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Chromatin-Associated Periodicity in Genetic Variation Downstream of Transcriptional Start Sites

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Science  16 Jan 2009:
Vol. 323, Issue 5912, pp. 401-404
DOI: 10.1126/science.1163183

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  1. Fig. 1.

    Diversity rates and nucleosome positions around TSSs. (A) The x axis shows the distance from the representative TSSs in the medaka (Hd-rR) genome. Color key shows rates: blue line, mismatch mutation (substitution) rate; red line, indel mutation rate; and gray line, rate of indels of length 1 bp. For smoothing of lines, a running average over a 23-bp window (one full turn of the helix in each direction) is depicted. (B) (Top) Putative nucleosome dyads (red points, 73 bp from start of sequence read) and cores (gray bars; 147 bp). (Bottom) The distinct meanings of the three nucleosome indicators. (C) Distribution of nucleosomes, substitutions, and indels surrounding a TSS. Black boxes, exons of the gene; blue histograms, distributions of the three nucleosome indicators; green vertical bars, substitutions between the Hd-rR and HNI genomes; red bars, deletions from the Hd-rR genome; blue bars, insertions into the Hd-rR genome; and gray bars and boxes, failure of alignment. (D) The average local dyad positioning score.

  2. Fig. 2.

    Mutational spectra at positions around 8181 positioned dyads that are isolated from their neighboring dyads by >165 bp and are covered by an average of 5.44 putative nucleosome cores on a genome-wide scale (excluding TSSs and coding regions). (A) In nonpromoter regions, where transcription does not occur, the two locations in the distinct strands are positionally equivalent in a nucleosome core if they are the same distance from the dyad. The x axis presents the distance. Color key shows rates. (B) An expanded view of the indel rates enclosed in the green square in Fig. 2A is duplicated in tandem, and the two copies are overlaid for comparison with equivalent measurements relative to TSSs in Fig. 1A. (Bottom) The estimated dyads (arrows) aligned with dyad positioning score near TSSs (expanded from Fig. 1D).

  3. Fig. 3.

    (A) Base composition surrounding TSSs. Red line, the difference between guanines and cytosines; blue line, the difference between adenines and thymines. (B) Substitution rates around TSSs. Rates for each substitution and its complement and their 95% confidence intervals are indicated side by side for untranscribed and transcribed regions that are upstream and downstream of TSSs, respectively.

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