Description

This track shows the map of -log10(P-value) for ChIP-chip using 5 antibodies in Human Hela S3 cells hybridized to maskless photolithographic arrays with 50-mer oligonucleotides tiled with 12-nt overlaps covering most of the non-repetitive DNA sequence of the ENCODE regions.

This track shows the combined results of three multiple biological replicates. For all arrays, the ChIP DNA was labeled with Cy5 and the control DNA was labeled with Cy3. These data are available at NCBI GEO, which also provides additional information about the experimental protocols. The antibodies are described in the following section.

BAF155 and BAF170

The Swi-Snf chromatin-remodeling complex was first described in yeast, and similar proteins have been found in mammalian cells. The human Swi-Snf complex is comprised of at least nine polypeptides, including two ATPase subunits, Brm and Brg-1. Other members of the human Swi-Snf complex are termed BAFs for Brg1-associated factors. BAF155 and BAF170 are conserved (core) components that stimulate the chromatin remodeling activity of Brg1.

c-Fos

The transcriptional activity of the proto-oncogene c-Fos has been implicated in cell growth, differentiation, and development. Fos is induced by many stimuli, ranging from mitogens to pharmacological agents. c-Fos has been shown to be associated with another proto-oncogene, c-Jun, and together they bind to the AP-1 binding site to regulate gene transcription. Like CREB, c-Fos is regulated by p90Rsk.

c-Jun

C-Jun, also known as AP-1 (activator protein 1), is the cellular homologue of the avian sarcoma virus oncogene v-jun, and as such can be referred to as a proto-oncogene.

TAF1/TAF250

TAF250 (TBP associated factors, with molecular weight 250 kD, also known as TAF1), has histone acetyltransferase activity, which can relieve the binding between DNA and histones in the nucleosome.

Methods

The data from replicates were quantile-normalized and median-scaled to each other (both Cy3 and Cy5 channels). Using a 1000 bp sliding window centered on each oligonucleotide probe, a signal map (estimating the fold enrichment [log2 scale] of ChIP DNA) was generated by computing the pseudomedian signal of all log2(Cy5/Cy3) ratios (median of pairwise averages) within the window, including replicates. Using the same procedure, a -log10(P-value) map (measuring significance of enrichment of oligonucleotide probes in the window) for all sliding windows was made by computing P-values using the Wilcoxon paired signed rank test comparing fluorensent intensity between Cy5 and Cy3 for each oligonucleotide probe (Cy5 and Cy3 signals from the same array). A binding site was determined by thresholding oligonucleotide positions with -log10(P-value) (>= 4), extending qualified positions upstream and downstream 250 bp, and requiring 1000 bp space between two sites. Top 400 sites are retained.

Verification

ChIP-chip binding sites were verified by comparing "hit lists" generated from combinations of different biological replicates. Only experiments that yielded a significant overlap (greater than 50 percent) were accepted. As an independent check (for maskless arrays), data on the microarray were randomized with respect to position and re-scored; significantly fewer hits (consistent with random noise) were generated this way.

Credits

These data were generated and analyzed by the labs of Michael Snyder, Mark Gerstein and Sherman Weissman at Yale University.

References

Cawley, S., Bekiranov, S., Ng, H.H., Kapranov, P., Sekinger, E.A., Kampa, D., Piccolboni, A., Sementchenko, V., Cheng, J. et al. Unbiased mapping of transcription factor binding sites along human chromosomes 21 and 22 points to widespread regulation of noncoding RNAs. Cell 116(4), 499-509 (2004). Euskirchen, G., Royce, T.E., Bertone, P., Martone, R., Rinn, J.L., Nelson, F.K., Sayward, F., Luscombe, N.M., Miller, P. et al. CREB binds to multiple loci on human chromosome 22, Mol Cell Biol. 24(9), 3804-14 (2004). Martone, R., Euskirchen, G., Bertone, P., Hartman, S., Royce, T.E., Luscombe, N.M., Rinn, J.L., Nelson, F.K., Miller, P. et al. Distribution of NF-kappaB-binding sites across human chromosome 22. Proc Natl Acad Sci U S A. 100(21), 12247-52 (2003). Quackenbush, J.. Microarray data normalization and transformation, Nat Genet. 32(Suppl), 496-501 (2002).