Details

Autor(en) / Beteiligte

• Karpen, Gary H
• Park, Peter J
• Kharchenko, Peter V
• Alekseyenko, Artyom A
• Schwartz, Yuri B
• Minoda, Aki
• Riddle, Nicole C
• Ernst, Jason
• Sabo, Peter J
• Larschan, Erica
• Gorchakov, Andrey A
• Gu, Tingting
• Linder-Basso, Daniela
• Plachetka, Annette
• Shanower, Gregory
• Tolstorukov, Michael Y
• Luquette, Lovelace J
• Xi, Ruibin
• Jung, Youngsook L
• Park, Richard W
• Bishop, Eric P
• Canfield, Theresa P
• Sandstrom, Richard
• Thurman, Robert E
• MacAlpine, David M
• Stamatoyannopoulos, John A
• Kellis, Manolis
• Elgin, Sarah C. R
• Kuroda, Mitzi I
• Pirrotta, Vincenzo

Titel

Comprehensive analysis of the chromatin landscape in Drosophila melanogaster

Ist Teil von

• Nature (London), 2011-03, Vol.471 (7339), p.480-485

Ort / Verlag

London: Nature Publishing Group UK

Erscheinungsjahr

2011

Quelle

EBSCOhost Psychology and Behavioral Sciences Collection

Beschreibungen/Notizen

• 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. Elements of gene function Three papers in this issue of Nature report on the modENCODE initiative, which aims to characterize functional DNA elements in the fruitfly Drosophila melanogaster and the roundworm Caenorhabditis elegans . Kharchenko et al . present a genome-wide chromatin landscape of the fruitfly, based on 18 histone modifications. They describe nine prevalent chromatin states. Integrating these analyses with other data types reveals individual characteristics of different genomic elements. Graveley et al . have used RNA-Seq, tiling microarrays and cDNA sequencing to explore the transcriptome in 30 distinct developmental stages of the fruitfly. Among the results are scores of new genes, coding and non-coding transcripts, as well as splicing and editing events. Finally, Nègre et al . have produced a map of the regulatory part of the fruitfly genome, defining a vast array of putative regulatory elements, such as enhancers, promoters, insulators and silencers. As part of the modENCODE initiative, which aims to characterize functional DNA elements in D. melanogaster and C. elegans , this study presents a genome-wide chromatin landscape of the fruitfly, based on 18 histone modifications. Nine prevalent chromatin states are described. Integrating these analyses with other data types reveals individual characteristics of different genomic elements. The work provides a resource of unprecedented scale for future experimental investigations.