@article {152946, title = {Comprehensive analysis of the chromatin landscape in Drosophila melanogaster.}, journal = {Nature}, volume = {471}, number = {7339}, year = {2011}, month = {2011 Mar 24}, pages = {480-5}, abstract = { 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. }, keywords = {Animals, Cell Line, Chromatin, Chromatin Immunoprecipitation, Chromosomal Proteins, Non-Histone, Deoxyribonuclease I, Drosophila melanogaster, Drosophila Proteins, Exons, Gene Expression Regulation, Genes, Insect, Genome, Insect, Histones, Male, Molecular Sequence Annotation, Oligonucleotide Array Sequence Analysis, Polycomb Repressive Complex 1, RNA, Sequence Analysis, Transcription, Genetic}, issn = {1476-4687}, doi = {10.1038/nature09725}, author = {Kharchenko, Peter V and Alekseyenko, Artyom A and Schwartz, Yuri B and Minoda, Aki and Riddle, Nicole C and Ernst, Jason and Sabo, Peter J and Larschan, Erica and Gorchakov, Andrey A and Gu, Tingting and Linder-Basso, Daniela and Plachetka, Annette and Shanower, Gregory and Tolstorukov, Michael Y and Luquette, Lovelace J and Xi, Ruibin and Jung, Youngsook L and Park, Richard W and Bishop, Eric P and Canfield, Theresa K and Sandstrom, Richard and Thurman, Robert E and MacAlpine, David M and Stamatoyannopoulos, John A and Kellis, Manolis and Elgin, Sarah C R and Kuroda, Mitzi I and Pirrotta, Vincenzo and Karpen, Gary H** and Park, Peter J**} }