## Description

ENCODE region-wide location analyses of binding to the initiation-complex form of RNA polymerase II (Pol2), TATA-associated factor (TAF1), acetylated histone H3 (H3ac), lysine-4-dimethylated H3 (H3K4me2), SUZ12, and H3K27me3 were conducted using chromatin extracted from IMR90 (lung fibroblast), HCT116 (colon epithelial carcinoma), HeLa (cervix epithelial adenocarcinoma), and THP1 (blood monocyte leukemia) cells. The initiation-complex form of Pol2 is associated with the transcription start site, as is TAF1. Both H3ac and H3K4me2 are associated with transcriptionally active "open" chromatin.

## Display Conventions and Configuration

Data for each antibody is displayed in a separate track in the UCSC browser. In cases where experiments involve multiple cell types, the data for each cell line is displayed in an individual subtrack. The complete set of tracks and subtracks for this annotation includes:

- Pol2 (HeLa, THP1, IMR90, HCT116)
- TAF1 (HeLa, THP1, IMR90, HCT116)
- H3ac (IMR90)
- H3K4me2 (IMR90)
- SUZ12 (unstimulated HeLa)
- H3K27me3 (unstimulated HeLa)

The specific antibody against Pol2, 8WG16 from the Abcom catalog, binds specifically to the non-phosphorylated form of Pol2 which is associated with the pre-initiation complex.

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 each of the four cell lines was separately cross-linked, precipitated with antibody to one of the four proteins, sheared, amplified and hybridized to a PCR DNA tiling array produced at the Ren Lab at UC San Diego. The array is composed of 24,537 non-repetitive sequences within the 44 ENCODE regions.

For each marker, there were three biological replicates. Each experiment was normalized using the median values. 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

There were three biological replicates for each of the eight experiments. 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.

## 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, 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, 2306-2309 (2000).