| Loren Hansen | at 11:00 |
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Sequence specific chromatin modifying proteins binding motifs show strong positional preferences for potential regulatory regions.
The initiation and regulation of gene expression programs is critically dependent on temporal and position specific binding of transcriptional regulators. Many transcriptional regulators recognize and bind to specific DNA motifs. Due to the size and degeneracy of these motifs they are frequently found many hundreds or thousands of times in the genome with only a small subset serving as binding platforms. By occupying potential binding sites nucleosome placement can specify which out of a pool of sequence motifs are available to DNA binding regulatory factors. This raises the question how nucleosome placement is specified such that access is granted to transcriptional regulators when and where required. Here we show that many DNA binding motifs in the yeast, Sachharomyces cerevisiae show a strong positional preference to only occur in potential regulatory regions. Furthermore we demonstrate a correlation between positional preference and nucleosome occupancy, indicating proteins whose binding motifs show the strongest positional preference may also have a tendency to have chromatin modifying properties. This suggests that some DNA binding proteins may depend to a stronger degree on the distribution of their binding motifs across the genome to assist in the determination of specificity. Since many of these DNA binding proteins have chromatin remodeling properties, they can then alter the local nucleosome structure to a more permissive and/or restrictive state thereby assisting in determining DNA binding protein specificity.
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