1. Center for Gene Regulation, and,
2. Center for Comparative Genomics and Bioinformatics, Department of Biochemistry and Molecular Biology, The Pennsylvania State University, University Park, Pennsylvania 16802, USA
3. Department of Biomedical Informatics and Department of Molecular and Cellular Biochemistry, Davis Heart and Lung Research Institute, The Ohio State University, Columbus, Ohio 43210, USA
4. Berkeley Drosophila Transcription Network Project, Genomics Division, Lawrence Berkeley National Laboratory, One Cyclotron Road, Berkeley, California 94720, USA
5. Wadsworth Center, New York State Department of Health and Department of Biomedical Sciences, State University of New York, Albany, New York 12201-2002, USA
6. These authors contributed equally to this work.

Correspondence to: B. Franklin Pugh^1,2 Correspondence and requests for materials should be addressed to B.F.P. (Email: bfp2@psu.edu).

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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