title: Comprehensive analysis of the chromatin landscape in Drosophila melanogaster.
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.
authors.affiliation: Center for Biomedical Informatics, Harvard Medical School, Boston, Massachusetts 02115, USA.
authors.forename: Peter V
authors.initials: PV
authors.lastname: Kharchenko
authors.forename: Artyom A
authors.initials: AA
authors.lastname: Alekseyenko
authors.forename: Yuri B
authors.initials: YB
authors.lastname: Schwartz
authors.forename: Aki
authors.initials: A
authors.lastname: Minoda
authors.forename: Nicole C
authors.initials: NC
authors.lastname: Riddle
authors.forename: Jason
authors.initials: J
authors.lastname: Ernst
authors.forename: Peter J
authors.initials: PJ
authors.lastname: Sabo
authors.forename: Erica
authors.initials: E
authors.lastname: Larschan
authors.forename: Andrey A
authors.initials: AA
authors.lastname: Gorchakov
authors.forename: Tingting
authors.initials: T
authors.lastname: Gu
authors.forename: Daniela
authors.initials: D
authors.lastname: Linder-Basso
authors.forename: Annette
authors.initials: A
authors.lastname: Plachetka
authors.forename: Gregory
authors.initials: G
authors.lastname: Shanower
authors.forename: Michael Y
authors.initials: MY
authors.lastname: Tolstorukov
authors.forename: Lovelace J
authors.initials: LJ
authors.lastname: Luquette
authors.forename: Ruibin
authors.initials: R
authors.lastname: Xi
authors.forename: Youngsook L
authors.initials: YL
authors.lastname: Jung
authors.forename: Richard W
authors.initials: RW
authors.lastname: Park
authors.forename: Eric P
authors.initials: EP
authors.lastname: Bishop
authors.forename: Theresa K
authors.initials: TK
authors.lastname: Canfield
authors.forename: Richard
authors.initials: R
authors.lastname: Sandstrom
authors.forename: Robert E
authors.initials: RE
authors.lastname: Thurman
authors.forename: David M
authors.initials: DM
authors.lastname: MacAlpine
authors.forename: John A
authors.initials: JA
authors.lastname: Stamatoyannopoulos
authors.forename: Manolis
authors.initials: M
authors.lastname: Kellis
authors.forename: Sarah C R
authors.initials: SC
authors.lastname: Elgin
authors.forename: Mitzi I
authors.initials: MI
authors.lastname: Kuroda
authors.forename: Vincenzo
authors.initials: V
authors.lastname: Pirrotta
authors.forename: Gary H
authors.initials: GH
authors.lastname: Karpen
authors.forename: Peter J
authors.initials: PJ
authors.lastname: Park
mesh_terms: D000818:Animals; D002460:Cell Line; D002843:Chromatin / Q000235:genetics* / Q000378:metabolism*; D047369:Chromatin Immunoprecipitation; D002868:Chromosomal Proteins, Non-Histone / Q000032:analysis / Q000378:metabolism; D003850:Deoxyribonuclease I / Q000378:metabolism; D029721:Drosophila Proteins / Q000235:genetics; D004331:Drosophila melanogaster / Q000196:embryology / Q000235:genetics* / Q000254:growth & development; D005091:Exons / Q000235:genetics; D005786:Gene Expression Regulation / Q000235:genetics; D017344:Genes, Insect / Q000235:genetics; D049750:Genome, Insect / Q000235:genetics; D006657:Histones / Q000737:chemistry / Q000378:metabolism; D008297:Male; D058977:Molecular Sequence Annotation; D020411:Oligonucleotide Array Sequence Analysis; D063150:Polycomb Repressive Complex 1; D012313:RNA / Q000032:analysis / Q000235:genetics; D017421:Sequence Analysis; D014158:Transcription, Genetic / Q000235:genetics
chemical_list: D002843:Chromatin; D002868:Chromosomal Proteins, Non-Histone; D029721:Drosophila Proteins; D006657:Histones; C066770:Pc protein, Drosophila; D012313:RNA; D063150:Polycomb Repressive Complex 1; D003850:Deoxyribonuclease I