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Nucleosome organization in the Drosophila genome

Abstract

Comparative genomics of nucleosome positions provides a powerful means for understanding how the organization of chromatin and the transcription machinery co-evolve. Here we produce a high-resolution reference map of H2A.Z and bulk nucleosome locations across the genome of the fly Drosophila melanogaster and compare it to that from the yeast Saccharomyces cerevisiae. Like Saccharomyces, Drosophila nucleosomes are organized around active transcription start sites in a canonical -1, nucleosome-free region, +1 arrangement. However, Drosophila does not incorporate H2A.Z into the -1 nucleosome and does not bury its transcriptional start site in the +1 nucleosome. At thousands of genes, RNA polymerase II engages the +1 nucleosome and pauses. How the transcription initiation machinery contends with the +1 nucleosome seems to be fundamentally different across major eukaryotic lines.

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Figure 1: H2A.Z nucleosomal organization around the 5′ end of Drosophila genes.
Figure 2: Organization of conserved DNA motifs around TSSs (left) and nucleosomes (right).
Figure 3: Positioning properties of Drosophila nucleosomes and DNA.
Figure 4: H2A.Z nucleosomal organization around the 3′ end of Drosophila genes.
Figure 5: Distribution of Pol II and Pol II-engaged nucleosomes around the 5′ end of genes.

Accession codes

Primary accessions

ArrayExpress

Data deposits

Sequence data are deposited in the NCBI Trace Archives TI SRA000283 under the Sequencing Center designation ‘CCGB’, and microarray data are deposited in the ArrayExpress under accession numbers E-MEXP-1515, E-MEXP-1519 and E-MEXP-1520.

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Acknowledgements

This work was supported by grants HG004160 (B.F.P.) and GM47477 (D.S.G.). We thank M. Biggin for early access to the Pol II chromatin immunoprecipitation (ChIP)–chip data, R. Fan for supplying the antibody raised against the Drosophila Pol II subunit Rpb3, and C. Lee for help in identifying paused Pol II.

Author Contributions T.N.M. prepared and purified the nucleosomes including Pol II-bound nucleosomes; C.J. analysed the nucleosome-mapping data and its relationship to other genomic features; I.P.I. performed computational analyses related to nucleosome-positioning sequences; X.L. conducted ChIP–chip on Pol II; B.J.V. conducted ChIP–chip and analysis on GAF; S.J.Z. provided bioinformatics support; L.P.T. constructed libraries and sequenced nucleosomal DNA; J.Q. mapped sequencing reads to the yeast genome; R.L.G. provided H2A.Z antibodies; S.C.S. directed the DNA-sequencing phase; D.S.G. directed embryo preparations and helped to interpret the data; I.A. developed computational approaches to derive nucleosome maps from the read locations and developed the associated browser; and B.F.P. directed the project, interpreted the data and wrote the paper.

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Correspondence to B. Franklin Pugh.

Supplementary information

Supplementary information

The file contains Supplementary Figures 1-19 with Legends. (PDF 3877 kb)

Supplementary information

The file contains Supplementary Table S1 including H2A.Z nucleosome consensus start and end points, peak height, read counts, and standard deviation of read distribution. (TXT 40634 kb)

Supplementary information

The file contains Supplementary Table S2 - TAB file containing all gene lists used in this study. (DOC 954 kb)

Supplementary information

The file contains Supplementary Table S3 - TAB file containing the genomic coordinates of all GAGA motifs. (DOC 4329 kb)

Supplementary information

The file contains Supplementary Table S4 - XLS file containing the plotted data for Fig. 2 (XLS 3111 kb)

Supplementary information

The file contains Supplementary Table S5 - TAB file containing the start and end coordinates of bulk nucleosomes. (DOC 9676 kb)

Supplementary information

The file contains Supplementary Table S6 - TXT file containing the start and end coordinates of Pol II peaks. (TXT 21615 kb)

Supplementary information

The file contains Supplementary Table S7 - TAB file containing the start and end coordinates of Pol II bound nucleosomes. (DOC 1936 kb)

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Mavrich, T., Jiang, C., Ioshikhes, I. et al. Nucleosome organization in the Drosophila genome. Nature 453, 358–362 (2008). https://doi.org/10.1038/nature06929

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