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Chromosome four, heterochromatin, and euchromatin (metagenes in Figure S4 and S5, heatmaps in Figure S6). H3K9me2 is the only mark on chromosome four preferentially linked with repressed gene bodies. The higher levels of POF and HP1a associated with transcribed genes on chromosome 4 confirm prior findings by Johannson and colleagues [17]. The enrichment of H3K9me3 in these regions of active transcription is unexpected and suggests a special mechanism regulating H3K9 methylation on chromosome 4.Chromosome 4 genes seldom display RNA polymerase pausingAs previously reported, silencing marks are depleted in the TSSs [15]. Figure three compares the chromatin composition in the TSS and also the gene body for chromosome four genes. The distinctive enrichment patterns observed for TSSs and gene bodies suggested a doable role for this chromatin structure in regulation in the TSS. Given the anticipated difficulty in transcribing via a area with HP1a and H3K9me3, we viewed as adjustments in polymerase dynamics, like pausing, to be likely affected. For a important variety of active genes, RNA pol II initiates transcription but pauses just after 250 nt, remaining there till pausing is relieved. We investigated polymerase association with genes and polymerase pausing on chromosome 4 working with global runon followed by sequencing (GRO-seq) with data from PubMed ID:http://www.ncbi.nlm.nih.gov/pubmed/20030704 S2 cells produced by Larschan and colleagues [26]. First, we compared the association of polymerase with genes in euchromatin, pericentric heterochromatin, and chromosome 4. RNA-seq data derived from steady state mRNA revealed that, even though pericentric heterochromatin features a reduce gene density, the fraction of active genes is roughly the same among heterochromatin (pericentric heterochromatin and chromosome 4) and euchromatin (54 vs. 52 inActive genes on chromosome 4 are characterized by a distinct combination of POF, H3K36me3, HP1a, and H3K9me2/Previous perform by us and by others has indicated that HP1a correlates well with H3K9me2 and H3K9me3 in pericentric heterochromatin [14,15]. Having said that, H3K9me2 and H3K9me3 have distinct distributions on chromosome four (Figure 1A, compare states A ), top us to re-examine the correlation of those marks as well as some others in chromosome four and pericentric heterochromatin. Though pericentric heterochromatin maintains the expected association among silencing marks, we find that HP1a and H3K9me3 correlate positively with active marks POFPLOS Genetics | www.plosgenetics.orgDrosophila Chromosome 4 Chromatin StructureFigure 2. The partnership amongst marks of classical heterochromatin and gene expression are altered on chromosome 4. The strength of correlation amongst marks is illustrated within this diagram by the colour intensity (red – constructive correlation; blue – adverse correlation). In pericentric heterochromatin, the black outline demarcates the powerful correlation structure observed amongst H3K9me2, H3K9me3, and HP1a (suitable). This sturdy correlation is not present on chromosome four; HP1a and H3K9me3 as an alternative are positively correlated with H3K36me3, a mark of elongation, plus the chromosome 4-specific protein POF (left). doi:10.1371/journal.pgen.1002954.gS2 cells). GRO-seq information confirmed this assessment, indicating that 47.six of euchromatic genes have been becoming actively transcribed in S2 cells, in MedChemExpress CXCR2-IN-1 comparison to 40.4 of those in heterochromatin. On chromosome 4, 54.three from the genes were associated with GRO-seq signal, a fraction slightly larger but not significantly different from that of euchro.