Comparative analysis of human and mouse 3′ Igh regulatory regions identifies distinctive structural features

Molecular Immunology

Volumn 42, Issue 5, 2005, Pages 605-615

  Sepulveda, Manuel A ^a   Garrett, Francine E ^a   Price Whelan, Alexa ^a   Birshtein, Barbara K ^a  

^a ALBERT EINSTEIN COLLEGE OF MEDICINE   (United States)

Author keywords

3 Untranslated regions immunology; B lymphocytes immunology; Conserved sequence; Enhancer elements (genetics) immunology; Evolution; Heavy chain genetics; Immunoglobulins; Molecular; Molecular sequence data; Nucleic acid; Phylogeny; Regulatory sequences

Indexed keywords

IMMUNOGLOBULIN HEAVY CHAIN; REPETITIVE DNA;

ARTICLE; CHIMPANZEE; CONTROLLED STUDY; GENE SEQUENCE; GENETIC CONSERVATION; HUMAN; IMMUNOGLOBULIN GENE; MOUSE; NONHUMAN; NUCLEOTIDE SEQUENCE; PRIORITY JOURNAL; RAT; REGULATOR GENE; RESTRICTION FRAGMENT LENGTH POLYMORPHISM; SEQUENCE HOMOLOGY; SINGLE NUCLEOTIDE POLYMORPHISM; SPECIES COMPARISON; TANDEM REPEAT;

3' UNTRANSLATED REGIONS; ANIMALS; BASE SEQUENCE; CHROMOSOMES, ARTIFICIAL, BACTERIAL; DNA; EVOLUTION, MOLECULAR; GENE REARRANGEMENT, B-LYMPHOCYTE; GENES, IMMUNOGLOBULIN; GENES, REGULATOR; HUMANS; MICE; MULTIGENE FAMILY; PAN TROGLODYTES; POLYMORPHISM, RESTRICTION FRAGMENT LENGTH; RATS; REPETITIVE SEQUENCES, NUCLEIC ACID; REVERSE TRANSCRIPTASE POLYMERASE CHAIN REACTION; SPECIES SPECIFICITY;

MURINAE; PAN TROGLODYTES; PRIMATES; RODENTIA;

EID: 10844228012     PISSN: 01615890     EISSN: None     Source Type: Journal    
DOI: 10.1016/j.molimm.2004.09.006     Document Type: Article

References (43)

1. K. Araki, H. Maeda, J. Wang, D. Kitamura, and T. Watanabe Purification of a nuclear trans-acting factor involved in the regulated transcription of a human immunoglobulin heavy chain gene Cell 53 1988 723 730
2. N.A. Barlev, A.V. Emelyanov, P. Castagnino, P. Zegerman, A.J. Bannister, M.A. Sepulveda, F. Robert, L. Tora, T. Kouzarides, B.K. Birshtein, and S.L. Berger A novel human Ada2 homologue functions with Gcn5 or Brg1 to coactivate transcription Mol. Cell Biol. 23 2003 6944 6957
3. G. Benson Tandem repeats finder: a program to analyze DNA sequences Nucleic Acids Res. 27 1999 573 580
4. P.L. Bergsagel, and W.M. Kuehl Chromosome translocations in multiple myeloma Oncogene 20 2001 5611 5622
5. M. Bulger, J.H. van Doorninck, N. Saitoh, A. Telling, C. Farrell, M.A. Bender, G. Felsenfeld, R. Axel, M. Groudine, and J.H. von Doorninck Conservation of sequence and structure flanking the mouse and human beta-globin loci: the beta-globin genes are embedded within an array of odorant receptor genes (published erratum appears in Proc. Natl. Acad. Sci. USA 1999 July 6;96(14):8307) Proc. Natl. Acad. Sci. USA 96 1999 5129 5134
6. C. Chauveau, and M. Cogne Palindromic structure of the IgH 3′locus control region Nat Genet. 14 1996 15 16 (letter)
7. C. Chen, and B.K. Birshtein A region of 20 bp repeats lies 3′ of human Ig Cα1 and Cα2 genes Int. Immunol. 8 1996 115 122
8. C. Chen, and B.K. Birshtein Virtually identical enhancers containing a segment of homology to murine 3′IgH-E (hs1,2) lie downstream of human Ig C alpha 1 and C alpha 2 genes J. Immunol. 159 1997 1310 1318
9. S. Codlin, C. Soh, T. Lee, and P. Lavender Characterization of a palindromic enhancer element in the promoters of IL4, IL5, and IL13 cytokine genes J. Allergy Clin. Immunol. 111 2003 826 832
10. Y. Denizot, E. Pinaud, C. Aupetit, C. Le Morvan, E. Magnoux, J.C. Aldigier, and M. Cogne Polymorphism of the human alpha1 immunoglobulin gene 3′ enhancer hs1 2 and its relation to gene expression Immunology 103 2001 35 40
11. O. Dunda, and D. Corcos Recombining sequence recombination in normal kappa-chain-expressing B cells J. Immunol. 159 1997 4362 4366
12. M. Enjoji, T. Iwaki, H. Nawata, and T. Watanabe IgH intronic enhancer element HE2 (mu B) functions as a cis-activator in choroid plexus cells at the cellular level as well as in transgenic mice J. Neurochem. 64 1995 961 966
13. C. Gaillard, and F. Strauss Association of poly(CA).poly(TG) DNA fragments into four-stranded complexes bound by HMG1 and 2 Science 264 1994 433 436
14. C. Gaillard, and F. Strauss DNA loops and semicatenated DNA junctions BMC Biochem. 1 2000 1
15. S.J. Gordon, S. Saleque, and B.K. Birshtein Yin Yang 1 is a lipopolysaccharide-inducible activator of the murine 3′ Igh enhancer, hs3 J. Immunol. 170 2003 5549 5557
16. P.D. Gregor, and S.L. Morrison Myeloma mutant with a novel 3′ flanking region: loss of normal sequence and insertion of repetitive elements leads to decreased transcription but normal processing of the alpha heavy-chain gene products Mol. Cell. Biol. 6 1986 1903 1916
17. R. Heilig, R. Eckenberg, J.L. Petit, N. Fonknechten, C. Da Silva, L. Cattolico, M. Levy, V. Barbe, V. de Berardinis, A. Ureta-Vidal, E. Pelletier, V. Vico, V. Anthouard, L. Rowen, A. Madan, S. Qin, H. Sun, H. Du, K. Pepin, F. Artiguenave, C. Robert, C. Cruaud, T. Bruls, O. Jaillon, L. Friedlander, G. Samson, P. Brottier, S. Cure, B. Segurens, F. Aniere, S. Samain, H. Crespeau, N. Abbasi, N. Aiach, D. Boscus, R. Dickhoff, M. Dors, I. Dubois, C. Friedman, M. Gouyvenoux, R. James, B. Mairey-Estrada, S. Mangenot, N. Martins, M. Menard, S. Oztas, A. Ratcliffe, T. Shaffer, B. Trask, B. Vacherie, C. Bellemere, C. Belser, M. Besnard-Gonnet, D. Bartol-Mavel, M. Boutard, S. Briez-Silla, S. Combette, V. Dufosse-Laurent, C. Ferron, C. Lechaplais, C. Louesse, D. Muselet, G. Magdelenat, E. Pateau, E. Petit, P. Sirvain-Trukniewicz, A. Trybou, N. Vega-Czarny, E. Bataille, E. Bluet, I. Bordelais, M. Dubois, C. Dumont, T. Guerin, S. Haffray, R. Hammadi, J. Muanga, V. Pellouin, D. Robert, E. Wunderle, G. Gauguet, A. Roy, L. Sainte-Marthe, J. Verdier, C. Verdier-Discala, L. Hillier, L. Fulton, J. McPherson, F. Matsuda, R. Wilson, C. Scarpelli, G. Gyapay, P. Wincker, W. Saurin, F. Quetier, R. Waterston, L. Hood, and J. Weissenbach The DNA sequence and analysis of human chromosome 14 Nature 421 2003 601 607
18. B.G. Herrmann, and A.M. Frischauf Isolation of genomic DNA Methods Enzymol. 152 1987 180 183
19. A.C. Hollmann, Q. Gong, and T. Owens CD40-mediated apoptosis in murine B-lymphoma lines containing mutated p53 Exp. Cell. Res. 280 2002 201 211
20. K. Kanda, H.M. Hu, L. Zhang, J. Grandchamps, and L.M. Boxer NF-kappa B activity is required for the deregulation of c-myc expression by the immunoglobulin heavy chain enhancer J. Biol. Chem. 275 2000 32338 32346
21. M.A. Karim, K. Ohta, M. Egashira, Y. Jinno, N. Niikawa, I. Matsuda, and Y. Indo Human ESP1/CRP2, a member of the LIM domain protein family: characterization of the cDNA and assignment of the gene locus to chromosome 14q32.3 Genomics 31 1996 167 176
22. M. Kaushik, R. Kukreti, D. Grover, S.K. Brahmachari, and S. Kukreti Hairpin-duplex equilibrium reflected in the A → B transition in an undecamer quasi-palindrome present in the locus control region of the human beta-globin gene cluster Nucleic Acids Res. 31 2003 6904 6915
23. A.A. Khamlichi, E. Pinaud, C. Decourt, C. Chauveau, and M. Cogne The 3′ IgH regulatory region: a complex structure in a search for a function Adv. Immunol. 75 2000 317 345
24. P.C. Kulakosky, M.A. McCarty, S.C. Jernigan, K.E. Risinger, and C.M. Klinge Response element sequence modulates estrogen receptor alpha and beta affinity and activity J. Mol. Endocrinol. 29 2002 137 152
25. L. Madisen, and M. Groudine Identification of a locus control region in the immunoglobulin heavy-chain locus that deregulates c-myc expression in plasmacytoma and Burkitt's lymphoma cells Genes Dev. 8 1994 2212 2226
26. H. Maeda, K. Araki, D. Kitamura, J. Wang, and T. Watanabe Nuclear factors binding to the human immunoglobulin heavy-chain gene enhancer Nucleic Acids Res. 15 1987 2851 2869
27. R.G. Mage, B.A. Newman, N. Harindranath, K.E. Bernstein, R.S. Becker, and K.L. Knight Evolutionary conservation of splice sites in sterile C mu transcripts and of immunoglobulin heavy chain (IgH) enhancer region sequences Mol. Immunol. 26 1989 1007 1010
28. E.E. Max Immunoglobulins: molecular genetics W.E. Paul Fundamental Immunology fifth ed. 2003 Lippincott Williams & Wilkins New York 107 158
29. E.E. Max, M. Mitchell, and F.C. Mills Multiple recombination events near the 3′ boundary of the human IgH locus duplication Mamm. Genome 11 2000 938 940
30. T.J. McConnell, W.S. Talbot, R.A. McIndoe, and E.K. Wakeland The origin of MHC class II gene polymorphism within the genus Mus Nature 332 1988 651 654
31. R. Melfi, F. Palla, P. Di Simone, C. Alessandro, L. Cali, L. Anello, and G. Spinelli Functional characterization of the enhancer blocking element of the sea urchin early histone gene cluster reveals insulator properties and three essential cis-acting sequences J. Mol. Biol. 304 2000 753 763
32. F.C. Mills, J.S. Brooker, and R.D. Camerini-Otero Sequences of human immunoglobulin switch regions: implications for recombination and transcription Nucleic Acids Res. 18 1990 7305 7316
33. F.C. Mills, N. Harindranath, M.a. Mitchell, and E.E. Max Enhancer complexes located downstream of both human immunoglobulin Cα genes J. Exp. Med. 186 1997 845 858
34. M.G. Morgado, E. Jouvin-Marche, C. Gris-Liebe, F. Bonhomme, R. Anand, G.P. Talwar, and P.A. Cazenave Restriction fragment length polymorphism and evolution of the mouse immunoglobulin constant region gamma loci Immunogenetics 38 1993 184 192
35. A.L. Nesset, and D.M. Bader Hole is a novel gene product expressed in the developing heart and brain Mech. Dev. 117 2002 347 350
36. E. Pinaud, C. Aupetit, C. Chauveau, and M. Cogne Identification of a homolog of the C alpha 3′/hs3 enhancer and of an allelic variant of the 3′IgH/hs1 2 enhancer downstream of the human immunoglobulin alpha 1 gene Eur. J. Immunol. 27 1997 2981 2985
37. E. Pinaud, A.A. Khamlichi, C. Le Morvan, M. Drouet, V. Nalesso, M. Le Bert, and M. Cogne Localization of the 3′ IgH locus elements that effect long-distance regulation of class switch recombination Immunity 15 2001 187 199
38. S. Saleque, M. Singh, and B.K. Birshtein IgH expression and class switching in vitro from an allele lacking the 3′ enhancers DNase I-hypersensitive hs3A and hs1,2 J. Immunol. 162 1999 2791 2803
39. S. Saleque, M. Singh, R.D. Little, S.L. Giannini, J.S. Michaelson, and B.K. Birshtein Dyad symmetry within the mouse 3′ IgH regulatory region includes two virtually identical enhancers (C alpha3′E and hs3) J. Immunol. 158 1997 4780 4787
40. S. Schwartz, Z. Zhang, K.A. Frazer, A. Smit, C. Riemer, J. Bouck, R. Gibbs, R. Hardison, and W. Miller PipMaker - a web server for aligning two genomic DNA sequences Genome Res. 10 2000 577 586
41. M.A. Sepulveda, A.V. Emelyanov, and B.K. Birshtein NF-kappaB and Oct-2 synergize to activate the human 3′ Igh hs4 enhancer in B cells J. Immunol. 172 2004 1054 1064
42. C.M. Wade, E.J. Kulbokas 3rd., A.W. Kirby, M.C. Zody, J.C. Mullikin, E.S. Lander, K. Lindblad-Toh, and M.J. Daly The mosaic structure of variation in the laboratory mouse genome Nature 420 2002 574 578
43. J. Zhou, N. Ashouian, M. Delepine, F. Matsuda, C. Chevillard, R. Riblet, C.L. Schildkraut, and B.K. Birshtein The origin of a developmentally regulated Igh replicon is located near the border of regulatory domains for Igh replication and expression Proc. Natl. Acad. Sci. USA 99 2002 13693 13698