E2F4 and Myc ChIP-chip perfomed on Nimblegen hg17 ENCODE arrays

Identifying the chromosomal targets of transcription factors is important for reconstructing the transcriptional regulatory networks underlying global gene expression programs. ChIP-chip is a powerful technique to map chromosomal targets of transcription factors. We applied ChIP-chip to map downstream targets of the transcription factor E2F4 and c-Myc. E2F4 is a member of the E2F family of transcriptional regulators that functions as a repressor in quiescent and early G1 cells. c-Myc is a oncogenic transcription factor implicated in almost all aspects of tumorigenesis. We mapped E2F4 and c-Myc binding sites in 1% of the human genome using Nimblegen hg17 ENCODE arrays. Keywords: ChIP-chip Cultured cells are cross-linked in vivo using 1% formaldehyde and chromatin is sheared to less than 1 kb fragments using a sonicator. Specific protein-dna complexes are pulled down using a specific antibody. After adequate washing, the protein-dna complexes are eluted, reverse cross-linked and the DNA purified by phenol-chloroform extraction. ChIP-enriched DNA is now labeled with Cy5 while DNA derived from a mock IP is used as a reference and labeled with Cy3. Samples are then hybridized on ENCODE arrays.