Use of chromatin immunoprecipitation (ChIP) to detect transcription factor binding to highly homologous promoters in chromatin isolated from unstimulated and activated primary human B cells

Biological Procedures Online

Volumn 8, Issue 1, 2006, Pages 44-54

  Dryer, Rebecca L ^a   Covey, Lori R ^a  

^a RUTGERS UNIVERSITY   (United States)

Author keywords

B cells; Chromatin immunoprecipitation; Gene expression regulation; Transcription factors

Indexed keywords

CD19 ANTIGEN; CD40 ANTIGEN; CYCLIC AMP RESPONSIVE ELEMENT BINDING PROTEIN; IMMUNOGLOBULIN ENHANCER BINDING PROTEIN; IMMUNOGLOBULIN G; IMMUNOGLOBULIN HEAVY CHAIN; PROTEIN P300; TRANSCRIPTION FACTOR;

AMINO ACID SEQUENCE; ARTICLE; B LYMPHOCYTE ACTIVATION; BLOOD SAMPLING; CELL COUNT; CELL ISOLATION; CELL SELECTION; CHROMATIN; CHROMATIN IMMUNOPRECIPITATION; CONTROLLED STUDY; CROSS HYBRIDIZATION; EXON; FLOW CYTOMETRY; GENE LOCUS; GENE MUTATION; HUMAN; HUMAN CELL; IN VIVO STUDY; INFORMATION PROCESSING; INTRON; PERIPHERAL BLOOD MONONUCLEAR CELL; POLYMERASE CHAIN REACTION; PROMOTER REGION; PROTEIN BINDING; PROTEIN INTERACTION; SEQUENCE HOMOLOGY; SIGNAL TRANSDUCTION;

EID: 33645959504     PISSN: 14809222     EISSN: 14809222     Source Type: Journal    
DOI: 10.1251/bpo117     Document Type: Article

References (30)

1. Kuo MH, Allis CD. In vivo cross-linking and immunoprecipitation for studying dynamic Protein:DNA associations in a chromatin environment. Methods 1999; 19:425-433.
2. Wells J, Farnham PJ. Characterizing transcription factor binding sites using formaldehyde crosslinking and immunoprecipitation. Methods 2002; 26:48-56.
3. Stavnezer J. Molecular processes that regulate class switching. Curr Top Microbiol Immunol 2000; 245:127-168.
4. Stavnezer J, Amemiya CT. Evolution of isotype switching. Semin Immunol 2004; 16:257-275.
5. Gaff C, Gerondakis S. RNA splicing generates alternate forms of germline immunoglobulin alpha heavy chain transcripts. Int Immunol 1990; 2:1143-1148.
6. Gerondakis S. Structure and expression of murine germ-line immunoglobulin epsilon heavy chain transcripts induced by interleukin 4. Proc Natl Acad Sci USA 1990; 87:1581-1585.
7. Lebman DA, Nomura DY, Coffman RL, Lee FD. Molecular characterization of germ-line immunoglobulin A transcripts produced during transforming growth factor type beta-induced isotype switching. Proc Natl Acad Sci USA 1990; 87:3962-3966.
8. Lutzker S, Rothman P, Pollock R, Coffman R, Alt FW. Mitogen and IL-4 regulated expression of germline Ig γ2b transcripts: evidence for directed heavy chain class switching. Cell 1988; 53:177-184.
9. Radcliffe G, Lin YC, Julius M, Marcu KB, Stavnezer J. Structure of germ line immunoglobulin alpha heavy-chain RNA and its location on polysomes. Mol Cell Biol 1990; 10:382-386.
10. Rothman P, Chen YY, Lutzker S, Li SC, Stewart V, Coffman R, Alt FW. Structure and expression of germline immunoglobuin heavy-chain epsilon transcripts: interleukin-4 plus lipopolysaccharide-directed switching to C epsilon. Mol Cell Biol 1990; 10:1672-1679.
11. Rothman P, Lutzker S, Gorham B, Stewart V, Coffman R, Alt FW. Structure and expression of germline immunoglobulin γ3 heavy chain gene transcripts: implications for mitogen and lymphokine directed class switching. Int Immunol 1990; 2:621-627.
12. Ford GS, Yin CH, Barnhart B, Sztam K, Covey LR. CD40 ligand exerts differential effects on the expression of Iγ transcripts in subdones of an IgM+ human B cell lymphoma line. J Immunol 1998; 160:595-605.
13. Bhushan A, Covey LR. CREB/ATF proteins enhance the basal and CD154- and IL-4-induced transcriptional activity of the human Igamma1 proximal promoter. Eur J Immunol 2001; 31:653-664.
14. Dryer RL, Covey LR. A Novel NF-{kappa}B-Regulated Site within the Human I{gamma}1 Promoter Requires p300 for Optimal Transcriptional Activity. J Immunol 2005; 175:4499-4507.
15. Lin S-C, Stavnezer J. Activation of NF-κB/Rel by CD40 engagement induces the mouse germ line immunoglobulin Cγ1 promoter. Mol Cell Biol 1996; 16:4591-4603.
16. Lin S-C, Wortis HH, Stavnezer J. The ability of CD40L, but not lipopolysaccharide, to initiate immunoglobulin switching to immunoglobulin G1 is explained by differential induction of NF-κB/ Rel Proteins. Mol Cell Biol 1998; 18:5523-5532.
17. Snapper CM, Rosas FR, Zelazowski P, Moorman MA, Kehry MR, Bravo R, Weih F. B cells lacking relB are decfective in proliferative responses, but undergo normal B cell maturation to Ig secretion and Ig class switching. J Exp Med 1996; 184:1537-1541.
18. Jumper MD, Nishioka U, Davis LS, Lipsky PE, Meek K. Regulation of human B cell function by recombinant CD40 ligand and other TNF-related ligands. J Immunol 1995; 155:2369-2378.
19. Jumper MD, Splawski JB, Lipsky PE, Meek K. Ligation of CD40 induces sterile transcripts of multiple Ig H chain isotypes in human B cells. J Immunol 1994; 152:438-445.
20. Fujieda S, Zhang K, Saxon A. IL-4 plus CD40 monoclonal antibody induces human B cells γ subclass-specific isotype switch: Switching to γ1, γ3, and γ4, but not γ2. J Immunol 1995; 155:2318-2328.
21. Dignam J, Lebovitz RM, Roeder RD. Accurate transcription initiation by RNA polymerase II in a soluble extract from isolated mammalian nuclei. Nucl Acids Res 1983; 11:1475-1489.
22. Orlando V, Strutt H, Paro R. Analysis of chromatin structure by in vivo formaldehyde cross-linking. Methods 1997; 11:205-214.
23. Parekh BS, Maniatis T. Virus infection leads to localized hyperacetylation of histones H3 and H4 at the IFN-beta promoter. Mol Cell 1999; 3:125-129.
24. Orlando V. Mapping chromosomal proteins in vivo by formaldehyde-crosslinked-chromatin immunoprecipitation. Trends Biochem Sci 2000; 25:99-104.
25. Weinmann AS. Novel ChIP-based strategies to uncover transcription factor target genes in the immune system. Nat Rev Immunol 2004; 4:381-386.
26. Schaffer A, Cerutti A, Shah S, Zan H, Casali P. The evolutionarily conserved sequence upstream of the human Ig heavy chain S gamma 3 region is an inducible promoter: synergistic activation by CD40 ligand and IL-4 via cooperative NF-kappa B and STAT-6 binding sites. J Immunol 1999; 162:5327-5336.
27. Warren WD, Roberts KL, Linehan LA, Berton MT. Regulation of the germline immunoglobulin Cgamma1 promoter by CD40 ligand and IL-4: dual role for tandem NF-kappaB binding sites. Mol Immunol 1999; 36:31-44.
28. Rust S, Funke H, Assmann G. Mutagenically separated PCR (MS-PCR): a highly specific one step procedure for easy mutation detection. Nucl Acids Res 1993; 21:3623-3629.
29. Schluter B, Erren M, Schotte H, Junker R, Rust S, Assmann, G. The mutagenically separated polymerase chain reaction is a rapid and reliable method for genotyping of the tumour necrosis factor-alpha promoter polymorphism (-308 G/A). Clin Chim Acta 2002; 320:135-138.
30. Sideras P, Mizuta TR, Kanamori H, Suzuki N, Okamoto M, Kuze K, Ohno H, Doi S, Fukuhara S, Hassan MS, et al. Production of sterile transcripts of C gamma genes in an IgM-producing human neoplastic B cell line that switches to IgG-producing cells. Int Immunol 1989; 1:631-642.