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Volume 1, Issue 2 , Pages 138-143 , September 2007

Identifying estrogen receptor target genes

Willem-Jan Welboren
- Department of Molecular Biology, NCMLS Radboud University Nijmegen, Nijmegen, The Netherlands
- Department of Chemical Endocrinology, Radboud University Nijmegen Medical Center, Nijmegen, The Netherlands
Henk G. Stunnenberg
- Department of Molecular Biology, NCMLS Radboud University Nijmegen, Nijmegen, The Netherlands
Fred C.G.J. Sweep
- Department of Chemical Endocrinology, Radboud University Nijmegen Medical Center, Nijmegen, The Netherlands
Paul N. Span
- Department of Chemical Endocrinology, Radboud University Nijmegen Medical Center, Nijmegen, The Netherlands
- Corresponding author. Department of Chemical Endocrinology 479, Radboud University Nijmegen Medical Center, PO Box 9101, NL-6500 HB, Nijmegen, The Netherlands. Tel.: +31 24 3614279; fax: +31 24 3541484.

Received 28 March 2007 ,Revised 26 April 2007 ,Accepted 27 April 2007.

Overview of ChIP-chip. (A) Using formaldehyde protein–protein and protein–DNA are cross-linked in vivo. The cross-linked chromatin is subsequently isolated. (B) The isolated chromatin is sheared in sm

Overview of ChIP-chip. (A) Using formaldehyde protein–protein and protein–DNA are cross-linked in vivo. The cross-linked chromatin is subsequently isolated. (B) The isolated chromatin is sheared in smaller fragments by sonication yielding fragments of 500–1000bp. The protein or histone modification of interest is precipitated using an antibody. The cross-linked DNA is co-precipitated. (C) The unbound chromatin is washed away. (D) The cross-linking is reversed and the DNA is isolated. The DNA is amplified by either LM-PCR or T7 linear amplification of DNA. (E) Total genomic DNA and ChIP DNA are differently labeled with Cy3 and Cy5. (F) Labeled DNA is hybridized on promoter arrays or arrays spanning the total non-repetitive genome.
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