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A genomic code for nucleosome
positioning
Eran Segal1,
Yvonne Fondufe-Mittendorf2, Lingyi
Chen2, AnnChristine Thåström2,
Yair Field1, Irene K. Moore2,
Ji-Ping Z. Wang3 and Jonathan
Widom2
(1)Department 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,
Illinois 60208, USA. (3)Department of Statistics, Northwestern
University, 2006 Sheridan Road, Evanston, Illinois 60208, USA.
Correspondence to: Eran Segal1 Jonathan
Widom2 Correspondence and requests for
materials should be addressed to E.S. (Email: eran.segal@weizmann.ac.il)
or J.W. (Email: j-widom@northwestern.edu).
Received 16 March 2006; Accepted 14 June 2006; Published online 19
July 2006.
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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.
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