BioVyon Protein A, an alternative solid-phase affinity matrix for chromatin immunoprecipitation

Analytical Biochemistry

Volumn 412, Issue 2, 2011, Pages 183-188

  Chernukhin, Igor ^a   Kang, Sung Yun ^a   Brown, Sam ^b   Gretton, Svetlana ^a   Mendez Catala, Claudia Fabiola ^a   Cowieson, Dave ^b   Klenova, Elena ^a  

^a UNIVERSITY OF ESSEX   (United Kingdom)

^b Porvair Technology   (United Kingdom)

Author keywords

BioVyon Protein A; CCCTC binding factor (CTCF); Chromatin immunoprecipitation (ChIP); CTCF binding (target) sites (CTSs); Dynabeads Protein A; Protein A Sepharose; Quantitative real time polymerase chain reaction (Q PCR); RNA polymerase II; TATA box

Indexed keywords

BINDING SITES; CHROMOSOMES; DNA; PROTEINS;

CCCTC BINDING FACTORS; CHROMATIN IMMUNOPRECIPITATION; CTCF BINDING (TARGET) SITES (CTSS); PROTEIN A; QUANTITATIVE REAL-TIME POLYMERASE CHAIN REACTION; RNA POLYMERASE II; TATA BOX;

POLYMERASE CHAIN REACTION;

ANTIBODY; B LYMPHOCYTE INDUCED MATURATION PROTEIN 1; BETA GLOBIN; BIOVYON PROTEIN A; DNA; DYNABEAD PROTEIN A; IMMUNOGLOBULIN G; MATRIX PROTEIN; POLO LIKE KINASE; POLYETHYLENE; PROTEIN; PROTEIN A; PROTEIN A SEPHAROSE; PROTEIN KINASE PIM 1; RNA H19; RNA POLYMERASE II; TRANSCRIPTION FACTOR CTCF; UNCLASSIFIED DRUG;

ANIMAL CELL; ARTICLE; CHROMATIN; CHROMATIN IMMUNOPRECIPITATION; CONTROLLED STUDY; DNA BINDING; DNA DETERMINATION; MOUSE; NONHUMAN; ONCOGENE C MYB; PRIORITY JOURNAL; PROTEIN ANALYSIS; PROTEIN DNA BINDING; REAL TIME POLYMERASE CHAIN REACTION;

EID: 79953192129     PISSN: 00032697     EISSN: 10960309     Source Type: Journal    
DOI: 10.1016/j.ab.2011.01.036     Document Type: Article

References (31)

1. O. Aparicio, J.V. Geisberg, and K. Struhl Chromatin immunoprecipitation for determining the association of proteins with specific genomic sequences in vivo Curr. Protoc. Cell Biol. 2004 Unit 17.7
2. C.E. Massie, and I.G. Mills ChIPping away at gene regulation EMBO Rep. 9 2008 337 343
3. P. Dasgupta, and S.P. Chellappan Chromatin immunoprecipitation assays: molecular analysis of chromatin modification and gene regulation Methods Mol. Biol. 383 2007 135 152
4. P. Collas, and J.A. Dahl Chop it, ChIP it, check it: The current status of chromatin immunoprecipitation Front. Biosci. 13 2008 929 943 (Pubitemid 351594738)
5. M.H. Kuo, and C.D. Allis In vivo cross-linking and immunoprecipitation for studying dynamic protein:DNA associations in a chromatin environment Methods 19 1999 425 433 (Pubitemid 30028602)
6. D.S. Hage Affinity chromatography: a review of clinical applications Clin. Chem. 45 1999 593 615 (Pubitemid 29220320)
7. J. Wu, L.T. Smith, C. Plass, and T.H. Huang ChIP-chip comes of age for genome-wide functional analysis Cancer Res. 66 2006 6899 6902 (Pubitemid 44197662)
8. M.L. Bulyk DNA microarray technologies for measuring protein-DNA interactions Curr. Opin. Biotechnol. 17 2006 422 430 (Pubitemid 44177668)
9. D. Schmidt, M.D. Wilson, C. Spyrou, G.D. Brown, J. Hadfield, and D.T. Odom ChIP-seq: using high-throughput sequencing to discover protein-DNA interactions Methods 48 2009 240 248
10. I. Chernukhin, S. Shamsuddin, S.Y. Kang, R. Bergstrom, Y.W. Kwon, W. Yu, J. Whitehead, R. Mukhopadhyay, F. Docquier, D. Farrar, I. Morrison, M. Vigneron, S.Y. Wu, C.M. Chiang, D. Loukinov, V. Lobanenkov, R. Ohlsson, and E. Klenova CTCF interacts with and recruits the largest subunit of RNA polymerase II to CTCF target sites genome-wide Mol. Cell. Biol. 27 2007 1631 1648
11. S. Cuddapah, R. Jothi, D.E. Schones, T.Y. Roh, K. Cui, and K. Zhao Global analysis of the insulator binding protein CTCF in chromatin barrier regions reveals demarcation of active and repressive domains Genome Res. 19 2009 24 32
12. V. Parelho, S. Hadjur, M. Spivakov, M. Leleu, S. Sauer, H.C. Gregson, A. Jarmuz, C. Canzonetta, Z. Webster, T. Nesterova, B.S. Cobb, K. Yokomori, N. Dillon, L. Aragon, A.G. Fisher, and M. Merkenschlager Cohesins functionally associate with CTCF on mammalian chromosome arms Cell 132 2008 422 433
13. S.R. Frank, M. Schroeder, P. Fernandez, S. Taubert, and B. Amati Binding of c-Myc to chromatin mediates mitogen-induced acetylation of histone H4 and gene activation Genes Dev. 15 2001 2069 2082 (Pubitemid 32762051)
14. Diagenode, Rapid Chromatin Immunoprecipitation Kit instruction manual, Diagenode, Liege, Belgium, 2011, p. 19.
15. J. den Hollander, S. Rimpi, J.R. Doherty, M. Rudelius, A. Buck, A. Hoellein, M. Kremer, N. Graf, M. Scheerer, M.A. Hall, A. Goga, N. von Bubnoff, J. Duyster, C. Peschel, J.L. Cleveland, J.A. Nilsson, and U. Keller Aurora kinases A and B are up-regulated by Myc and are essential for maintenance of the malignant state Blood 116 2010 1498 1505
16. D. Toniolo, M. Filippi, R. Dono, T. Lettieri, and G. Martini The CpG island in the 5′ region of the G6PD gene of man and mouse Gene 102 1991 197 203
17. R. Ohlsson, R. Renkawitz, and V. Lobanenkov CTCF is a uniquely versatile transcription regulator linked to epigenetics and disease Trends Genet. 17 2001 520 527 (Pubitemid 32763050)
18. E.M. Klenova, H.C. Morse 3rd, R. Ohlsson, and V.V. Lobanenkov The novel BORIS + CTCF gene family is uniquely involved in the epigenetics of normal biology and cancer Semin. Cancer Biol. 12 2002 399 414
19. G.N. Filippova Genetics and epigenetics of the multifunctional protein CTCF Curr. Top. Dev. Biol. 80 2008 337 360
20. T.H. Kim, Z.K. Abdullaev, A.D. Smith, K.A. Ching, D.I. Loukinov, R.D. Green, M.Q. Zhang, V.V. Lobanenkov, and B. Ren Analysis of the vertebrate insulator protein CTCF-binding sites in the human genome Cell 128 2007 1231 1245 (Pubitemid 46427876)
21. M. Lutz, L.J. Burke, P. LeFevre, F.A. Myers, A.W. Thorne, C. Crane-Robinson, C. Bonifer, G.N. Filippova, V. Lobanenkov, and R. Renkawitz Thyroid hormone-regulated enhancer blocking: cooperation of CTCF and thyroid hormone receptor EMBO J. 22 2003 1579 1587 (Pubitemid 36417406)
22. G.N. Filippova, C.P. Thienes, B.H. Penn, D.H. Cho, Y.J. Hu, J.M. Moore, T.R. Klesert, V.V. Lobanenkov, and S.J. Tapscott CTCF-binding sites flank CTG/CAG repeats and form a methylation-sensitive insulator at the DM1 locus Nat. Genet. 28 2001 335 343 (Pubitemid 32702422)
23. C.M. Farrell, A.G. West, and G. Felsenfeld Conserved CTCF insulator elements flank the mouse and human β-globin loci Mol. Cell. Biol. 22 2002 3820 3831 (Pubitemid 34525223)
24. A.C. Bell, and G. Felsenfeld Methylation of a CTCF-dependent boundary controls imprinted expression of the Igf2 gene Nature 405 2000 482 485 (Pubitemid 30367427)
25. D. Takai, F.A. Gonzales, Y.C. Tsai, M.J. Thayer, and P.A. Jones Large scale mapping of methylcytosines in CTCF-binding sites in the human H19 promoter and aberrant hypomethylation in human bladder cancer Hum. Mol. Genet. 10 2001 2619 2626 (Pubitemid 33133402)
26. A.J. Wilson, D.S. Byun, S. Nasser, L.B. Murray, K. Ayyanar, D. Arango, M. Figueroa, A. Melnick, G.D. Kao, L.H. Augenlicht, and J.M. Mariadason HDAC4 promotes growth of colon cancer cells via repression of p21 Mol. Biol. Cell 19 2008 4062 4075
27. J.W. Kim, P. Gao, Y.C. Liu, G.L. Semenza, and C.V. Dang Hypoxia-inducible factor 1 and dysregulated c-Myc cooperatively induce vascular endothelial growth factor and metabolic switches hexokinase 2 and pyruvate dehydrogenase kinase 1 Mol. Cell. Biol. 27 2007 7381 7393 (Pubitemid 350033646)
28. J.A. Dahl, and P. Collas MicroChIP: chromatin immunoprecipitation for small cell numbers Methods Mol. Biol. 567 2009 59 74
29. J.A. Dahl, A.H. Reiner, and P. Collas Fast genomic muChIP-chip from 1000 cells Genome Biol. 10 2009 R13
30. S. Flanagin, J.D. Nelson, D.G. Castner, O. Denisenko, and K. Bomsztyk Microplate-based chromatin immunoprecipitation method matrix ChIP: a platform to study signaling of complex genomic events Nucleic Acids Res. 36 2008 e17
31. A.R. Wu, J.B. Hiatt, R. Lu, J.L. Attema, N.A. Lobo, I.L. Weissman, M.F. Clarke, and S.R. Quake Automated microfluidic chromatin immunoprecipitation from 2000 cells Lab Chip 9 2009 1365 1370