Long-range interactions between three transcriptional enhancers, active Vκ gene promoters, and a 3′ boundary sequence spanning 46 kilobases

Molecular and Cellular Biology

Volumn 25, Issue 8, 2005, Pages 3220-3231

  Liu, Zhe ^a   Garrard, William T ^a  

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

Author keywords

[No Author keywords available]

Indexed keywords

2 AMINO 4 PHOSPHONOBUTYRIC ACID; IMMUNOGLOBULIN ENHANCER BINDING PROTEIN; IMMUNOGLOBULIN KAPPA CHAIN;

ALLELE; ANIMAL CELL; ARTICLE; B LYMPHOCYTE; CHROMATIN; CHROMOSOME; CONTROLLED STUDY; ENHANCER REGION; GENE LOCUS; GENE SEQUENCE; GENETIC TRANSCRIPTION; GERM LINE; HOUSEKEEPING GENE; IMMUNOPRECIPITATION; MASTOCYTOMA; MOUSE; NONHUMAN; PLASMACYTOMA; PRIORITY JOURNAL; PROMOTER REGION; T LYMPHOCYTE;

3' FLANKING REGION; ANIMALS; B-LYMPHOCYTES; CELL LINE, TUMOR; CHROMATIN; CHROMATIN IMMUNOPRECIPITATION; DNA; DNA-BINDING PROTEINS; ENHANCER ELEMENTS (GENETICS); GLOBINS; IMMUNOGLOBULIN KAPPA-CHAINS; IMMUNOGLOBULIN VARIABLE REGION; LOCUS CONTROL REGION; MICE; NF-KAPPA B; NUCLEIC ACID CONFORMATION; PLASMACYTOMA; PROMOTER REGIONS (GENETICS); T-LYMPHOCYTES; TCF TRANSCRIPTION FACTORS; TRANSCRIPTION FACTOR RELA; TRANSCRIPTION FACTORS; TRANSCRIPTION, GENETIC;

EID: 16244398049     PISSN: 02707306     EISSN: None     Source Type: Journal    
DOI: 10.1128/MCB.25.8.3220-3231.2005     Document Type: Article

References (68)

1. Abney, J. R., B. Butler, M. L. Fillbach, D. Axelrod, and B. A. Scalettar. 1997. Chromatin dynamics in interphase nuclei and its implications for nuclear structure. J. Cell Biol. 137:1459-1468.
2. Aranburu, A., R. Carlsson, C. Persson, and T. Leanderson. 2001. Transcription factor AP-4 is a ligand for immunoglobulin-κ promoter E-box elements. Biochem. J. 354:431-438.
3. Atchison, M. L., and R. P. Perry. 1987. The role of the κ enhancer and its binding factor NF-κB in the developmental regulation of κ gene transcription. Cell 48:121-128.
4. Bain, G., E. C. R. Maandag, H. P. J. te Riele, A. J. Freeney, A. Sheehy, M. Schlissel, S. A. Shinton, R. R. Hardy, and C. Murre. 1997. Both E12 and E47 allow commitment to the B cell lineage. Immunity 6:145-154.
5. Baxter, J., M. Merkenschlager, and A. G. Fisher. 2002. Nuclear organization and gene expression. Curr. Opin. Cell Biol. 14:372-376.
6. Blasquez, V. C., M. A. Hale, K. W. Trevorrow, and W. T. Garrard. 1992. Immunoglobulin κ gene enhancers synergistically activate gene expression but independently determine chromatin structure. J. Biol. Chem. 267:23888-23893.
7. Bradney, C., M. Hjelmeland, Y. Komatsu, M. Yoshida, T.-P. Yao, and Y. Zhuang. 2003. Regulation of E2A activities by histone acetyltransferases in B lymphocyte development. J. Biol. Chem. 278:2370-2376.
8. Brekke, K. M., and W. T. Garrard. 2004. Assembly and analysis of the mouse immunoglobulin kappa gene sequence. Immunogenetics 56:490-505.
9. Brown, K. E., J. Baxter, D. Graf, M. Merkenschlager, and A. G. Fisher. 1999. Dynamic repositioning of genes in the nucleus of lymphocytes preparing for cell division. Mol. Cell 3:207-217.
10. Brown, K. E., S. S. Guest, S. T. Smale, K. Hahm, M. Merkenschlager, and A. G. Fisher. 1997. Association of transcriptionally silent genes with ikaros complexes at centromeric heterochromatin. Cell 91:845-854.
11. Carter, D., L. Chakalova, C. S. Osborne, Y.-F. Dai, and P. Fraser. 2002. Long-range chromatin regulatory interactions in vivo. Nat. Genet. 32:623-626.
12. Casellas, R., M. Jankovic, G. Meyer, A. Gazumyan, Y. Luo, R. G. Roeder, and M. C. Nussenzweig. 2002. OcaB is required for normal transcription and V(D)J recombination in a subset of immunoglobulin genes. Cell 110:575-585.
13. Choi, E., M. Kuehl, and R. Wall. 1980. RNA splicing generates a variant light chain from an aberrantly rearranged kappa gene. Nature 286:776-779.
14. Chubb, J. R., S. Boyle, P. Perry, and W. A. Bickmore. 2002. Chromatin motion is constrained by association with nuclear compartments in human cells. Curr. Biol. 12:439-445.
15. Chubb, J. R., and W. Bickmore. 2003. Considering nuclear compartmentalization in the light of nuclear dynamics. Cell 112:403-406.
16. Cockerill, P. N., and W. T. Garrard. 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.
17. Coligan, J. E., A. M. Kruisbeek, D. H. Margulies, E. M. Sherach, and W. Strober. 1994. Current protocols in immunology, p. 1.9.1-1.9.3, 6.4.5-6.4.6. John Wiley & Sons, New York, N.Y.
18. Cook, P. R. 1999. The organization of replication and transcription. Science 284:1790-1795.
19. Dekker, J. 2003. A closer look a long-range chromosomal interactions. Trends Biochem. Sci. 28:277-280.
20. Dekker, J., K. Rippe, M. Dekker, and N. Kleckner. 2002. Capturing chromosome conformation. Science 295:1306-1311.
21. de Laat, W., and F. Grosveld. 2003. Spatial organization of gene expression: the active chromatin hub. Chromosome Res. 11:447-459.
22. Eckner, R., T.-P. Yao, E. Oldread, and D. M. Livingston. 1996. Interaction and functional collaboration of p300/CBP and bHLH proteins in muscle and B-cell differentiation. Genes Dev. 10:2478-2490.
23. Fernandez, L., M. Winkler, and R. Grosschedl. 2001. Matrix attachment region-dependent function of the immunoglobulin μ enhancer involves histoneacetylation at a distance without changes in enhancer occupancy. Mol. Cell. Biol. 21:196-208.
24. Franzoso, G., L. Carlson, L. Xing, L. Poljak, E. W. Shores, K. D. Brown, A. Leonardi, T. Tran, B. F. Boyce, and U. Siebenlist. 1997. Requirement for NF-κB in osteoclast and B-cell development. Genes Dev. 11:3482-3496.
25. Gellert, M. 2002. Recombination: RAG proteins, repair factors, and regulation. Annu. Rev. Biochem. 71:101-132.
26. George, J. B., S. Li, and W. T. Garrard. 1995. Yeast artificial chromosome contigs reveal that distal variable regions genes reside at least 3 megabases from the joining regions in the murine immunoglobulin κ locus. Proc. Natl. Acad. Sci. USA 92:12421-12425.
27. Gubin, A. N., and J. L. Miller. 2001. Human erythroid porphobilinogen deaminase exists in 2 splice variants. Blood 97:815-817.
28. Hale, M. A., and W. T. Garrard. 1998. A targeted kappa immunoglobulin gene containing a deletion of the nuclear matrix association region exhibits spontaneous hyper-recombination in pre-B cells. Mol. Immunol. 35:609-620.
29. Jackson, D. A. 2003. The principles of nuclear structure. Chromosome Res. 11:387-401.
30. Kosak, S. T., J. A. Skok, K. L. Medina, R. Riblet, M. M. Le Beau, A. G. Fisher, and H. Singh. 2002. Subnuclear compartmentalization of immunoglobulin loci during lymphocyte development. Science 296:158-162.
31. Kwan, S.-P., E. E. Max, S. G. Seidman, P. Leder, and M. D. Scharff. 1981. Two kappa immunoglobulin genes are expressed in the myeloma S107. Cell 26:57-66.
32. Kwan, S.-P., S. Rudikoff, S. G. Seidman, P. Leder, and M. D. Scharff. 1981. Nucleic acid and protein sequences of phosphocholine-binding light chains. J. Exp. Med. 153:1366-1370.
33. Labrador, M., and V. G. Corces. 2002. Setting the boundaries of chromatin domains and nuclear organization. Cell 111:151-154.
34. Lenardo, M., J. W., Pierce, and D. Baltimore. 1987. Protein-binding sites in Ig gene enhancers determine transcriptional activity and inducibility. Science 236:1573-1577.
35. Liu, X., A. Prabhu, and B. Van Ness. 1999. Developmental regulation of the κ locus involves both positive and negative sequence elements in the 3′ enhancer that affect synergy with the intron enhancer. J. Biol. Chem. 274: 3285-3296.
36. Liu, Z.-M., J. B. George-Raizen, S. Li, M. Y. Chang, K. C. Meyers, and W. T. Garrard. 2002. Chromatin structural analyses of the mouse Igκ gene locus reveal new hypersensitive sites specifying a transcriptional silencer and enhancer. J. Biol. Chem. 277:32640-32649.
37. Maitra, S., and M. Atchison. 2000. BSAP can repress enhancer activity by targeting PU.1 function. Mol. Cell. Biol. 20:1911-1922.
38. Manders, E., M. M., A. E. Visser, A. Koppen, W. C. de Leeuw, R. van Liere, G. J. Brakenhoff, and R. van Driel. 2003. Four-dimensional imaging of chromatin dynamics during the assembly of the interphase nucleus. Chromosome Res. 11:537-547.
39. Marshall, W. F. 2002. Order and disorder in the nucleus. Curr. Biol. 12: R185-R192.
40. Marshall, W. F., A. F. Dernburg, B. Harmon, D. A. Agard, and J. W. Sedat. 1996. Specific interactions of chromatin with the nuclear envelope: positional determination within the nucleus in Drosophila melanogaster. Mol. Biol. Cell. 7:825-842.
41. Marshall, W. F., A. Straight, J. F. Marko, J. Swedlow, A. Dernburg, A. Belmont, A. W. Murray, D. A. Agard, and J. W. Sedat. 1997. Interphase chromosomes undergo constrained diffusional motion in living cells. Curr. Biol. 7:930-939.
42. Massari, M. E., P. A. Grant, M. G. Pray-Grant, S. L. Berger, J. L. Workman, and C. Murre. 1999. A conserved motif present in a class of helix-loop-helix proteins activates transcription by direct recruitment of the SAGA complex. Mol. Cell 4:63-73.
43. Meyer, K. B., and M. S. Neuberger. 1989. The immunoglobulin κ locus contains a second, stronger B-cell-specific enhancer which is located downstream of the constant region. EMBO J. 8:1959-1964.
44. Murrell, A., S. Heeson, and W. Reik. 2004. Interaction between differentially methylated regions partitions the imprinted genes Igf2 and H19 into parent-specific chromatin loops. Nat. Genet. 36:889-893.
45. Palstra, R.-J., B. Tolhuis, E. Splinter, R. Nijmeijer, F. Grosveld, and W. de Laat. 2003. The β-globin nuclear compartment in development and erythroid differentiation. Nat. Genet. 35:190-194.
46. Parslow, T. G., D. L. Blair, W. J. Murphy, and D. K. Granner. 1984. Structure of the 5′ ends of immunoglobulin genes: a novel conserved sequence. Proc. Natl. Acad. Sci. USA 81:2650-2654.
47. Patrinos, G. P., M. de Krom, E. de Boer, A. Langeveld, A. M. Imam, J. Strouboulis, W. de Laat, and F. G. Grosveld. 2004. Multiple interacvtions between regulatory regions are required to stabilize an active chromatin hub. Genes Dev. 18:1495-1509.
48. Pederson, T. 2004. The spatial organization of the genome in mammalian cells. Curr. Opin. Genet. Dev. 14:203-209.
49. Perry, R. P., D. E. Kelley, C. Coleclough, J. G. Seidman, P. Leder, S. Tonegawa, G. Matthysssens, and M. Weigert. 1980. Transcription of mouse kappa chain genes: implications for allelic exclusion. Proc. Natl. Acad. Sci. USA 77:1937-1941.
50. Phair, R. D., P. Scaffidi, C. Elbi, J. Vecerova, A. S. Dey, K. Ozato, D. T. Brown, G. Hager, M. Bustin, and T. Misteli. 2004. Global nature of dynamic protein-chromatm interactions in vivo: three-dimensional genome scanning and dynamic interaction networks of chromatin proteins. Mol. Cell. Biol. 24:6393-6402.
51. Pongubala, J. M. R., and M. L. Atchison. 1991. Functional characterization of the developmentally controlled immunoglobulin kappa 3′ enhancer: regulation by Id, a repressor of helix-loop-helix transcription factors. Mol. Cell. Biol. 11:1040-1047.
52. Queen, C., and D. Baltimore. 1983. Immunoglobulin gene transcription is activated by downstream sequence elements. Cell 33:741-748.
53. Qui, Y., A. Sharma, and A. Stein. 1998. p300 mediates transcriptional stimulation by the basic helix-loop-helix factors of the insulin gene. Mol. Cell. Biol. 18:2957-2964.
54. Quong, M. W., W. J. Romanow, and C. Murre. 2002. E protein function in lymphocyte development. Annu. Rev. Immunol. 20:301-322.
55. Ragoczy, T., A. Telling, T. Sawado, M. Groudine, and S. T. Kosas. 2003. A genetic analysis of chromosome territory looping: diverse roles for distal regulatory elements. Chromosome Res. 11:513-525.
56. Roque, M. A., P. A. Smith, and V. C. Blasquez. 1996. A developmentally modulated chromatin structure at the mouse immunoglobulin κ 3′ enhancer. Mol. Cell. Biol. 16:3138-3155.
57. Rose, S. M., and W. T. Garrard. 1984. Differentiation-dependent chromatin alterations precede and accompany transcription of immunoglobulin light chain genes. J. Biol. Chem. 259:8534-8544.
58. 1 to S phase transition. Nucleic Acids Res. 30:4176-4185.
59. Schibler, U., K. B. Marcu, and R. P. Perry. 1978. The synthesis and processing of the messenger RNAs specifying heavy and light chain immunoglobulins in MPC-11 cells. Cell 15:1495-1509.
60. Seidman, J. G., and P. Leder. 1980. A mutant immunoglobulin light chain is formed by aberrant DNA-and RNA-splicing events. Nature 286:779-783.
61. Shaffer, A. L., A. Peng, and M. S. Schlissel. 1997. In vivo occupancy of the κ light chain enhancers in primary pro- and pre-B cells: a model for κ locus activation. Immunity 6:131-143.
62. Skok, J. A., K. E. Brown, V. Azuara, M.-L. Caparros, J. Baxter, K. Takacs, N. Dillon, D. Gray, R. P. Perry, M. Merkenschlager, and A. G. Fisher. 2001. Nonequivalent nuclear location of immunoglobulin alleles in B lymphocytes. Nat. Immunol. 2:848-853.
63. Spiliankis, C. G., and R. A. Flavell. 2004. Long-range intrachromosomal interactions in the T helper type 2 cytokine locus. Nat. Immunol. 5:1017-1027.
64. Tolhuis, B., R.-J. Palstra, E. Splinter, F. Grosveld, and W. de Laat. 2002. Looping and interaction between hypersensitive sites in the active β-globin locus. Mol. Cell 10:1453-1465.
65. Williams, R. R. E. 2003. Transcription and the territory: the ins and outs of gene positioning. Trends Genet. 19:298-302.
66. Xu, M., M. B. Barnard, S. M. Rose, P. N. Cockerill, S.-Y. Huang, and W. T. Garrard. 1986. Transcription termination and chromatin structure of the active immunoglobulin κ gene locus. J. Biol. Chem. 261:3838-3845.
67. Yancopoulos, G. D., and F. W. Alt. 1985. Developmental controlled and tissue-specific expression of unrearranged Vκ gene segments. Cell 40:271-281.
68. Yusufzai, T. M., H. Tagami, Y. Nakatani, and G. Felsenfeld. 2004. CTCF tethers an insulator to subnuclear sites, suggesting shared insulator mechanisms across species. Cell 13:291-298.