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Bioinformatics Advance Access published online on July 1, 2009
Bioinformatics, doi:10.1093/bioinformatics/btp413
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© The Author (2009). Published by Oxford University Press. All rights reserved. For Permissions, please email: journals.permissions@oxfordjournals.org

Genome-wide maps of mono- and di-nucleosomes of Aspergillus fumigatus

Hiromi Nishida 1,*, Takayuki Motoyama 2, Shogo Yamamoto 3, Hiroyuki Aburatani 3 and Hiroyuki Osada 2

1 Agricultural Bioinformatics Research Unit, Graduate School of Agricultural and Life Sciences, University of Tokyo, Tokyo 113-8657, Japan
2 Antibiotics Laboratory, Advanced Science Institute, RIKEN, Wako, Saitama 351-0198, Japan
3 Research Center for Advance Science and Technology, University of Tokyo, Tokyo 153-8904, Japan

*To whom correspondence should be addressed. Dr. Hiromi Nishida, E-mail: hnishida{at}iu.a.u-tokyo.ac.jp


  Abstract

We identified 6 499 428 mono- and 7 545 410 di-nucleosome positions of the fungus Aspergillus fumigatus, which was detected at high resolution based on the DNA sequence data obtained from both mono- and dinucleosomal DNA fragments. We show that the distribution of lengths of the mononucleosomal DNA fragments has two peaks at 134 nt and 149 nt, whereas the distribution of di-nucleosomal DNA fragment lengths has a single peak at 285 nt. Although the gene bodies of the active and inactive genes and the inactive gene promoters had the two peaks of the mono-nucleosomal DNA fragment lengths, the active gene promoter lost the longer peak at 149-nt. Our findings strongly suggest that the nucleosomes protecting longer DNA fragments against MNase at the promoters, thereby inhibiting high gene expression.

Contact: hnishida{at}iu.a.u-tokyo.ac.jp

Supplementary information: Supplementary data are available at Bioinformatics online.

Associate Editor: Prof. Dmitrij Frishman

Received on April 30, 2009; revised on June 11, 2009; accepted on June 29, 2009

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