Microplate-based chromatin immunoprecipitation method, Matrix ChIP: A platform to study signaling of complex genomic events

Nucleic Acids Research

Volumn 36, Issue 3, 2008, Pages

  Flanagin, Steve ^a   Nelson, Joel D ^b   Castner, David G ^c   Denisenko, Oleg ^a   Bomsztyk, Karol ^a,b  

^a UNIVERSITY OF WASHINGTON   (United States)

^b UNIVERSITY OF WASHINGTON   (United States)

^c University of Washington   (United States)

Author keywords

[No Author keywords available]

Indexed keywords

DNA; PHOSPHOTRANSFERASE; ANTIBODY; EARLY GROWTH RESPONSE FACTOR 1; PROTEIN KINASE;

ANIMAL CELL; ARTICLE; AUTOMATION; CALCULATION; CHROMATIN IMMUNOPRECIPITATION; CONTROLLED STUDY; DNA PURIFICATION; GENE EXPRESSION; GENETIC TRANSCRIPTION; GENOME ANALYSIS; IN VIVO STUDY; MESANGIUM CELL; MICROPLATE BASED CHROMATIN IMMUNOPRECIPITATION; NONHUMAN; PRIORITY JOURNAL; RAT; REAL TIME POLYMERASE CHAIN REACTION; SENSITIVITY ANALYSIS; ANIMAL; CELL CULTURE; CHEMISTRY; CHROMATIN; GENETICS; ISOLATION AND PURIFICATION; KINETICS; METABOLISM; METHODOLOGY; SIGNAL TRANSDUCTION; VALIDATION STUDY;

ANIMALS; ANTIBODIES; CELLS, CULTURED; CHROMATIN; CHROMATIN IMMUNOPRECIPITATION; DNA; EARLY GROWTH RESPONSE PROTEIN 1; KINETICS; PROTEIN KINASES; RATS; SIGNAL TRANSDUCTION; TRANSCRIPTION, GENETIC;

EID: 39449114225     PISSN: 03051048     EISSN: 13624962     Source Type: Journal    
DOI: 10.1093/nar/gkn001     Document Type: Article

References (70)

1. Felsenfeld,G. and Groudine,M. (2003) Controlling the double helix. Nature, 421, 448-453.
2. Sims,R.J. III, Mandal,S.S. and Reinberg,D. (2004) Recent highlights of RNA-polymerase-II-mediated transcription. Curr. Opin. Cell Biol., 16, 263-271.
3. Thiriet,C. and Hayes,J.J. (2005) Chromatin in need of a fix: phosphorylation of H2AX connects chromatin to DNA repair. Mol. Cell 18, 617-622.
4. Kuo,M.H. and Allis,C.D. (1999) In vivo cross-linking and immunoprecipitation for studying dynamic Protein:DNA associations in a chromatin environment. Methods, 19, 425-433.
5. Impey,S., McCorkle,S.R., Cha-Molstad,H., Dwyer,J.M., Yochum,G.S., Boss,J.M., McWeeney,S., Dunn,J.J., Mandel,G. and Goodman,R.H. (2004) Defining the CREB regulon: A genome-wide analysis of transcription factor regulatory regions. Cell, 119, 1041-1054.
6. Dundr,M., Hoffmann-Rohrer,U., Hu,Q., Grummt,I., Rothblum,L.I., Phair,R.D. and Misteli,T. (2002) A kinetic framework for a mammalian RNA polymerage in vivo. Science, 298, 1623-1626.
7. Cheutin,T., McNairn,A.J., Jenuwein,T., Gilbert,D.M., Singh,P.B. and Misteli,T. (2003) Maintenance of stable heterochromatin domains by dynamic HP1 binding. Science, 299, 721-725.
8. Spector,D.L. (2003) The dynamics of chromosome organization and gene regulation. Annu. Rev. Biochem., 72, 573-608.
9. Lorincz,M.C. and Schubeler,D. (2007) RNA polymerase II: Just stopping by. Cell, 130, 16-18.
10. Bannister,A.J. and Kouzarides,T. (2005) Reversing histone methylation. Nature, 436, 1103-1106.
11. Belotserkovskaya,R., Oh,S., Bondarenko,V.A., Orphanides,G., Studitsky,V.M. and Reinberg,D. (2003) FACT facilitates transcription-dependent nucleosome alteration. Science, 301, 1090-1093.
12. Bernstein,E. and Allis,C.D. (2005) RNA meets chromatin. Genes Dev. 19, 1635-1655.
13. Festenstein,R., Pagakis,S.N., Hiragami,K., Lyon,D., Verreault,A., Sekkali,B. and Kioussis,D. (2003) Modulation of heterochromatin protein 1 dynamics in primary Mammalian cells. Science, 299, 719-721.
14. Koch,C.M., Andrews,R.M., Flicek,P., Dillon,S.C., Karaoz,U., Clelland,G.K., Wilcox,S., Bare,D.M., Fowler,J.C:, Couttet,P. et al. (2007) The landscape of histone modifications across 1% of the human genome in five human cell lines. Genome Res., 17, 691-707.
15. Kouzarides,T. (2007) Chromatin modifications and their function. Cell 128, 693-705.
16. Jones,P.A. and Baylin,S.B. (2007) The epigenomics of cancer. Cell, 128, 683-692.
17. Guenther,M.G., Levine,S.S., Boyer,L.A., Jaenisch,R. and Young,R.A. (2007) A chromatin landmark and transcription initiation at most promoters in human cells. Cell, 130, 77-88.
18. Bernstein,B.E., Meissner,A. and Lander,E.S. (2007) The mammalian epigenome. Cell, 128, 669-681.
19. Berger,S.L. (2007) The complex language of chromatin regulation during transcription. Nature, 447, 407-412.
20. Nelson,J.D., Denisenko,O., Sova,P. and Bomsztyk,K. (2006) Fast chromatin immunoprecipitation assay. Nucleic Acids Res., 34, e2.
21. L'Honore,A., Rana,V., Arsic,N., Franckhauser,C, Lamb,N.J. and Fernandez,A. (2007) Identification of a new hybrid serum response factor and myocyte enhancer factor 2-binding element in MyoD enhancer required for MyoD expression during myogenesis. Mol. Biol. Cell, 18, 1992-2001.
22. Prieto,J.L. and McStay,B. (2007) Recruitment of factors linking transcription and processing of pre-rRNA to NOR chromatin is UBF-dependent and occurs independent of transcription in human cells. Genes Dev., 21, 2041-2054.
23. Montgomery,R.L., Davis,C.A., Potthoff,M.J, Haberland,M., Fielitz,J., Qi,X., Hill,J.A., Richardson,J.A. and Olson,E.N. (2007) Histone deacetylases 1 and 2 redundantly regulate cardiac morphogenesis, growth, and contractility. Genes Dev., 21, 1790-1802.
24. Seger,R. and Krebs,E.G. (1995) The MAPK signaling cascade. Faseb J. 9, 726-735.
25. Gschwendt,M. (1999) Protein kinase Cd. Eur. J. Biochem., 259 555-564.
26. Resh,M.D. (1998) Fyn, a Src family tyrosine kinase. Int. J. Biochem. Cell Biol., 30, 1159-1162.
27. Ostrowski,J., Kawata,Y., Schullery,D.S., Denisenko,O.N. and Bomsztyk,K. (2003) Transient recruitment of the hnRNP K protein to inducibly transcribed gene loci. Nucleic Acids Res., 31, 3954-3962.
28. Chow,C.W. and Davis,R.J. (2006) Proteins kinases: Chromatin-associated enzymes? Cell, 127, 887-890.
29. Vicent,G.P., Ballare,C., Nacht,A.S., Clausell,J., Subtil-Rodriguez, A., Quiles,I., Jordan,A. and Beato,M. (2006) Induction of progesterone target genes requires activation of Erk and Msk kinases and phosphorylation of histone H3. Mol. Cell, 24, 367-381.
30. Simone,C., Forcales,S.V., Hill,D.A., Imbalzano,A.N., Latella,L. and Puri,P.L. (2004) p38 pathway targets SWI-SNF chromatin-remodeling complex to muscle-specific loci. Nat. Genet., 36, 738-743.
31. Edmunds,J.W. and Mahadevan,L.C. (2006) Cell signaling. Protein kinases seek close encounters with active genes. Science, 313, 449-451.
32. Pokholok,D.K., Zeitlinger,J., Hannett,N.M., Reynolds,D.B. and Young,R.A. (2006) Activated signal transduction kinases frequently occupy target genes. Science, 313, 533-536.
33. Suzuki,H., O'Neill,B.C., Suzuki,Y., Denisenko,O.N. and Bomsztyk,K. (1996) Activation of a nuclear DNA-binding protein recognized by a transcriptional element, bcn-1, from the laminin B2 chain gene promoter. J. Biol. Chem., 271, 18981-18988.
34. Nelson,J.D., Denisenko,O. and Bomsztyk,K. (2006) Protocol for the fast chromatin immunoprecipitation (ChIP) method. Nat. Protoc., 1 179-185.
35. Chen,R., Weng,L., Sizto,N.C., Osorio,B., Hsu,C.J., Rodgers,R. and Litman,D.J. (1984) Ultrasound-accelerated immunoassay, as exemplified by enzyme immunoassay of choriogonadotropin. Clin. Chem., 30, 1446-1451.
36. Mendoza,L.G., McQuary,P., Mongan,A., Gangadharan,R., Brignac,S. and Eggers,M. (1999) High-throughput microarray-based enzyme-linked immunosorbent assay (ELISA). Biotechniques, 27, 778-788.
37. Desai,S. and Dworecki,B.R. (2004) Coated microwell plate-based affinity purification of antigens. Anal. Biochem., 328, 162-165.
38. Peluso,P., Wilson,D.S., Do,D., Tran,H., Venkatasubbaiah,M., Quincy,D., Heidecker,B., Poindexter,K., Tolani,N., Phelan,M. et al. (2003) Optimizing antibody immobilization strategies for the construction of protein microarrays. Anal. Biochem., 312, 113-124.
39. Briand,E., Salmain,M., Compere,C. and Pradier,C.M. (2006) Immobilization of Protein A on SAMs for the elaboration of immunosensors. Colloids Surf B Biointerfaces, 53, 215-224.
40. Dai,J., Bao,Z., Sun,L., Hong,S.U., Baker,G.L. and Bruening,M.L. (2006) High-capacity binding of proteins by poly(acrylic acid) brushes and their derivatives. Langmuir, 22, 4274-4281.
41. Hollmann,O., Gutberlet,T. and Czeslik,C. (2007) Structure and protein binding capacity of a planar PAA brush. Langmuir, 23, 1347-1353.
42. Tanaka,G, Funabashi,H., Mie,M. and Kobatake,E. (2006) Fabrication of an antibody microwell array with self-adhering antibody binding protein. Anal. Biochem., 350, 298-303.
43. Danczyk,R., Krieder,B., North,A., Webster,T., HogenEsch,H. and Rundell,A. (2003) Comparison of antibody functionality using different immobilization methods. Biotechnol. Bioeng., 84, 215-223.
44. Anderson,G.P., Jacoby,M.A., Ligler,F.S. and King,K.D. (1997) Effectiveness of protein A for antibody immobilization for a fiber optic biosensor. Biosens. Bioelectron., 12, 329-336.
45. Struhl,K. (2007) Transcriptional noise and the fidelity of initiation by RNA polymerase II. Nat. Struct. Mol. Biol., 14, 103-105.
46. Bomsztyk,K., Denisenko,G. and Ostrowski.J. (2004) hnRNP K: One protein multiple processes. Bioessays, 26, 629-638.
47. Chang,L. and Karin,M. (2001) Mammalian MAP kinase signalling cascades. Nature, 410, 37-40.
48. Denis,V. and Cyert,M.S. (2005) Molecular analysis reveals localization of Saccharomyces cerevisiae protein kinase C to sites of polarized growth and Pkclp targeting to the nucleus and mitotic spindle. Eukaryot. Cell, 4, 36-45.
49. Timms,J.F., Swanson,K.D., Marie-Cardine,A., Raab,M., Rudd,C.E., Schraven,B. and Neel,B.G. (1999) SHPS-1 is a scaffold for assembling distinct adhesion-regulated multi-protein complexes in macrophages. Curr. Biol., 9, 927-930.
50. Murphy,L.O. and Blenis,J. (2006) MAPK signal specificity: The right place at the right time. Trends Biochem. Sci., 31, 268-275.
51. Rongish,B.J. and Kinsey,W.H. (2000) Transient nuclear localization of Fyn kinase during development in zebrafish. Anat. Rec., 260, 115-123.
52. Wong,W. and Scott,J.D. (2004) AKAP signalling complexes: Focal points in space and time. Nat. Rev. Mol. Cell Biol., 5, 959-970.
53. Heintzman,N.D., Stuart,R.K., Hon,G., Fu,Y., Ching,C.W., Hawkins,R.D., Barrera,L.O., Van Calcar,S., Qu,C., Ching,K.A. et al. (2007) Distinct and predictive chromatin signatures of transcriptional promoters and enhancers in the human genome. Nat. Genet., 39 311-318.
54. Barski,A., Cuddapah,S., Cui,K., Roh,T.Y., Schones,D.E., Wang,Z., Wei,G., Chepelev,I. and Zhao.K. (2007) High-resolution profiling of histone methylations in the human genome. Cell, 129, 823-837.
55. Vakoc,C.R., Mandat,S.A., Olenchock,B.A. and Blobel,G.A. (2005) Histone H3 lysine 9 methylation and HP1 gamma are associated with transcription elongation through mammalian chromatin. Mol. Cell, 19, 381-391.
56. Ostrowski,J., Schullery,D.S., Denisenko,O.N., Higaki,Y., Watts,J., Aebersold,R., Stempka,L., Gschwendt,M. and Bomsztyk,K. (2000) Role of tyrosine phosphorylation in the regulation of the interaction of heterogenous nuclear ribonucleoprotein K protein with its protein and RNA partners. J. Biol. Chem., 275, 3619-3628.
57. Adolph,D., Flach,N., Mueller,K., Ostareck,D.H. and Ostareck-Lederer,A. (2006) Deciphering the crosstalk between hnRNP K and c-Src: The c-Src activation domain in hnRNP K is distinct from a second interaction site. Mol. Cell Biol., 27, 1758-1770.
58. Grewal,S.I. and Jia,S. (2007) Heterochromatin revisited. Nat. Rev. Genet., 8, 35-46.
59. Clayton,A.L., Hazzalin,C.A. and Mahadevan,L.C. (2006) Enhanced histone acetylation and transcription: A dynamic perspective. Mol. Cell, 23, 289-296.
60. Miao,F. and Natarajan,R. (2005) Mapping global histone methylation patterns in the coding regions of human genes. Mol. Cell Biol., 25, 4650-4661.
61. Morillon,A., Karabetsou,N., Nair,A. and Mellor,J. (2005) Dynamic lysine methylation on histone H3 defines the regulatory phase of gene transcription. Mol. Cell, 18, 723-734.
62. Santos-Rosa,H., Schneider,R., Bannister,A.J., Sherriff,J., Bernstein,B.E., Emre,N.C., Schreiber,S.L., Mellor,J. and Kouzarides,T. (2002) Active genes are tri-methylated at K4 of histone H3. Nature 419, 407-411.
63. Schwabish,M.A. and Struhl,K. (2004) Evidence for eviction and rapid deposition of histones upon transcriptional elongation by RNA polymerase II. Mol. Cell Biol., 24, 10111-10117.
64. Shilatifard,A. (2004) Transcriptional elongation control by RNA polymerase II: A new frontier. Biochim. Biophys. Acta, 1677, 79-86.
65. Cao,R., Wang,L., Wang,H., Xia,L., Erdjument-Bromage,H., Tempst,P., Jones,R.S. and Zhang,Y. (2002) Role of histone H3 lysine 27 methylation in Polycomb-group silencing. Science, 298, 1039-1043.
66. Plath,K., Fang,J., Mlynarczyk-Evans,S.K., Cao,R., Worringer,K.A., Wang,H., de la Cruz,C.C., Otte,A.P., Panning,B. and Zhang,Y. (2003) Role of histone H3 lysine 27 methylation in X inactivation. Science, 300, 131-135.
67. Wu,S.Q., Minami,T., Donovan,D.J: And Aird,W.C. (2002) The proximal serum response element in the Egr-1 promoter mediates response to thrombin in primary human endothelial cells. Blood, 100, 4454-4461.
68. Selvaraj,A. and Prywes,R. (2004) Expression profiling of serum inducible genes identifies a subset of SRF target genes that are MKL dependent. BMC Mol. Biol., 5, 13.
69. Cooper,S.J., Trinklein,N.D., Nguyen,L. and Myers,R.M. (2007) Serum response factor binding sites differ in three human cell types. Genome Res, 17, 136-144.
70. Li,B., Carey,M. and Workman,J.L. (2007) The role of chromatin during transcription. Cell, 128, 707-719.