Comprehensive analysis of the chromatin landscape in Drosophila melanogaster.
Nature, 2011/3/24;471(7339):480-5.
Kharchenko PV[1], Alekseyenko AA, Schwartz YB, Minoda A, Riddle NC, Ernst J, Sabo PJ, Larschan E, Gorchakov AA, Gu T, Linder-Basso D, Plachetka A, Shanower G, Tolstorukov MY, Luquette LJ, Xi R, Jung YL, Park RW, Bishop EP, Canfield TK, Sandstrom R, Thurman RE, MacAlpine DM, Stamatoyannopoulos JA, Kellis M, Elgin SC, Kuroda MI, Pirrotta V, Karpen GH, Park PJ
Affiliations
PMID: 21179089DOI: 10.1038/nature09725
Impact factor: 69.504
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.
MeSH terms
Animals; Cell Line; Chromatin; Chromatin Immunoprecipitation; Chromosomal Proteins, Non-Histone; Deoxyribonuclease I; Drosophila Proteins; Drosophila melanogaster; 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
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