38

Noda Institute for Scientific Research GRANT
2012 Research Grant

Study of Aspergillus nucleosome positioning
Hiromi Nishida
Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University

Research aims
Eukaryotic genomic DNA is packaged with histones toform chromatin. The most fundamental repeating unit ofchromatin is the nucleosome. Nucleosome positioning is
not only related to genomic DNA compaction but also toother biological functions, such as gene transcription.
Nucleosome positioning differs even among phylogenetically close ascomycetous yeasts.1) To date, fungal nucleosome positioning data has been reported only for ascomycetous yeasts. Thus, we sequenced and mapped the pairends of nucleosomal DNA fragments of the filamentous
ascomycete Aspergillus fumigatus.2)
It has been reported that the GC content of the exons ishigher than that of the introns in the genes of Arabidopsis
thaliana, Homo sapiens, and Oryza sativa.3) In addition,
GC content and nucleosome positioning are related to thestructure of the exons and introns.4)
In this study, we mapped the Aspergillus nidulans and A.
oryzae nucleosomal DNA fragments and compared the nucleosome density in the exons and introns of their genes.
Methods
A. nidulans A4 and A. oryzae RIB40 were used in thisstudy. Micrococcal nuclease digestions were performed,
and the resulting cleavage products were analyzed using
agarose gel electrophoresis. The nucleosomal DNA fragments were excised from the gel. Both ends (each 101 bpFig. 1.

long) of the DNA fragments were sequenced using an Illumina GAIIx, and only the uniquely mapped read-pairs wereused in the subsequent analyses. The midpoint of the region
mapped in each nucleosomal DNA fragment was used as
the nucleosome position. In this study, nucleosome density
is defined as the number of the nucleosome positions perexon or intron.
Results
We examined the positions of 36,871,528 and
43,690,293 nucleosomes in the genomes of A. nidulans andA. oryzae, respectively. The means of the exon GC content
in the A. nidulans and A. oryzae genomes were 51.6%(sd=5.33) and 50.0% (sd=5.21), respectively. The means of
the intron GC content in the A. nidulans and A. oryzae genomes were 46.6% (sd=6.54) and 44.3% (sd=5.92), respectively. Figure 1 shows scatter plots of GC content vs.
nucleosome density for the protein-coding regions in thegenomes of A. nidulans and A. oryzae, comparing 9,616
orthologous genes from A. nidulans and A. oryzae. The
Spearman’s rank correlation coefficient was 0.084 for
A. nidulans and 0.15 for A. oryzae. Figure 2 shows scatterplots comparing the genomes of A. nidulans and A. oryzae
with respect to the GC content of protein-coding regions
and exon nucleosome density. The Spearman’s rank correlation coefficient was 0.51 for GC content and 0.31 fornucleosome density.

Scatter plots of the GC content vs. nucleosome density of protein-coding regions in orthologous genes of A. nidulans and A. oryzae.

		39Fig. 2.

Scatter plots of the GC content of protein-coding regions and the nucleosome density in exons in A. nidulans vs. those in A. oryzae.

Conclusion

References

The highest nucleosome density in the A. nidulans and A.
oryzae genomes was found to be in areas with a GC contentof 54%. The GC content and nucleosome density in exons
are higher than in introns. However, the conservation levelof the GC content is higher than that of the nucleosome
density in the exons, suggesting that the variation in the location of the nucleosome may be species-specific.

1) Tsankov, A. M., Thompson, D. A., Socha, A., Regev, A., and Rando,
O. J. (2010) The role of nucleosome positioning in the evolution ofgene regulation. PLOS Biol. 8: e1000414.
2) Nishida, H., Motoyama, T., Yamamoto, S., Aburatani, H., and Osada,
H. (2009) Genome-wide maps of mono- and di-nucleosomes ofAspergillus fumigatus. Bioinformatics 25: 2295–2297.
3) Yu, J. et al. (2002) A draft sequence of the rice genome (Oryzasativa L. ssp. indica). Science 296: 79–92.
4) Schwartz, S., Meshorer, E., and Ast, G. (2009) Chromatin organization marks exon-intron structure. Nat. Struct. Mol. Biol. 16: 990–995.
5) Nishida, H., Katayama, T., Suzuki, Y., Kondo, S., and Horiuchi, H.
(2013) Base composition and nucleosome density in exonic and intronic regions in genes of the filamentous ascomycetes Aspergillus
nidulans and Aspergillus oryzae. Gene 525: 5–10.