Figure 3

Method-independent consistency of MNase cut sites and nucleosome positions within the fission yeast ade6 gene region. The horizontal axis and transcription diagram at the bottom of this figure are common to panels A and B. Thick blue bars represent the CoDing Sequences (CDS) of the indicated genes. The narrow green bars represent the 5' untranslated regions (5'-UTRs) of these genes, while the narrow red pointed bars represent their 3'-UTRs. (a) Histogram (vertical orange bars) displaying the frequencies (tags at the indicated position per million tags genome-wide) of 36-nt sequence tags in mononucleosomal DNA (LFN sample; Figure 2f and Additional File 1C), which map uniquely to the forward (upward scale) and reverse (downward scale) strands of a 4-kbp region of S. pombe chromosome 3 centered on the ade6 gene. (b) Profiles of relative MNase protection. For the orange (LFN sample) and green (LUN sample) lines, this is defined as the frequency, relative to the genome average (horizontal black, dotted line), with which the indicated nucleotide position is crossed by computer-generated 3'-extrapolations of forward- and reverse-strand sequence tags to 120 bp. The pink line shows relative MNase protection based on the microarray results published by Lantermann et al. [21]. The percent GC (150-bp window) over the region is indicated by the gray line and right-hand vertical axis. The vertical black arrows and lines mark the positions of MNase cuts mapped within the ade6 gene by Lantermann et al. [7] using the traditional indirect-end-labeling method