Greenleaf (RNA pol II), G. factors, transcripts, small RNAs, and origins of replication in and genomea. A 9-state model of prevalent chromatin states found in S2 and BG3 cells. Each chromatin state (row) is defined by a combinatorial pattern of enrichment (red) or depletion (blue) for specific chromatin marks (first panel, columns). For instance, state 1 is distinguished by enrichment in H3K4me2/me3 and H3K9ac, typical of transcription start sites (TSS) in expressed genes. The enrichments/depletions are shown relative to chromatin input S2 data shown, see (Supp. Figure 3 for BG3 data and histone density normalization). The second panel shows average enrichment of chromosomal proteins. The third panel shows fold over/under-representation of genic and TSS-proximal (1kb) regions relative to the entire tiled genome. The enrichment of intronic regions is relative to genic regions associated with each state. b. A genome-wide karyotype view of OC 000459 the domains defined by Rabbit polyclonal to TRAIL the 9-state model in S2 cells. Centromeres are shown as open circles, and dashed lines span gaps in the genome assembly. Several prominent chromatin organization features are illustrated (color code in a), including the extent of pericentromeric heterochromatin (state 7), and the H4K16ac-driven signature of the dosage-compensated male X chromosome (state 5). (BG3 genome in Supp. Figure 4.) c-e. Examples of chromatin annotation at specific loci. c. Two distinct chromatin signatures of transcriptionally active genes: one (left) is associated with enrichment in marks of states 3 and 4, while the other (right) is limited to states 1 and 2, recapitulating well-established TSS and elongation signatures (note: small patches of state 7 in CG13185 illustrate H3K9me2 found at some expressed genes in S2 cells16). d. A locus containing two Polycomb-associated domains, silent (left) and balanced (right). e. A large state 8 domain located within euchromatic sequence in BG3 cells, enriched for chromatin marks typically associated with heterochromatic regions, but at lower levels than in pericentromeric heterochromatin (state 7). Most distinct chromatin states are associated with transcriptionally active genes. Active promoter and transcription start site (TSS)-proximal regions are identified by state 1 (Figure 1; red), marked by prominent enrichment in H3K4me3/me2 and H3K9ac. The transcriptional elongation signature associated with H3K36me3 enrichment is OC 000459 captured by state 2 (purple), found preferentially over exonic regions of transcribed genes. State 3 (brown), typically found within intronic regions, is distinguished by high enrichment in H3K27ac, H3K4me1, and H3K18ac. A related chromatin signature is captured by state 4 (coral), distinguished by enrichment of H3K36me1, but notably lacking H3K27ac. The number of genes associated with each chromatin state and the distribution of states within genes are shown in Supp. Figure 5. Several aspects of large-scale organization are revealed by the karyotype view (Figure 1b). Chromosome X is strikingly enriched for state 5 (green), distinguished by high levels of H4K16ac in combination with some enrichment in H3K36me3 and other marks of elongation state 2 (a pattern associated with dosage compensation in male cells15). Pericentromeric heterochromatin domains and chromosome 4 are characterized by high levels of H3K9me2/me3 (state 7, dark blue)10. Finally, the model distinguishes OC 000459 another set of heterochromatin-like regions containing moderate OC 000459 levels of H3K9me2/me3 (state 8, light blue, Figure 1e). Surprisingly, this state occupies extensive domains in autosomal euchromatic arms in BG3 cells, and in chromosome X in both cell lines16. Further aspects of chromatin organization can be visualized by folding the chromosome using a Hilbert curve (Figure 2a)17, which maintains the spatial.