Quantitative analysis of H3K4me3 across metaphase chromosome 1 and comparison with interphase transcription. (a) Scanning of human chromosome 1 immunostained with antibodies to H3K4me3. Scans from each sister chromatid are shown (dotted and solid lines). The blue line on the immunostained chromosome was inserted manually to mark the centromere prior to scanning (see Materials and methods for details). Note that peak positions differ slightly between sister chromatids, presumably due to differential stretching during preparation. (b) Transcription from 3,071 RefSeq genes across chromosome 1 in human LCLs was measured by expression microarray and summed within 10-Mb windows across the chromosome. Transcription (open bars) is plotted as the sum of normalized gene expression values per 10-Mb window. H3K4me3 levels across chromosome 1 (solid line) were obtained by scanning (a). To obtain the mean distribution shown, each scanned chromatid was divided linearly into 25 equal segments (nominally 10 Mb each) and fluorescence values within each segment (expressed as percent maximum value for that scan) were summed. Each value shown is the average of 24 chromatids. The minimum value at the centromere (120 to 130 Mb) was used as a background value and subtracted. There is some broadening of peaks derived from multiple scans compared to single chromatid scans because of the shifts in peak position caused by differential stretching (a). A standard chromosome 1 ideogram showing major G bands is aligned with the histogram. FITC, fluorescein isothiocyanate.