Genome-wide maps of nucleosomes of the trichostatin A treated and untreated archiascomycetous yeast <em>Saitoella complicata</em>

Kenta Yamauchi; Shinji Kondo; Makiko Hamamoto; Yutaka Suzuki; Hiromi Nishida; Kenta Yamauchi; Shinji Kondo; Makiko Hamamoto; Yutaka Suzuki; Hiromi Nishida

doi:10.3934/microbiol.2016.1.69

AIMS Microbiology

2016, Volume 2, Issue 1: 69-91. doi: 10.3934/microbiol.2016.1.69

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Genome-wide maps of nucleosomes of the trichostatin A treated and untreated archiascomycetous yeast Saitoella complicata

1.
Biotechnology Research Center and Department of Biotechnology, Toyama Prefectural University, Imizu, Toyama 939-0398, Japan
2.
National Institute of Polar Research, Tokyo, Japan
3.
Department of Life Sciences, School of Agriculture, Meiji University, Kanagawa, Japan
4.
Department of Medical Genome Sciences, Graduate School of Frontier Sciences, University of Tokyo, Kashiwa, Japan

Received: 28 January 2016 Accepted: 11 March 2016 Published: 15 March 2016

We investigated the effects of trichostatin A (TSA) on gene expression and nucleosome position in the archiascomycetous yeast Saitoella complicata. The expression levels of 154 genes increased in a TSA-concentration-dependent manner, while the levels of 131 genes decreased. Conserved genes between S. complicata and Schizosaccharomyces pombe were more commonly TSA-concentration-dependent downregulated genes than upregulated genes. We calculated the correlation coefficients of nucleosome position profiles within 300 nucleotides (nt) upstream of a translational start of S. complicata grown in the absence and the presence of TSA (3 μg/mL). We found that 20 (13.0%) of the 154 TSA-concentration-dependent upregulated genes and 22 (16.8%) of the 131 downregulated genes had different profiles (r < 0.4) between TSA-free and TSA-treated. Additionally, 59 (38.3%) of the 154 upregulated genes and 58 (44.3%) of the 131 downregulated genes had similar profiles (r > 0.8). We did not observe a GC content bias between the 300 nt upstream of the translational start of the TSA-concentration-dependent genes with conserved nucleosome positioning and the genes with different nucleosome positioning, suggesting that TSA-induced nucleosome position change is likely not related to DNA sequence. Most gene promoters maintained their nucleosome positioning even after TSA treatment, which may be related to DNA sequence. Enriched and depleted dinucleotides distribution of S. complicata around the midpoints of highly positioned nucleosome dyads was not similar to that of the phylogenetically close yeast Schizosaccharomyces pombe but similar to the basidiomycete Mixia osmundae, which has similar genomic GC content to that of S. complicata.
- archiascomycetes,
- histone acetylation,
- nucleosome position,
- Saitoella complicata,
- transcription,
- trichostatin A
Citation: Kenta Yamauchi, Shinji Kondo, Makiko Hamamoto, Yutaka Suzuki, Hiromi Nishida. Genome-wide maps of nucleosomes of the trichostatin A treated and untreated archiascomycetous yeast Saitoella complicata[J]. AIMS Microbiology, 2016, 2(1): 69-91. doi: 10.3934/microbiol.2016.1.69

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Abstract

We investigated the effects of trichostatin A (TSA) on gene expression and nucleosome position in the archiascomycetous yeast Saitoella complicata. The expression levels of 154 genes increased in a TSA-concentration-dependent manner, while the levels of 131 genes decreased. Conserved genes between S. complicata and Schizosaccharomyces pombe were more commonly TSA-concentration-dependent downregulated genes than upregulated genes. We calculated the correlation coefficients of nucleosome position profiles within 300 nucleotides (nt) upstream of a translational start of S. complicata grown in the absence and the presence of TSA (3 μg/mL). We found that 20 (13.0%) of the 154 TSA-concentration-dependent upregulated genes and 22 (16.8%) of the 131 downregulated genes had different profiles (r < 0.4) between TSA-free and TSA-treated. Additionally, 59 (38.3%) of the 154 upregulated genes and 58 (44.3%) of the 131 downregulated genes had similar profiles (r > 0.8). We did not observe a GC content bias between the 300 nt upstream of the translational start of the TSA-concentration-dependent genes with conserved nucleosome positioning and the genes with different nucleosome positioning, suggesting that TSA-induced nucleosome position change is likely not related to DNA sequence. Most gene promoters maintained their nucleosome positioning even after TSA treatment, which may be related to DNA sequence. Enriched and depleted dinucleotides distribution of S. complicata around the midpoints of highly positioned nucleosome dyads was not similar to that of the phylogenetically close yeast Schizosaccharomyces pombe but similar to the basidiomycete Mixia osmundae, which has similar genomic GC content to that of S. complicata.

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