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The Scientific World Journal
Volume 2012 (2012), Article ID 298174, 26 pages
http://dx.doi.org/10.1100/2012/298174
Research Article

Conservation of Nucleosome Positions in Duplicated and Orthologous Gene Pairs

Agricultural Bioinformatics Research Unit, Graduate School of Agriculture and Life Sciences, The University of Tokyo, Bunkyo-ku, Tokyo 113-8657, Japan

Received 5 October 2011; Accepted 8 December 2011

Academic Editor: David E. Misek

Copyright © 2012 Hiromi Nishida. This is an open access article distributed under the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.

Abstract

Although nucleosome positions tend to be conserved in gene promoters, whether they are conserved in duplicated and orthologous genes is unknown. In order to elucidate how nucleosome positions are conserved between duplicated and orthologous gene pairs, I performed 2 comparative studies. First, I compared the nucleosome position profiles of duplicated genes in the filamentous ascomycete Aspergillus fumigatus. After identifying 63 duplicated gene pairs among 9630 protein-encoding genes, I compared the nucleosome position profiles of the paired genes. Although nucleosome positions are conserved more in gene promoters than in gene bodies, their profiles were diverse, suggesting evolutionary changes after gene duplication. Next, I examined the conservation of nucleosome position profiles in 347 A. fumigatus orthologs of S. cerevisiae genes that showed notably high conservation of nucleosome positions between the parent strain and 2 deletion mutants. In only 11 (3.2%) of the 347 gene pairs, the nucleosome position profile was highly conserved (Spearman’s rank correlation coefficient > 0.7). The absence of nucleosome position conservation in promoters of orthologous genes suggests organismal specificity of nucleosome arrangements.

1. Introduction

Nucleosomes are histone octamers around which DNA is wrapped in 1.65 turns [1]. Neighboring nucleosomes are separated by unwrapped linker DNA. Nucleosome density is lower, and nucleosome position is more conserved in the promoters than in the bodies of genes [25]. It is thought that nucleosome positioning in the gene promoter plays an important role in transcriptional regulation.

Although nucleosome positions can be partially simulated using a DNA-sequence-based approach [6], these simulations are limited due to variations between species. The nucleosome positioning mechanism varies between the 2 ascomycetous yeasts, Saccharomyces cerevisiae, and Schizosaccharomyces pombe [7]. Nucleosome positioning differs even among phylogenetically close ascomycetous yeast species [5].

Gene duplication is a driving force behind gene creation, and generating novel functions in newly created genes. Approximately one-half of cellular functions have been gained through gene duplication [8]. The duplicated genes encode similar amino acid sequences and often similar protein functions. It is uncertain, however, whether duplicated genes have similar nucleosome position profiles. In this study, I compared nucleosome positions in the promoter and body regions of duplicated gene pairs in the filamentous ascomycete Aspergillus fumigatus.

Previous analyses have found that nucleosome positions in A. fumigatus are conserved more in gene promoters than in gene bodies, even after treatment with the histone deacetylase inhibitor trichostatin A [4, 9]. In addition, nucleosome positions in S. cerevisiae are more conserved in gene promoters than in gene bodies between the control and the histone acetyltransferase gene ELP3 deletion mutant, and between the control and the histone deacetylase gene HOS2 deletion mutant [10]. The proteins Elp3 and Hos2 show the highest and the third highest evolutionary conservation, respectively, among the fungal histone modification proteins [11].

How well are nucleosome positions conserved in genes of the same origins? If there is a “nucleosome position code” that regulates nucleosome positioning, common nucleosome positions should remain in the promoters of orthologous genes across distinct species. In this study, I compared nucleosome positions in the promoters of duplicated and orthologous genes in A. fumigatus and S. cerevisiae.

2. Materials and Methods

2.1. Identification of Duplicated Gene Pairs in Aspergillus fumigates

Protein-coding gene pairs aligned over more than 80% of query length and more than 70% aminoacid sequence identity were selected by performing a BLAST search of 9630 A. fumigatus proteins at Fungal Genomes Central on NCBI (http://www.ncbi.nlm.nih.gov/projects/genome/guide/fungi/). Pairs in which the lengths differ by more than 25% were not used. Thus, we identified 63 duplicated A. fumigatus gene pairs (Tables 1 and 2).

tab1
Table 1: Duplicated gene pairs in Aspergillus fumigatus.
tab2
Table 2: Spearman's rank correlation coefficients of nucleosome position profiles in the promoter and body regions of 63 duplicated gene pairs in Aspergillus fumigatus.
2.2. Identification of Orthologous Gene Pairs in Aspergillus fumigates and Saccharomyces cerevisiae

In a comparison of nucleosome positioning between A. fumigatus and S. cerevisiae, I focused on 466 genes (Table 3) that showed notably high conservation of nucleosome positioning in the promoters of the control and the ELP3 and HOS2 deletion mutants from the previous study [10].

tab3
Table 3: Genes of Saccharomyces cerevisiae with highly conserved nucleosome positions in the promoters of the control and histone modification gene deletion mutants.

A total of 3339 ortholog clusters were identified (See table 1 in Supplementary Material available at doi: 10.1100/2012/298174) between A. fumigatus and S. cerevisiae by ortholog cluster analysis in the Microbial Genome Database for Comparative Analysis (MBGD, http://mbgd.nibb.ac.jp/) [12]. Of these orthologous gene pairs, 347 (Table 4) are yeast genes that showed a high level of nucleosome positioning conservation in the control and deletion mutants. I focused on these 347 orthologous pairs to compare nucleosome positioning between species. The same number of pairs of A. fumigatus and S. cerevisiae genes chosen at random were used as a control.

tab4
Table 4: Spearman's rank correlation coefficients between nucleosome position profiles in the promoters of 347 orthologous gene pairs between Aspergillus fumigatus and Saccharomyces cerevisiae.
2.3. Nucleosome Position Profile

Nucleosome mapping numbers at each genomic position were determined [13] based on genome-wide nucleosome mapping data for A. fumigatus [9] and S. cerevisiae [10]. In this analysis, a 1-kb region upstream of the translational start site was defined as a gene promoter. When the length of the gene body region is more than 1 kb, a 1-kb region downstream of the translational start site was defined as the gene body. When the length of the gene body is less than 1 kb, the region between the translational start and end sites was defined as the gene body. Analyses of nucleosome position data including calculation of Spearman’s rank correlation coefficient were performed using the statistics software R (http://www.r-project.org/).

3. Results and Discussion

3.1. Nucleosome Position Profiles of Duplicated Genes in Aspergillus fumigates

I compared nucleosome position profiles in each of the 63 duplicated gene pairs. Nucleosome positioning was conserved more in gene promoters than in gene bodies (Figure 1), as observed in the comparison of nucleosome positioning between trichostatin A-treated and -untreated A. fumigatus [4]. This result suggests that nucleosome positioning in the gene promoter plays an important role in transcriptional regulation [14].

298174.fig.001
Figure 1: Boxplots of Spearman’s rank correlation coefficients of nucleosome position profiles in the promoter and body regions of 63 duplicated gene pairs. Circles represent the correlation coefficients and values of the same genes are connected by lines.

Single-gene duplications and gene cluster duplications consisting of multiple genes were identified. One cluster of 4 genes (AFUA_1G00420 to AFUA_1G00470) is a duplication of another 4-gene cluster (AFUA_8G04120 to AFUA_8G04080) (Table 2). Among these gene pairs, the nucleosome position profile was poorly conserved in the gene promoter between AFUA_1G00470 and AFUA_8G04080 and in the gene body between AFUA_1G00440 and AFUA_8G04110 (Spearman’s rank correlation coefficients were 0.43 and 0.23, resp.) (Table 2). With the exception of these 2 cases, the nucleosome position profile was highly conserved (correlation coefficients were higher than 0.7) (Table 2).

We analyzed another pair of duplicated clusters (9 genes) (AFUA_1G16030 to AFUA_1G16120 and AFUA_5G14930 to AFUA_5G15030). The genes in each cluster have evolved for the same period after the duplication (Table 2). At present, conservation of the nucleosome position profiles varies among the 9 genes (Table 2). For example, the nucleosome position profile is poorly conserved in the gene promoters of 3 gene pairs (AFUA_1G16050 and AFUA_5G14950, AFUA_16110 and AFUA_15020, AFUA_1G16120 and AFUA_15030) (Spearman’s rank correlation coefficients are −0.35, −0.26, and −0.14, resp.). On the other hand, the nucleosome position profile is highly conserved in the promoters of AFUA_16070 and AFUA_5G14980 and was strongly correlated (correlation coefficient = 0.93). These results suggest that transcriptional regulation of duplicated genes is associated with nucleosome positions in the gene promoters.

3.2. Nucleosome Position Profiles of Orthologous Gene Promoters in Aspergillus fumigates and Saccharomyces cerevisiae

I compared the nucleosome position profiles in the promoters of 347 orthologous pairs of yeast genes that showed notably high conservation in the control and mutant strains. In the 63 duplicated A. fumigatus gene pairs, 13 (20.6%) gene promoter profiles and 11 (17.5%) gene body profiles were highly correlated (Spearman’s rank correlation coefficient > 0.7) (Table 1, Figure 1). On the other hand, of the 347 orthologous gene pairs, only 11 (3.2%) nucleosome position profiles were highly correlated (Spearman’s rank correlation coefficient > 0.7) (Table 4, Figure 2). The distribution of correlation coefficients of the 347 orthologous gene promoters did not significantly differ from that of the control (gene pairs chosen at random) ( 𝑃 -value = 0.28 Kolmogorov-Smirnov test). One potential cause of this low conservation is the large evolutionary distance between the 2 fungi. A. fumigatus and S. cerevisiae belong to the subphyla Pezizomycotina and Saccharomycotina, respectively. Alternatively, this low conservation may represent a difference in mechanisms regulating the nucleosome arrangement, since the nucleosomal (nucleosome-bound) DNA lengths differ between the 2 fungi [9, 10].

298174.fig.002
Figure 2: Boxplots of Spearman’s rank correlation coefficients between nucleosome position profiles in the promoters of 347 orthologous gene pairs between Aspergillus fumigatus and Saccharomyces cerevisiae. The same number of gene pairs was chosen at random to serve as a control. Dots indicate correlation coefficients. The distributions of correlation coefficients did not significantly differ ( 𝑃 -value = 0.28 in Kolmogorov-Smirnov test) between the orthologous gene promoters and the controls.

Nucleosome position profiles in gene promoters are thought to be related to gene function. For example, YIR038C of S. cerevisiae encodes an amino acid sequence protein (glutathione S-transferase) similar to 3 genes (AFUA_1G17010, AFUA_2G17300, and AFUA_8G02500) in A. fumigatus (Table 4). Although the nucleosome position profiles show some conservation between YIR038C and AFUA_8G02500 (Spearman’s rank correlation coefficient = 0.55, except for one nucleosome position loss in A. fumigatus), they are poorly conserved between YIR038C and AFUA_1G17010 (Spearman’s rank correlation coefficient = −0.03) and between YIR038C and AFUA_2G17300 (Spearman’s rank correlation coefficient = −0.07) (Table 4, Figure 3).

fig3
Figure 3: Mapping numbers of nucleosomes and transcription start sites in the promoter regions of YIR038C, AFUA_8G02500, AFUA_1G17010, and AFUA_2G17300. Position 0 indicates the translational start site.

Interestingly, although the nucleosome position profile of AFUA_8G02500 is completely different from that of AFUA_2G17300, the transcription start site patterns are very similar between these genes (Figure 3), suggesting that the relationship between transcription start site and nucleosome position in the gene promoter varies.

Acknowledgments

The author thanks Dr. Shinji Kondo for helpful comments and critical review of the paper. This study was supported in part by a grant from the Institute for Fermentation, Osaka (IFO), Japan.

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