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The role of chromatin accessibility in directing the widespread, overlapping patterns of Drosophila transcription factor binding

Xiao-Yong Li12, Sean Thomas3, Peter J Sabo3, Michael B Eisen124, John A Stamatoyannopoulos3* and Mark D Biggin1*

Author Affiliations

1 Genomics Division, Lawrence Berkeley National Laboratory, 1 Cyclotron Road MS 84-171, Berkeley, CA 94720, USA

2 Howard Hughes Medical Institute, University of California Berkeley, 176 Stanley Hall #3220, Berkeley, CA 94720, USA

3 Department of Genome Sciences, University of Washington, Foege S310A, 1705 NE Pacific Street, Box 355065, Seattle, WA 98195, USA

4 Department of Molecular and Cell Biology, University of California Berkeley, 176 Stanley Hall #3220, Berkeley, CA 94720, USA

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Genome Biology 2011, 12:R34  doi:10.1186/gb-2011-12-4-r34

Published: 7 April 2011

Additional files

Additional file 1:

Replica DNase-seq data closely agree.

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Additional file 2:

Summary of 5% FDR accessible regions in euchromatic DNA for stage 5, 9, 10, 11 and 14 embryos.

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Additional file 3:

5% FDR accessible regions in the euchromatic genome for stage 5, 9, 10, 11 and 14 embryos.

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Additional file 4:

ChIP-chip input crosslinked DNA is not appreciably enriched in either highly bound or highly accessible genomic regions.

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Additional file 5:

The overlap between 1% FDR ChIP-chip peaks versus 5% FDR accessible regions.

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Additional file 6:

Most highly accessible regions are bound by regulatory factors.

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Additional file 7:

The level of transcription factor occupancy correlates with the degree of DNaseI accessibility.

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Additional file 8:

Comparison of ChIP-chip scores for occurrences of DNA recognition sequences in accessible versus closed chromatin regions.

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Additional file 9:

Levels of MED factor occupancy and DNaseI accessibility change between developmental stages.

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Additional file 10:

Change in DNA binding levels in vivo between developmental stages.

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Additional file 11:

Temporal changes in levels of MED occupancy correlate with changes in DNaseI accessibility.

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Additional file 12:

1% and 25% FDR ChIP-chip bound regions for HB at stage 9 and MED at stages 10 and 14.

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Additional file 13:

Position weight matrices of factors' intrinsic DNA recognition properties used.

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