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Bioinformatics Advance Access originally published online on July 1, 2009
Bioinformatics 2009 25(18):2295-2297; 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

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

*To whom correspondence should be addressed.


  Abstract

We identified 5 975 567 mono- and 6 995 122 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 di-nucleosomal DNA fragments. We show that the distribution of lengths of the mono-nucleosomal DNA fragments has two peaks at 135 and 150 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 150 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: Dmitrij Frishman

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

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