Chromosome band features analyzed by hidden Markov modeling with Viterbi segmentations. (A, top) Giemsa annotated, shows the whole chr 17 Giemsa banding pattern obtained from http://genome.ucsc.edu that is derived from measurement of Giemsa bands relative to whole chromosome length. (Bottom) Predicted, shows the whole chr 17 banding pattern predicted from the enriched histone domains shown in (B) that is based on a nonsynchronized, mainly interphase cell population. Gray shading indicates the predicted relationship between the two binding patterns. Light bands: gene-rich domains enriched for H3K27me3, H3Ac, H4Ac, H4K20me1, and SINEs. Dark bands: gene-poor domains enriched for H3K9me3, H4K20me3, and LINEs/LTRs. Domains sizes larger than 2.5 Mbp are shown and an asterisk marks the imprinted Igf2r cluster analyzed in Figure 4. (B) Hidden Markov modeling with Viterbi segmentations (HMM-Seg) for H3K27me3, H3Ac, H4Ac and H4K20me1 ChIP-chip hybridizations shown as blue boxes, separately for MEFF and MEFB1 cells. Note that all four histone modifications identify the same domains in two independent MEF cell lines. HMM-Seg for H3K9me3 and H3K20me3 is shown as green boxes using the combined MEFF and MEFB1 data. HMM-Seg is shown separately for LINEs + LTRs and for SINEs (black boxes). Note that areas of LINE and LTR density are distinct from areas of SINE density. HMM-Seg for gene density is shown underneath as dark gray boxes. (C) Quantitative analysis comparing the similarity of the above sets of HMM-Seg analyses. Pie charts show the amount of overlap of two groups of segments (similar: black) and the amount of nonoverlap (different: gray). Blue: H3K27me3, H3Ac, H4Ac, and H4K20me1.
