For example, we observe that chromatin patterns most accurately reflect the replication timing of the S2 genome at scales of ~170kb (Supp

For example, we observe that chromatin patterns most accurately reflect the replication timing of the S2 genome at scales of ~170kb (Supp. DNA Elements (modENCODE) project is usually generating a comprehensive map of chromatin components, transcription factors, transcripts, small RNAs, and origins of replication inD. melanogasterandC. elegans1,2. Drosophila has been used as a model system for over a century to study chromosome structure and function, gene regulation, development, and evolution. The availability of high-quality euchromatic and heterochromatic sequence assemblies3-5, considerable annotation of functional elements6, and a vast repertoire of experimental manipulations enhance the value of epigenomic studies in Drosophila. Genome-wide profiling of chromatin components provides a rich annotation of the potential functions of the underlying DNA sequences. Previous work has recognized patterns of post-translational histone modifications and nonhistone proteins associated with specific elements (e.g. transcription start sites, enhancers), as well as delineating the transcriptional status of DAB genes and large domains7,8. Here, we present a comprehensive picture of the chromatin scenery in a model eukaryotic genome. We define combinatorial chromatin says at different levels of business, from individual regulatory units to the chromosome level, and relate individual says to genome functions. == Combinatorial chromatin says == We performed chromatin immunoprecipitation (ChIP)-array analysis for numerous histone modifications and chromosomal proteins (Supp. Table 1), using antibodies tested for specificity and cross-reactivity9(Supp. Physique 1). Here, we describe analyses of cell lines S2-DRSC (S2) and ML-DmBG3-c2 (BG3), derived from late male embryonic tissues (stages 16-17) and the central nervous system of male third instar larvae, respectively (seehttp://www.modencode.orgfor data from other cell lines and animal stages). Analysis discloses groups of correlated features, including those associated with heterochromatic regions10, Polycomb-mediated repression11, and active transcription12(Supp. Physique 2), much like those observed in other organisms13,14. This suggests that specific histone modifications work together to achieve unique chromatin says. We utilized a machine-learning approach to identify the prevalent combinatorial patterns of 18 histone modifications, capturing the overall complexity of chromatin profiles observed in S2 and BG3 genomes with 9 combinatorial says (Physique 1a, Methods). The model associates each genomic location with a particular state, generating a chromatin-centric annotation of the genome (Physique 1b). We examined each state for enrichment in non-histone proteins (Physique 1a,Supp. Physique 3) and gene elements, as DAB well as distribution across the karyotype (Physique 1b,Supp. Physique 4) and finer-scale levels (Physique 1c-e). == Physique 1. Chromatin annotation of theDrosophila melanogastergenome. == a. A 9-state model of prevalent chromatin says found in S2 and BG3 cells. Each chromatin state (row) is defined by a combinatorial pattern of enrichment (reddish) or depletion (blue) for specific chromatin marks (first panel, columns). For instance, state 1 is usually distinguished by enrichment in H3K4me2/me3 and H3K9ac, DAB common of transcription start sites (TSS) in expressed genes. The enrichments/depletions are shown relative to chromatin input S2 data shown, see (Supp. Physique 3for 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 Ntf5 and TSS-proximal (1kb) regions relative to the entire tiled genome. The enrichment of intronic regions is usually relative to genic regions associated with each state. b. A genome-wide karyotype view of the domains defined by 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 business 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 inSupp. Physique 4.) c-e. Examples of chromatin annotation at specific loci.c. Two unique chromatin signatures of transcriptionally active genes: one (left) is associated with enrichment in marks of says 3 and 4, while the other (right) is limited to says 1 and 2, recapitulating well-established TSS and elongation signatures (notice: small patches of state 7 in CG13185 illustrate DAB H3K9me2 found at some expressed genes in S2 cells16).d. A locus made up of two Polycomb-associated domains, silent (left) and balanced (right).e. A large state 8 domain name 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 unique chromatin says are associated with transcriptionally active genes. Active promoter and transcription start site (TSS)-proximal regions are recognized by state 1 (Physique 1; reddish), noticeable by prominent.