Description

This track shows an estimate of the binding activity of 24 transcription factors in the D. melanogaster embryo. Chromatin immunoprecipitation and whole-genome tiling arrays (ChIP/chip) were used (see Li, MacArthur et al.) to map the genomic regions bound by 22 sequence specific transcription factors and two general transcription factors: TFIIB and the transcriptionally active phosphorylated form of RNA polymerase II. The sequence specific factors (except for Zeste), described in the table below, fall into three regulatory classes: anterior-posterior (A-P) early, A-P pair rule, and dorsal-ventral (D-V). Data for all proteins except Zeste are for stage 4-5 blastoderm embryos. Data for Zeste are for stage 11 embryos. Enrichment factors (1 = no enrichment) are shown in separate subtracks for 36 antibodies at false discovery rates (FDR) of 1% and 25%.

Seq. Specific Factor	Symbol	DNA binding domain	Regulatory Class
Bicoid	bcd	homeodomain	A-P early maternal
Caudal	cad	homeodomain	A-P early maternal
Giant	gt	b-zip domain	A-P early gap
Hunchback	hb	C2H2 Zinc finger	A-P early gap
Knirps	kni	receptor Zinc finger	A-P early gap
Krüppel	Kr	C2H2 Zinc finger	A-P early gap
Huckebein	hkb	C2H2 Zinc finger	A-P early terminal
Tailless	tll	receptor Zinc finger	A-P early terminal
Dichaete	D	HMG/SOX class	A-P early gap-like
Fushi tarazu	ftz	homeodomain	A-P pair rule
Hairy	h	bHLH	A-P pair rule
Paired	prd	homeodomain / paired domain	A-P pair rule
Runt	run	runt domain	A-P pair rule
Sloppy paired 1	slp1	forkhead domain	A-P pair rule
Daughterless	da	bHLH	D-V maternal
Dorsal	dl	NFkB/rel	D-V maternal
Mothers against dpp	mad	SMAD-MH1	D-V zygotic
Medea	med	SMAD-MH1	D-V zygotic
Schnurri	shn	C2H2 Zinc finger	D-V zygotic
Snail	sna	C2H2 Zinc finger	D-V zygotic
Twist	twi	bHLH	D-V zygotic
Zeste	z	unique	ubiquitous

Display Conventions and Configuration

By default, values are displayed in grayscale ("dense" mode) instead of graphing ("full" mode), and only 24 of the 72 subtracks are shown: only those with FDR of 1% and only one antibody per factor (the antibody with the most bound regions at FDR of 1%). To change the configuration, click on the blue or gray button to the left of the track or click on the track title in the controls below the image.

The subtracks within this composite annotation track may be configured in a variety of ways to highlight different aspects of the displayed data. 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.

Subtracks are colored according to regulatory class: green for A-P early, orange for A-P pair rule, blue for D-V, brown for stage 11 zeste, and red for general transcription factors.

Methods

Where practicable two antibody preparations that were independently purified against nonoverlapping epitopes were used. For each purified antibody, two independent replicates of three different sample types were analyzed on separate arrays:

"Factor immunoprecipitates (IPs)" obtained by immunoprecipitation using a factor-specific antibody
"immunoglobulin G (IgG) control IPs" obtained by immunoprecipitation using a normal IgG antibody
"input DNA" obtained from the chromatin prior to immunoprecipitation

for a total of six arrays per antibody. Mean hybridization intensities for transcription factor IP replicates and IgG control IP replicates were divided by the mean probe intensity in the input DNA samples to produce oligonucleotide ratio values. The logarithms of the oligonucleotide ratios were averaged in windows of 675 bp centered around each probe (after discarding the highest and lowest values, to produce a "trimmed mean") to produce window scores. Bound regions were identified by comparing window scores to expected score distributions computed from a symmetric null distribution. The symmetric null method assumes that the background window score distribution is symmetric about its mean, and estimates the distribution from values less than the observed mode. This estimated null distribution was used to assign p-values to each window score, and these were corrected for multiple testing to control the FDR. A separate FDR estimation method that uses the IgG control data to estimate the null distribution defines a similar number of bound regions (not shown here, see Li et al., 2008).

Credits

Thanks to the Berkeley Drosophila Transcription Network Project's In Vivo DNA Binding collaboration, and Stewart MacArthur and Mark Biggin in particular, for these data.

References

Li XY, MacArthur S, Bourgon R, Nix D, Pollard DA, Iyer VN, Hechmer A, Simirenko L, Stapleton M, Luengo Hendriks CL et al. Transcription factors bind thousands of active and inactive regions in the Drosophila blastoderm. PLoS Biol. 2008 Feb;6(2):e27.

MacArthur S, Li XY, Li J, Brown JB, Chu HC, Zeng L, Grondona BP, Hechmer A, Simirenko L, Keränen SV et al. Developmental roles of 21 Drosophila transcription factors are determined by quantitative differences in binding to an overlapping set of thousands of genomic regions. Genome Biol. 2009;10(7):R80.

Moses AM, Pollard DA, Nix DA, Iyer VN, Li XY, Biggin MD, Eisen MB. Large-scale turnover of functional transcription factor binding sites in Drosophila. PLoS Comput Biol. 2006 Oct;2(10):e130.

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.