The DNA-encoded nucleosome organization of a eukaryotic genome

Noam Kaplan, Irene K. Moore, Yvonne Fondufe-Mittendorf, Andrea J. Gossett, Desiree Tillo, Yair Field, Emily M. LeProust, Timothy R. Hughes, Jason D. Lieb, Jonathan Widom, Eran Segal

Research output: Contribution to journalArticlepeer-review

944 Scopus citations

Abstract

Nucleosome organization is critical for gene regulation. In living cells this organization is determined by multiple factors, including the action of chromatin remodellers, 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 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, indicating that nucleosome depletion at these sites in vivo is partly 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 150-base-pair 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 Caenorhabditis elegans. Our results indicate that the intrinsic DNA sequence preferences of nucleosomes have a central role in determining the organization of nucleosomes in vivo.

Original languageEnglish
Pages (from-to)362-366
Number of pages5
JournalNature
Volume458
Issue number7236
DOIs
StatePublished - Mar 19 2009

Bibliographical note

Funding Information:
Acknowledgements We thank H. Kelkar for bioinformatics support in handling the sequencing files, P. Mieczkowski and J. McPherson for Illumina sequencing (library preparation and instrument operation), and the members of our respective laboratories for technical assistance, discussions and comments on the manuscript. The UNC sequencing facility is funded by the Lineberger Comprehensive Cancer Center and University Cancer Research Funds. J.W. acknowledges the use of instruments at Northwestern University’s Keck Biophysics Facility. This work was supported by a grant from CIHR to T.R.H. and C. Nislow, a grant from the NIH to J.D.L., a grant from the NIH to J.W., and grants from the European Research Council (ERC) and NIH to E.S. D.T. holds an NSERC postgraduate scholarship. N.K. is a Clore scholar. E.S. is the incumbent of the Soretta and Henry Shapiro career development chair.

ASJC Scopus subject areas

  • General

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