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
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
display peaks. The peaks in one set were determined using PeakFinder
software supplied by NimbleGen. A false positive rate (FPR) was estimated for
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
configuration help link. Note that the graphical configuration options are
available only for the Signal subtrack; the Peaks subtracks are fixed.
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
The data were verified using PCR with primers designed to promoters enriched
with FAIRE and downstream coding regions.
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.
Buck, M.J., Nobel, A.B., and Lieb, J.D.
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).