publication . Article . 2008

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

Flanagin, Steve; Nelson, Joel D.; Castner, David G.; Denisenko, Oleg; Bomsztyk, Karol;
Open Access
  • Published: 18 Jan 2008 Journal: Nucleic Acids Research, volume 36, page e17 (issn: 0305-1048, eissn: 1362-4962, Copyright policy)
  • Publisher: Oxford University Press (OUP)
Abstract
The chromatin immunoprecipitation (ChIP) assay is a major tool in the study of genomic processes in vivo. This and other methods are revealing that control of gene expression, cell division and DNA repair involves multiple proteins and great number of their modifications. ChIP assay is traditionally done in test tubes limiting the ability to study signaling of the complex genomic events. To increase the throughput and to simplify the assay we have developed a microplate-based ChIP (Matrix ChIP) method, where all steps from immunoprecipitation to DNA purification are done in microplate wells without sample transfers. This platform has several important advantages...
Subjects
free text keywords: Genetics, Chromatin immunoprecipitation, Chip, Molecular biology, DNA, chemistry.chemical_compound, chemistry, Chromatin, ChIP-sequencing, DNA repair, Immunoprecipitation, DNA extraction, Biology, Methods Online
Related Organizations
Funded by
NIH| Nanoscale Investigation of Protein-Surface Interactions
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5R01GM074511-03
  • Funding stream: NATIONAL INSTITUTE OF GENERAL MEDICAL SCIENCES
,
NIH| LAMININ GENE EXPRESSION IN GLOMERULAR CELLS
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5R37DK045978-16
  • Funding stream: NATIONAL INSTITUTE OF DIABETES AND DIGESTIVE AND KIDNEY DISEASES
,
NIH| Surface Analysis Facility for Biomedical Problems
Project
  • Funder: National Institutes of Health (NIH)
  • Project Code: 5P41EB002027-31
  • Funding stream: NATIONAL INSTITUTE OF BIOMEDICAL IMAGING AND BIOENGINEERING
70 references, page 1 of 5

Felsenfeld, G, Groudine, M. Controlling the double helix. Nature. 2003; 421: 448-453 [OpenAIRE] [PubMed]

Sims, RJ, Mandal, SS, Reinberg, D. Recent highlights of RNA-polymerase-II-mediated transcription. Curr. Opin. Cell Biol. 2004; 16: 263-271 [OpenAIRE] [PubMed]

Thiriet, C, Hayes, JJ. Chromatin in need of a fix: phosphorylation of H2AX connects chromatin to DNA repair. Mol. Cell. 2005; 18: 617-622 [OpenAIRE] [PubMed]

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 [OpenAIRE] [PubMed]

Impey, S, McCorkle, SR, Cha-Molstad, H, Dwyer, JM, Yochum, GS, Boss, JM, McWeeney, S, Dunn, JJ, Mandel, G, Goodman, RH. Defining the CREB regulon: a genome-wide analysis of transcription factor regulatory regions. Cell. 2004; 119: 1041-1054 [OpenAIRE] [PubMed]

Dundr, M, Hoffmann-Rohrer, U, Hu, Q, Grummt, I, Rothblum, LI, Phair, RD, Misteli, T. A kinetic framework for a mammalian RNA polymerase in vivo. Science. 2002; 298: 1623-1626 [OpenAIRE] [PubMed]

Cheutin, T, McNairn, AJ, Jenuwein, T, Gilbert, DM, Singh, PB, Misteli, T. Maintenance of stable heterochromatin domains by dynamic HP1 binding. Science. 2003; 299: 721-725 [OpenAIRE] [PubMed]

Spector, DL. The dynamics of chromosome organization and gene regulation. Annu. Rev. Biochem. 2003; 72: 573-608 [PubMed]

Lorincz, MC, Schubeler, D. RNA polymerase II: just stopping by. Cell. 2007; 130: 16-18 [OpenAIRE] [PubMed]

Bannister, AJ, Kouzarides, T. Reversing histone methylation. Nature. 2005; 436: 1103-1106 [OpenAIRE] [PubMed]

Belotserkovskaya, R, Oh, S, Bondarenko, VA, Orphanides, G, Studitsky, VM, Reinberg, D. FACT facilitates transcription-dependent nucleosome alteration. Science. 2003; 301: 1090-1093 [OpenAIRE] [PubMed]

Bernstein, E, Allis, CD. RNA meets chromatin. Genes Dev. 2005; 19: 1635-1655 [PubMed]

Festenstein, R, Pagakis, SN, Hiragami, K, Lyon, D, Verreault, A, Sekkali, B, Kioussis, D. Modulation of heterochromatin protein 1 dynamics in primary Mammalian cells. Science. 2003; 299: 719-721 [PubMed]

Koch, CM, Andrews, RM, Flicek, P, Dillon, SC, Karaoz, U, Clelland, GK, Wilcox, S, Beare, DM, Fowler, JC, Couttet, P. The landscape of histone modifications across 1% of the human genome in five human cell lines. Genome Res. 2007; 17: 691-707 [OpenAIRE] [PubMed]

Kouzarides, T. Chromatin modifications and their function. Cell. 2007; 128: 693-705 [OpenAIRE] [PubMed]

70 references, page 1 of 5
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publication . Article . 2008

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

Flanagin, Steve; Nelson, Joel D.; Castner, David G.; Denisenko, Oleg; Bomsztyk, Karol;