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The DNA-Encoded Nucleosome Organization of a Eukaryotic Genome

Noam Kaplan^1*, Irene Moore^2*, Yvonne Fondufe-Mittendorf², Andrea J. Gossett³, Desiree Tillo⁴, Yair Field¹, Emily M. LeProust⁵, Timothy R. Hughes^4,6,7,†, Jason D. Lieb^3,†, Jonathan Widom^2,†, Eran Segal^1,8,†

Nucleosome organization is critical for gene regulation. In living cells, this organization is determined by multiple factors, including the action of chromatin remodelers, competition with site-specific DNA-binding proteins, and the DNA sequence preferences of the nucleosomes themselves. However, it has been difficult to estimate the relative importance of each of these mechanisms in vivo, because in vivo nucleosome maps reflect the combined action of all influencing factors. Here, we determine the importance of nucleosome DNA sequence preferences experimentally by measuring the genome-wide occupancy of nucleosomes assembled on purified yeast genomic DNA. The resulting map, in which nucleosome occupancy is governed only by the intrinsic sequence preferences of nucleosomes, is remarkably similar to in vivo nucleosome maps generated in three different growth conditions. In vitro, nucleosome depletion is evident at many transcription factor binding sites and around gene start and end sites, suggesting that nucleosome depletion at these sites in vivo is partially encoded in the genome. We confirm these results with a micrococcal nuclease-independent experiment that measures the relative affinity of nucleosomes for ~40,000 double-stranded 150bp oligonucleotides. Using our in vitro data, we devise a computational model of nucleosome sequence preferences that is significantly correlated with in vivo nucleosome occupancy in C. elegans. Our results indicate that the intrinsic DNA sequence preferences of nucleosomes play a central role in determining the organization of nucleosomes in vivo.

Illustration: The intrinsic DNA-encoded nucleosome organization at a typical genomic region. Shown are the four different maps of nucleosome occupancy measured in this study for a typical 20,000bp-long genomic region: the in vitro map, which reflects only the intrinsic nucleosome sequence preferences, and in vivo maps for three different growth conditions, YPD, ethanol, and galactose. Each track plots the measured nucleosome occupancy per basepair, computed by summing all of the nucleosome reads obtained in that experiment, and dividing that number with the average number of reads per basepair across the genome. The line of Y=1 thus represents the genome-wide average and is shown as a dotted orange line. The average nucleosome occupancy predictions from our model are shown in blue.

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^* These authors contributed equally to this work.
^† Correspondence should be addressed to T.R.H. , J.D.L , J.W. or E.S.
¹ Dept. of Computer Science and Applied Mathematics, Weizmann Institute of Science, Rehovot 76100, Israel.
² Department of Biochemistry, Molecular Biology, and Cell Biology, Northwestern University, 2153 Sheridan Road, Evanston, IL 60208 USA.
³ Department of Biology, Carolina Center for Genome Sciences, and Lineberger Comprehensive Cancer Center, University of North Carolina at Chapel Hill, Chapel Hill, North Carolina 27599, USA.
⁴ Department of Molecular Genetics, University of Toronto, Toronto, Ontario M5S 1A8, Canada.
⁵ Agilent Technologies Inc., Genomics ? LSSU, 5301 Stevens Creek Blvd., MS 3L/MT Santa Clara, CA 95051, USA.
⁶ Terrence Donnelly Centre for Cellular & Biomolecular Research, 160 College Street, Toronto, Ontario M5S 3E1, Canada.
⁷ Banting and Best Department of Medical Research, 160 College St., Toronto, Ontario M5S 3E1, Canada.
⁸ Department of. Molecular Cell Biology, Weizmann Institute of Science, Rehovot, 76100, Israel.