Chromatin is composed of DNA and a variety of modified histones and non-histone proteins, which have an impact on cell differentiation, gene regulation and other key cellular processes. Here we present a genome-wide chromatin landscape for Drosophila melanogaster based on eighteen histone modifications, summarized by nine prevalent combinatorial patterns. Integrative analysis with other data (non-histone chromatin proteins, DNase I hypersensitivity, GRO-Seq reads produced by engaged polymerase, short/long RNA products) reveals discrete characteristics of chromosomes, genes, regulatory elements and other functional domains. We find that active genes display distinct chromatin signatures that are correlated with disparate gene lengths, exon patterns, regulatory functions and genomic contexts. We also demonstrate a diversity of signatures among Polycomb targets that include a subset with paused polymerase. This systematic profiling and integrative analysis of chromatin signatures provides insights into how genomic elements are regulated, and will serve as a resource for future experimental investigations of genome structure and function.
The 9-state model is based on a machine-learning approach which was used to identify the prevalent combinatorial patterns of 18 histone modifications across the genome. A simplified intensity-based model with nine states captures the overall complexity of chromatin patterns observed in S2 and BG3 cell lines, and we used this model to associate each genomic location with a particular combinatorial 'state', generating a chromatin-centric annotation of the genome (colour-coded as shown in the legend below).
|1||Active promoter/transcription start site region|
|2||Actively transcribed exon|
|3||Actively transcribed intron (enhancer)|
|4||Other open chromatin|
|5||Actively transcribed exon on the male X chromosome (dosage compensation)|
|6||Region of Polycomb-mediated repression|
|8||Heterochromatin-like region embedded in euchromatin|
|9||Transcriptionally silent intergenic euchromatin|
Kharchenko PV., et al.
Comprehensive analysis of the chromatin landscape in Drosophila melanogaster.
Nature Volume: 471, Pages: 480-485 (24 March 2011)