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%.

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

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. PMID: 18271625; PMC: PMC2235902

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. PMID: 19627575; PMC: PMC2728534

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. PMID: 17040121; PMC: PMC1599766

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