Description

Formaldehyde-Assisted Isolation of Regulatory Elements (FAIRE) is a procedure used to isolate chromatin that is resistant to the formation of protein-DNA cross-links. These tracks display FAIRE data from 2091 fibroblast cells hybridized to high-resolution NimbleGen arrays that tile the ENCODE regions. The four datasets, in practical terms, can be thought of as independent replicates. However, because they were part of a series of experiments aimed at optimizing cross-linking conditions in human cells, the data represent different cross-linking times (1, 2, 4, and 7 minutes). Although the individual replicates are not displayed, the replicate data and also the signal averages and the peaks for the averages can be downloaded.

Display Conventions and Configuration

The FAIRE data are represented by three subtracks. One subtrack shows the average normalized log₂ ratios for the tiled probes; the other two subtracks display peaks. The peaks in one set were determined using PeakFinder software supplied by NimbleGen. A false positive rate (FPR) was estimated for the peak set using a permutation-based method. All peaks had an FPR of < 0.01. The peaks in the other set (Apr. 2006 update) were identified by ChIPOTle, a peak-finding algorithm that uses a sliding window to identify statistically significant signals that comprise a peak. A null distribution was determined by reflecting the negative data, which is presumed to be noise, about zero and a Gaussian distribution was fitted to it. Windows were considered significant with a p-value < 1e-25, after using the Benjamini-Hochberg correction for multiple tests.

This annotation follows the display conventions for composite 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 one subtrack, uncheck the box next to the track you wish to hide. For more information about the graphical configuration options, click the Graph configuration help link. Note that the graphical configuration options are available only for the Signal subtrack; the Peaks subtracks are fixed.

Methods

To perform FAIRE, proteins were cross-linked to DNA using 1% formaldehyde solution, the complex was sheared using sonication, and a phenol/chloroform extraction was performed to remove DNA fragments crosslinked to protein. The DNA recovered in the aqueous phase was fluorescently-labeled and hybridized to a microarray along with fluorescently-labeled genomic DNA as a control. Ratios were scaled by subtracting the Tukey Bi-weight mean for the log-ratio values from each log-ratio value, as recomended by NimbleGen. Results in yeast were consistent with enrichment for nucleosome-depleted regions of the genome. Therefore, the method may have utility as a positive selection for genomic regions with properties normally detected by assays like DNAse hypersensitivity.

Verification

The data were verified using PCR with primers designed to promoters enriched with FAIRE and downstream coding regions.

Credits

Cell culture, fixing, and DNA amplification were performed by Jonghwan Kim in the Vishy Iyer lab at the University of Texas, Austin. FAIRE was done by Paul Giresi in the Jason Lieb lab at the University of North Carolina at Chapel Hill. Paul Giresi of NimbleGen did the sample labeling and hybridization with the help of Mike Singer and Roland Green. Nan Jiang at NimbleGen supplied the Software used for the permutation analysis.

References

Buck, M.J., Nobel, A.B., and Lieb, J.D. ChIPOTle: a user-friendly tool for the analysis of ChIP-chip data. Genome Biol. 6(11), R97 (2005).

Nagy, P.L., Cleary, M.L., Brown, P.O., and Lieb, J.L. Genomewide demarcation of RNA polymerase II transcription units revealed by physical fractionation of chromatin. PNAS 100(11), 6364-9 (2003).