A genomic code for nucleosome positioning

Eran Segal (), Yvonne Fondufe-Mittendorf, Lingyi Chen, AnnChristine Thåström, Yair Field, Irene K. Moore, Ji-Ping Z. Wang and Jonathan Widom ()
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Eran Segal: Weizmann Institute of Science
Yvonne Fondufe-Mittendorf: Molecular Biology and Cell Biology, Northwestern University
Lingyi Chen: Molecular Biology and Cell Biology, Northwestern University
AnnChristine Thåström: Molecular Biology and Cell Biology, Northwestern University
Yair Field: Weizmann Institute of Science
Irene K. Moore: Molecular Biology and Cell Biology, Northwestern University
Ji-Ping Z. Wang: Northwestern University
Jonathan Widom: Molecular Biology and Cell Biology, Northwestern University

Nature, 2006, vol. 442, issue 7104, 772-778

Abstract: Abstract Eukaryotic genomes are packaged into nucleosome particles that occlude the DNA from interacting with most DNA binding proteins. Nucleosomes have higher affinity for particular DNA sequences, reflecting the ability of the sequence to bend sharply, as required by the nucleosome structure. However, it is not known whether these sequence preferences have a significant influence on nucleosome position in vivo, and thus regulate the access of other proteins to DNA. Here we isolated nucleosome-bound sequences at high resolution from yeast and used these sequences in a new computational approach to construct and validate experimentally a nucleosome–DNA interaction model, and to predict the genome-wide organization of nucleosomes. Our results demonstrate that genomes encode an intrinsic nucleosome organization and that this intrinsic organization can explain ∼50% of the in vivo nucleosome positions. This nucleosome positioning code may facilitate specific chromosome functions including transcription factor binding, transcription initiation, and even remodelling of the nucleosomes themselves.

Date: 2006
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DOI: 10.1038/nature04979

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