transcriptional repression of the cystic fibrosis transmembrane conductance regulator gene, mediated by CCAAT displacement protein/cut homolog, is associated with histone deacetylation. J Biol Chem 274:7803-7815.
33. Lichtenstein M, Keini G, Bergman Y (1994): B cell-specific demethylation: a novel role for the intronic kappa chain enhancer sequence. Cell 76:913-923.
34. Liu J, Barnett A, Neufeld EJ, Dudley JP (1999): Homeo-proteins CDP and SABT1 interact potential for tissue specific regulation. Mol Cell Biol 19:4918-4926.
35. Luderus ME, de Graaf A, Mattia E, den Blaauwen JL, Grande MA, de Jong L, van Driel R (1992): Binding of matrix attachment regions to lamin B1. Cell 70:949-959.
36. Nabirochkin S, Ossokina M, Heidmann T (1998): A nuclear matrix/scaffold attachment region co-localizes with the gypsy retrotransposon insulator sequence. J Biol Chem 273:2473-2479.
37. Nan X, Ng HH, Johnson CA, Laherty CD, Turner BM, Eisenman RN, Bird A (1998): Transcriptional repression by the methyl-CpG-binding protein MeCP2 involves a histone deacetylase complex [see comments]. Nature 393:386-389.
38. Neufeld EJ, Skalnik DG, Lievens PMJ, Orkin SH (1992): Human CCAAT displacement protein is homologous to the Drosophila homeoprotein, cut. Nat Genet 1:50-55.
39. Oancea AE, Berru M, Shulman MJ (1997): Expression of the (recombinant) endogenous immunoglobulin heavy-chain locus requires the intronic matrix attachment regions. Mol Cell Biol 17:2658-2668.
40. Reyes JC, Muchardt C, Yaniv M (1997): Components of the human SWI/SNF complex are enriched in active chromatin and are associated with the nuclear matrix. J Cell Biol 137:263-274.
41. Sakai E, Bottaro A, Davidson L, Sleckman BP, Alt FW (1999): Recombination and transcription of the endogenous Ig heavy chain locus is effected by the Ig heavy chain intronic enhancer core region in the absence of the matrix attachment regions. Proc Natl Acad Sci USA 96:1526-1531.
42. Schanke JT, Marcuzzi A, Podzorski RP, Van Ness B (1994): An AP1 binding site upstream of the kappa immunoglobulin intron enhancer binds inducible factors and contributes to expression. Nucleic Acids Res 22:5425-5432.
43. Scheuermann RH (1992): The tetrameric structure of NF-μNR provides a mechanism for cooperative binding to the immunoglobulin heavy chain μ enhancer. J Biol Chem 267:624-634.
44. Scheuermann RH, Chen U (1989): A developmental-specific factor binds to suppressor sites flanking the immunoglobulin heavy-chain enhancer. Genes Dev 3: 1255-1266.
45. Sperry AO, Blasquez VC, Garrard WT (1989): Dysfunction of chromosomal loop attachment sites: illegitimate recombination linked to matrix association regions and topoisomerase II. Proc Natl Acad Sci USA 86: 5497-5501.
46. Strissel-Broker P, Gill HS, Thirman M, Pomykala H, Yonebashi Y, Tanabe S, Zelenik-Le N, Rowley J (1996): Distribution of 11q23 breakpoints within the MLL breakpoint cluster region in de novo myeloid leukemia and in treatment-related acute myeloid leukemia: correlation with scaffold attachment regions and topoisomerase II binding sites. Blood 87:1912-1922.
47. Strouboulis J, Wolffe AP (1996): Functional compartmentalization of the nucleus. J Cell Sci 109:1991-2000.
48. Udvardy A (1999): Dividing the empire: boundary chromatir elements delimit the territory of enhancers EMBO J 18:1-8.
49. Valarche I, Tissier-Seta J-P, Hirsch M-R, Martinez S, Goridis C, Brunet J-F (1993): The mouse homeodomain protein Phox2 regulates Ncam promoter activity in concert with Cux/CDP and is a putative determinant of neurotransmitter phenotype. Development 119:881-896.
50. Van Wijnen A, Bidwell JP, Fey EG, Penman S, Lian JB, Stein JL, Stein GS (1993): Nuclear matrix association of multiple sequence-specific DNA binding activities related to SP-1, ATF, CCAAT, C/EBP, OCT-1, and AP-1. Biochemistry 32:8397-8402.
51. Wang Z, Goldstein A, Zong R-T, Lin D, Neufeld EJ, Scheuermann RH, Tucker PW (1999): Cux/CDP homeo-protein is a component of NF-μNR and represses the immunoglobulin heavy chain intronic enhancer by antagonizing the Bright transcription activator. Mol Cell Biol 19:284-295.
52. Webb CF, Das C, Eaton S, Calame K, Tucker PW (1991a): Novel protein-DNA interactions associated with increased immunoglobulin transcription in response to antigen plus interleukin-5. Mo1 Cell Biol 11:5197-5205.
53. Webb CF, Das C, Eneff KL, Tucker PW (1991b): Identification of a matrix-associated region 5′ of an immunoglobulin heavy chain variable region gene. Mol Cell Biol 11:5206-5211.
54. Webb CF, Zong R-T, Lin D, Wang Z, Kaplan M, Paulin Y, Smith E, Probst L, Bryant J, Goldstein A, Scheuermann R, Tucker P (1999): Differential regulation of immunoglobulin gene transcription via nuclear matrix associated regions. Cold Spring Harbor Symp Quant Biol (in press).
55. Whitehurst C, Henney HR, Max EE, Schroeder HW Jr, Stuber F, Siminovitch KA, Garrard WT (1992): Nucleotide sequence of the intron of the germline human kappa immunoglobulin gene connecting the J and C regions reveals a matrix association region (MAR) next to the enhancer. Nucleic Acids Res 20: 4929-4930.
56. Wiersma EJ, Ronai D, Berru M, Tsui FW, Shulman MJ (1999): 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 274:4858-4862.
57. Xu M, Hammer RE, Blasquez VC, Jones SL, Garrard WT (1989): Immunoglobulin K gene expression after stable integration. II. Role of the intronic MAR and enhancer in transgenic mice. J Biol Chem 264:21190-21195.
58. Yi M, Wu P, Trevorrow KW, Claflin L, Garrard WT (1999): Evidence that the Igkappa gene MAR regulates the probability of premature V-J joining and somatic hypermutation. J Immunol 162:6029-6039.
59. Zhao K, Kas E, Gonzalez E, Laemmli U (1993): SAR-dependent mobilization of histone H1 by HMG-I/Y in vitro: HMG-I/Y is enriched in H1-depleted chromatin. EMBO J 12:3237-3247.
60. Zhong X-P, Carabana J, Krangel MS (1999): Flanking nuclear matrix attachment regions synergize with the T cell receptor δ enhancer to promote V(D)J recombination. Proc Natl Acad Sci USA (in press).
61. Zlatanova JS, van Holde KE (1992): Chromatin loops and transcriptional regulation. Crit Rev Eukaryot Gene Expression 2:211-224.
62. Zong R-T, Scheuermann RH (1995): Mutually exclusive interaction of a novel matrix attachment region binding protein and NF-μNR enhancer repressor: implications for regulation of immunoglobulin heavy-chain expression. J Biol Chem 270:24010-24018.