This track shows the accessibility of genomic DNA to DNase I digestion
in the D. melanogaster embryo for five stages of development: 5, 9,
10, 11 and 14 (Thomas et al.). These data have been used to show the
dynamics of chromatin accessibility during embryogenesis (Thomas et
al) and that chromatin accessibility plays a dominant role in
determining the widespread, overlapping patterns of binding by
functionally distinct transcription factors in Drosophila embryos (Li
et al.; Kaplan et al.).
Display Conventions and Configuration
Subtracks are provided showing either the density of DNA sequence tags
in 75 bp windows across the genome or the locations of 5% FDR
accessible regions. DNA sequence tag density data for independent
replica for each stage are provided, though by default only one
replica is shown. The DNA tag density subtracks are by default shown
in "full" and the locations of 5% FDR regions that are concordant
in both replicas are shown in "squish". Data for each stage is shown in
a different color: green for stage 5, orange for stage 9, red for
stage 10, light blue for stage 11 and purple for stage 14.
The graphical configuration options for the subtracks are shown at the
top of the track controls page, followed by a list of subtracks. To
show only selected subtracks, uncheck the boxes next to the tracks
that you wish to hide. For more information about the graphical
configuration options, click the Graph configuration help link.
One hour collections of wild type embryos were aged to the appropriate
developmental stage and then nuclei were isolated and briefly digested
with DNase I. The DNA released by digestion was size fractionated
through a sucrose gradient to capture 100 - 400 bp fragments, which
were then used to generate an average of ~14 million sequence tags per
sample to the Drosophila genome with an Illumina GA2.
The data were analyzed to determine short genomic regions that are
accessible to digestion at a 5% false discovery rate; see Thomas
et al. for further details.
Kaplan T, Li XY, Sabo PJ, Thomas S, Stamatoyannopoulos JA, Biggin MD, Eisen MB.
Quantitative models of the mechanisms that control genome-wide patterns of transcription factor
binding during early Drosophila development.
PLoS Genet. 2011 Feb 3;7(2):e1001290.
PMID: 21304941; PMC: PMC3033374
Li XY, Thomas S, Sabo PJ, Eisen MB, Stamatoyannopoulos JA, Biggin MD.
The role of chromatin accessibility in directing the widespread, overlapping patterns of Drosophila
transcription factor binding.
Genome Biol. 2011;12(4):R34.
PMID: 21473766; PMC: PMC3218860
Thomas S, Li XY, Sabo PJ, Sandstrom R, Thurman RE, Canfield TK, Giste E, Fisher W, Hammonds A,
Celniker SE et al.
Dynamic reprogramming of chromatin accessibility during Drosophila embryo development.
Genome Biol. 2011;12(5):R43.
PMID: 21569360; PMC: PMC3219966