All and only CpG containing sequences are enriched in promoters abundantly bound by RNA polymerase II in multiple tissues

Julian M Rozenberg¹ , Andrey Shlyakhtenko¹ , Kimberly Glass² , Vikas Rishi¹ , Maxim V Myakishev¹^,3 , Peter C FitzGerald⁴ and Charles Vinson¹

¹Laboratory of Metabolism, National Cancer Institute, Bethesda, MD 20892 USA

²Physics Department, University of Maryland, College Park, MD 20742, USA

³Department of Dermatology University of Rochester School of Medicine, Rochester, NY 14642, USA

⁴Genome Analysis Unit, National Cancer Institute, Bethesda, MD 20892 USA

author email corresponding author email

BMC Genomics 2008, 9:67doi:10.1186/1471-2164-9-67


Published:	5 February 2008

Additional files

Additional file 1:

The region of the promoter critical for the bimodal distribution of the 8-mer-association-with-RNAP. Histogram of the 8-mer-association-with-RNAP between -1,000 bp and +500 bp and in 200 bp increments from -1,200 bp to +1,000 bp for abundant 8-mers in the common RNAP promoters. 8-mers that contain a CpG are noted in black.

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Additional file 2:

Distribution of the 8-mer-association-with-RNAP for 8-mers containing particular dinucleotide. Histograms of the 8-mer-association-with-RNAP between -1,000 bp and +500 bp for abundant and all 8-mers with 8-mers containing each of the 10 dinucleotides noted in black.

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Additional file 5:

8-mer-association-with-RNAP for all 8-mers. Spreadsheet containing the 8-mer-association-with-RNAP for all 8-mers.

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Additional file 3:

Data presented at figures 2, 3(D–E), 5 and 6C for all 8-mers. The data presented at figures 2, 3(D–E), 5 and 6C is shown here for all 8-mers. Histograms and scatter plots for 8-mer-association-with-RNAP vs. 8-mer-association-with-H3K9me2, enrichment of 8-mers in 356 liver specific promoters vs. 8-mer-association-with-RNAP, clustering factor vs. 8-mer-association-with-RNAP.

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Additional file 4:

Supplementary tables. Table 1 shows the 120 statistically most non-randomly distributed sequences placed into 10 groups. Table 2 shows co-occurrence of the 10 proximal promoter motifs between -200 bp and the TSS in 14,790 mouse promoters, top 20% of common RNAP promoters and top 20% of promoters best bound by H3K9me2.

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