## Description

ENCODE region-wide location analysis of histones H3 and H4 with antibodies H3K4me2, H3K4me3, H3ac, H4ac, STAT1, RNA polymerase II and TAF1 was conducted with ChIP-chip, using chromatin extracted from HeLa cells induced for 30 min with interferon-gamma as well as uninduced cells. The H3K4me2, H3K4me3, H3ac form of histone H3, and H4ac form of histone H4 are associated with up-regulation of gene expression. STAT1 (signal transducer and activator of transcription) binds to DNA and activates transcription in response to various cytokines, including interferon-gamma.

## Display Conventions and Configuration

This annotation follows the display conventions for composite "wiggle" tracks. The subtracks within this annotation may be configured in a variety of ways to highlight different aspects of the displayed data. The graphical configuration options are shown at the top of the track description page, followed by a list of subtracks. To display only selected subtracks, uncheck the boxes next to the tracks you wish to hide. For more information about the graphical configuration options, click the Graph configuration help link.

## Methods

Chromatin from both induced and uninduced cells was separately cross-linked, precipitated with the antibodies, sheared, amplified and hybridized to a PCR DNA tiling array produced at the Ren Lab at UC San Diego. The array was composed of 24,537 non-repetitive sequences within the 44 ENCODE regions.

Each state had three or more biological replicates. Each experiment was loess-normalized using R. The P-value and R-value were calculated using the modified single array error model (Li, Z. et al., 2003). The P-value and R-value were then derived from the weighted average results of the replicates.

The displayed values were scaled to 0 - 16, corresponding to negative log base 10 of the P-value.

## Verification

Each of the two experiments has three biological replicates. The array platform, the raw and normalized data for each experiment, and the image files have all been deposited at the NCBI GEO Microarray Database (pending approval).

## Credits

The data for this track were generated at the Ren Lab, Ludwig Institute for Cancer Research at UC San Diego.

## References

Kim, T., Barrera, L.O., Qu, C., van Calcar, S., Trinklein, N., Cooper, S., Luna, R., Glass, C.K., Rosenfeld, M.G., Myers, R., Ren, B. Direct isolation and identification of promoters in the human genome. Genome Research 15,830-839 (2005).

Li, Z., Van Calcar, S., Qu, C., Cavenee, W.K., Zhang, M.Z., and Ren, B. A global transcriptional regulatory role for c-Myc in Burkitt's lymphoma cells. Proc. Natl. Acad. Sci. 100(14), 8164-8169 (2003).

Ren, B., Robert, F., Wyrick, J. W., Aparicio, O., Jennings, E. G., Simon, I., Zeitlinger, J., Schreiber, J., Hannett, N., Kanin, E., Volkert , T. L., Wilson, C., Bell, S. P. and Young, R. A. Genome-wide location and function of DNA-associated proteins Science 290(5500), 2306-2309 (2000).