Conservation of nucleosome positions in duplicated and orthologous gene pairs.

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 [2-5]. 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).

Table 1

Duplicated gene pairs in Aspergillus fumigatus.

Gene pair	Chromosome	Gene body region		Gene direction	Function
AFUA1G00150	1	25442	27017	+	RING finger protein
AFUA6G09370	6	2245549	2247121	+	RING finger protein
AFUA1G00420	1	135528	137781	+	Carboxypeptidase S1, putative
AFUA8G04120	8	897824	900076	−	Carboxypeptidase S1, putative
AFUA1G00440	1	138359	140093	−	DUF895 domain membrane protein
AFUA8G04110	8	895512	897246	+	DUF895 domain membrane protein
AFUA1G00450	1	143117	144466	+	N-acetylglucosamine-6-phosphate deacetylase(NagA), putative
AFUA8G04100	8	891135	892484	−	N-acetylglucosamine-6-phosphate deacetylase(NagA), putative
AFUA1G00470	1	148615	150219	+	Betaine aldehyde dehydrogenase, putative
AFUA8G04080	8	885376	886980	−	Betaine aldehyde dehydrogenase (BadH), putative
AFUA1G00530	1	164101	164771	−	Thermoresistant gluconokinase family protein
AFUA4G12050	4	3163747	3164530	−	Thermoresistant gluconokinase
AFUA1G00550	1	177114	178593	+	Hypothetical protein
AFUA1G00910	1	328785	330274	+	Hypothetical protein
AFUA1G00580	1	184790	186873	+	Acid phosphatase (PhoG), putative
AFUA8G04050	8	870757	872487	−	Acid phosphatase (PhoG), putative
AFUA1G00650	1	215584	217006	+	Alpha-1,3-glucanase, putative
AFUA7G08510	7	1973398	1974759	+	Alpha-1,3-glucanase, putative
AFUA1G00920	1	331676	332955	−	Hypothetical protein
AFUA3G06425	3	1582748	1584037	−	Hypothetical protein
AFUA1G01050	1	385302	386244	−	Hypothetical protein
AFUA8G06160	8	1465695	1466634	+	Hypothetical protein
AFUA1G02550	1	744583	746335	−	Tubulin alpha-1 subunit
AFUA2G14990	2	3947008	3948834	−	Tubulin alpha-2 subunit
AFUA1G02730	1	788249	789373	−	Mitochondrial phosphate carrier protein (Ptp), putative
AFUA1G15140	1	4070230	4071449	−	Mitochondrial phosphate carrier protein (Mir1), putative
AFUA1G05760	1	1658382	1659697	−	Arsenite efflux transporter
AFUA5G15010	5	3882425	3883746	+	Arsenite permease (ArsB), putative
AFUA1G05760	1	1658382	1659697	−	Arsenite efflux transporter
AFUA1G16100	1	4378898	4380216	+	Arsenite permease (ArsB), putative
AFUA1G10910	1	2848155	2850137	−	Tubulin beta, putative
AFUA7G00250	7	70221	71948	+	Tubulin beta-2 subunit
AFUA1G11260	1	2971529	2971889	−	Conserved hypothetical protein
AFUA6G00270	6	79542	79886	−	Conserved hypothetical protein
AFUA1G11610	1	3060058	3060510	+	3-Dehydroquinate dehydratase, type II
AFUA3G14850	3	3929721	3930173	+	3-Dehydroquinate dehydratase, type II
AFUA1G11890	1	3129447	3131489	+	Serine palmitoyltransferase 2, putative
AFUA6G00300	6	85851	87692	−	Serine palmitoyltransferase 1, putative
AFUA1G12850	1	3398837	3400611	+	Nitrate transporter (nitrate permease)
AFUA1G17470	1	4782320	4783995	+	High-affinity nitrate transporter NrtB
AFUA1G15970	1	4338407	4339712	+	Aldo-keto reductase (AKR13), putative
AFUA8G01560	8	401581	402815	−	Aldo-keto reductase (YakC), putative
AFUA1G16030	1	4358866	4360256	−	Conserved hypothetical protein
AFUA5G14930	5	3863218	3864521	−	Conserved hypothetical protein
AFUA1G16040	1	4363493	4365310	+	Metalloreductase, putative
AFUA5G14940	5	3867797	3869542	+	Cell surface metalloreductase (FreA), putative
AFUA1G16050	1	4366573	4368232	+	Hypothetical protein
AFUA5G14950	5	3870635	3872465	+	Hypothetical protein
AFUA1G16070	1	4370346	4373694	+	Conserved hypothetical protein
AFUA5G14980	5	3874539	3877890	+	Conserved hypothetical protein
AFUA1G16080	1	4374579	4375298	−	Hypothetical protein
AFUA5G14990	5	3878797	3879579	−	Hypothetical protein
AFUA1G16090	1	4377842	4378249	−	Arsenate reductase (ArsC), putative
AFUA5G15000	5	3881386	3881835	−	Arsenate reductase (ArsC), putative
AFUA1G16100	1	4378898	4380216	+	Arsenite permease (ArsB), putative
AFUA5G15010	5	3882425	3883746	+	Arsenite permease (ArsB), putative
AFUA1G16110	1	4380474	4381455	−	Arsenic methyltransferase (Cyt19), putative
AFUA5G15020	5	3883929	3884993	−	Arsenic methyltransferase (Cyt19), putative
AFUA1G16120	1	4385650	4386671	−	Arsenic resistance protein (ArsH), putative
AFUA8G07150	8	1751693	1752688	+	ArsH protein
AFUA1G16120	1	4385650	4386671	−	Arsenic resistance protein (ArsH), putative
AFUA5G15030	5	3887287	3888230	−	Arsenic resistance protein (ArsH), putative
AFUA2G00800	2	178081	179459	−	PelA protein
AFUA5G10380	5	2658656	2659968	+	Pectin lyase, putative
AFUA2G00800	2	178081	179459	−	PelA protein
AFUA7G05030	7	1182104	1183794	−	Pectin lyase B
AFUA2G04010	2	1092973	1094679	−	Alpha, alpha-trehalose-phosphate synthase subunit, putative
AFUA6G12950	6	3268958	3270783	+	Alpha, alpha-trehalose-phosphate Synthase subunitTPS1, putative
AFUA2G11270	2	2897275	2904954	−	Alpha-1,3-glucan synthase, putative
AFUA3G00910	3	210186	217666	+	Alpha-1,3-glucan synthase, putative
AFUA3G00340	3	71186	72734	+	Glycosyl hydrolase, putative
AFUA4G02720	4	751306	752715	−	Glycosyl hydrolase, putative
AFUA3G00680	3	151397	153549	−	Copper amine oxidase
AFUA7G04180	7	943893	946136	+	Amine oxidase
AFUA3G01560	3	393032	394802	−	Aminoacid permease, putative
AFUA5G04260	5	1140953	1142714	+	Arginine transporter, putative
AFUA3G02420	3	597476	598286	+	ThiJ/PfpI family protein
AFUA4G01400	4	369123	369944	−	ThiJ/PfpI family protein
AFUA3G03080	3	824479	825425	+	Endo-1,3(4)-beta-glucanase, putative
AFUA6G14540	6	3702416	3703383	−	Endo-1,3(4)-beta-glucanase, putative
AFUA3G03980	3	1134609	1136404	+	Cytochrome P450 monooxygenase, putative
AFUA5G10050	5	2589301	2591081	−	Cytochrome P450 monooxygenase, putative
AFUA3G08160	3	2094223	2095759	−	Eukaryotic translation initiation Factor eIF4A, putative
AFUA5G02410	5	621886	623486	−	DEAD/DEAH box helicase, putative
AFUA3G14420	3	3831868	3834921	+	Chitin synthase G
AFUA5G00760	5	211013	213795	+	Chitin synthase C
AFUA4G00510	4	133477	135102	−	Hypothetical protein
AFUA7G08600	7	2009436	2011052	+	Hypothetical protein
AFUA4G03110	4	868474	870249	−	Monosaccharide transporter
AFUA5G10690	5	2737348	2739178	−	Monosaccharide transporter
AFUA4G03680	4	1031586	1032539	−	Oxidoreductase, short-chain dehydrogenase/reductase family
AFUA6G03520	6	764308	765294	−	Short-chain dehydrogenase/reductase family protein, putative
AFUA4G09440	4	2462920	2466158	−	Sodium P-type ATPase, putative
AFUA6G03690	6	810027	813362	−	Sodium transport ATPase, putative
AFUA4G14360	4	3774307	3776166	+	Capsular associated protein, putative
AFUA5G07560	5	1889791	1891689	−	Capsular associated protein, putative
AFUA5G00145	5	15749	16327	−	Hypothetical protein
AFUA6G11710	6	2915903	2916483	+	Conserved hypothetical protein
AFUA5G00145	5	15749	16327	−	Hypothetical protein
AFUA7G08440	7	1942319	1942804	+	Hypothetical protein
AFUA5G01030	5	266294	267439	−	Glyceraldehyde 3-phosphate dehydrogenase(Ccg-7), putative
AFUA5G01970	5	503797	505194	+	Glyceraldehyde 3-phosphate dehydrogenase GpdA
AFUA5G06240	5	1494455	1495619	−	Alcohol dehydrogenase, putative
AFUA7G01010	7	270494	271675	−	Alcohol dehydrogenase, putative
AFUA5G07980	5	2019069	2020841	+	Hypothetical protein
AFUA5G14920	5	3857350	3859167	+	Hypothetical protein
AFUA5G09130	5	2345689	2346728	−	Polysaccharide deacetylase family protein
AFUA6G05030	6	1195846	1196956	+	Polysaccharide deacetylase family protein
AFUA5G15030	5	3887287	3888230	−	Arsenic resistance protein (ArsH), putative
AFUA8G07150	8	1751693	1752688	+	ArsH protein
AFUA6G06750	6	1475239	1476209	+	14-3-3 family protein
AFUA2G03290	2	867203	868250	−	14-3-3 family protein ArtA, putative
AFUA6G07070	6	1587643	1589124	+	Cellobiohydrolase D
AFUA6G11610	6	2878078	2879676	−	1,4-beta-D-glucan-cellobiohydrolyase, putative
AFUA6G11430	6	2837140	2839051	+	Aldehyde dehydrogenase, putative
AFUA7G01000	7	267518	269163	−	Aldehyde dehydrogenase, putative
AFUA6G11710	6	2915903	2916483	+	Conserved hypothetical protein
AFUA7G08440	7	1942319	1942804	+	Hypothetical protein
AFUA6G13490	6	3431912	3433612	−	Glutamate decarboxylase
AFUA8G06020	8	1428812	1430515	+	Glutamate decarboxylase
AFUA7G00360	7	102030	103064	−	UDP-galactose 4-epimerase, putative
AFUA8G00860	8	203496	204338	+	UDP-galactose 4-epimerase, putative
AFUA7G07050	7	1725686	1726402	−	Hypothetical protein
AFUA7G08300	7	1870244	1870960	−	Hypothetical protein
AFUA7G07060	7	1728876	1732992	−	Hypothetical protein
AFUA7G08310	7	1873437	1877817	−	Hypothetical protein

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.

Gene pair		Gene promoter	Gene body
AFUA1G00150	AFUA6G09370	0.750176913	0.215204254
AFUA1G00420	AFUA8G04120	0.80370974	0.723149072
AFUA1G00440	AFUA8G04110	0.856048561	0.225149091
AFUA1G00450	AFUA8G04100	0.9213602	0.94633912
AFUA1G00470	AFUA8G04080	0.433118045	0.818800395
AFUA1G00530	AFUA4G12050	0.326735006	−0.199291887
AFUA1G00550	AFUA1G00910	0.676910334	0.678763937
AFUA1G00580	AFUA8G04050	0.305291793	0.312927993
AFUA1G00650	AFUA7G08510	0.448171525	0.085599209
AFUA1G00920	AFUA3G06425	0.719748778	−0.340001527
AFUA1G01050	AFUA8G06160	0.635149308	0.176679577
AFUA1G02550	AFUA2G14990	0.139079116	−0.036644732
AFUA1G02730	AFUA1G15140	0.452193259	0.067186644
AFUA1G05760	AFUA5G15010	0.395849711	0.117006666
AFUA1G05760	AFUA1G16100	0.127911436	−0.397363108
AFUA1G10910	AFUA7G00250	0.310718577	0.665906466
AFUA1G11260	AFUA6G00270	0.617303556	−0.02397179
AFUA1G11610	AFUA3G14850	0.636281069	0.869300724
AFUA1G11890	AFUA6G00300	0.254487564	0.429087849
AFUA1G12850	AFUA1G17470	0.644447287	0.008468365
AFUA1G15970	AFUA8G01560	0.373850536	−0.106800689
AFUA1G16030	AFUA5G14930	0.618349765	0.858488283
AFUA1G16040	AFUA5G14940	0.481054005	0.017330056
AFUA1G16050	AFUA5G14950	−0.345037268	−0.392132138
AFUA1G16070	AFUA5G14980	0.930922124	0.902581516
AFUA1G16080	AFUA5G14990	0.559980787	0.136819379
AFUA1G16090	AFUA5G15000	0.773867924	0.338119153
AFUA1G16100	AFUA5G15010	0.681170098	0.70434823
AFUA1G16110	AFUA5G15020	−0.261864905	0.632982505
AFUA1G16120	AFUA8G07150	0.356869915	0.074502754
AFUA1G16120	AFUA5G15030	−0.135442129	−0.239074416
AFUA2G00800	AFUA5G10380	0.352063916	0.460712971
AFUA2G00800	AFUA7G05030	−0.114184443	0.457081245
AFUA2G04010	AFUA6G12950	0.134790545	−0.14813806
AFUA2G11270	AFUA3G00910	−0.004207858	0.192024608
AFUA3G00340	AFUA4G02720	−0.050259987	0.055757479
AFUA3G00680	AFUA7G04180	0.399912713	−0.044615588
AFUA3G01560	AFUA5G04260	0.179395067	0.125177632
AFUA3G02420	AFUA4G01400	0.662712481	0.646400554
AFUA3G03080	AFUA6G14540	0.3401707	−0.021961056
AFUA3G03980	AFUA5G10050	0.486726534	0.318475376
AFUA3G08160	AFUA5G02410	0.309645464	−0.255654021
AFUA3G14420	AFUA5G00760	0.917685134	0.415111431
AFUA4G00510	AFUA7G08600	0.578582743	0.441363777
AFUA4G03110	AFUA5G10690	0.721540193	0.176996881
AFUA4G03680	AFUA6G03520	0.662657833	−0.320417166
AFUA4G09440	AFUA6G03690	0.204159184	0.000609208
AFUA4G14360	AFUA5G07560	0.038083073	0.515103795
AFUA5G00145	AFUA6G11710	0.809402393	−0.741045496
AFUA5G00145	AFUA7G08440	0.019652845	−0.575600966
AFUA5G01030	AFUA5G01970	0.576211178	0.132479521
AFUA5G06240	AFUA7G01010	0.163674862	−0.552899419
AFUA5G07980	AFUA5G14920	0.669562689	−0.265207346
AFUA5G09130	AFUA6G05030	0.092452938	0.729278817
AFUA5G15030	AFUA8G07150	0.337482368	−0.502391454
AFUA6G06750	AFUA2G03290	0.333402926	−0.538389013
AFUA6G07070	AFUA6G11610	−0.048961745	−0.239430043
AFUA6G11430	AFUA7G01000	0.0145492	0.476692417
AFUA6G11710	AFUA7G08440	0.243362623	0.823124582
AFUA6G13490	AFUA8G06020	0.768186533	0.174847009
AFUA7G00360	AFUA8G00860	−0.115050268	0.03815086
AFUA7G07050	AFUA7G08300	0.70756842	0.778653567
AFUA7G07060	AFUA7G08310	0.906852725	0.919839072

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].

Table 3

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

Chromosome	Gene	Correlation coefficient between the control and the ELP3 deletion	Correlation coefficient between the control and the HOS2 deletion	Translational start site	Transcription direction
chr01	YAL064W-B	0.974719955	0.965814243	12047	+
chr01	YAL056W	0.989801003	0.982157328	39260	+
chr01	YAL047C	0.950243691	0.953129232	56858	−
chr01	YAR019C	0.970115162	0.960628643	175133	−
chr01	YAR033W	0.968807875	0.987221166	188101	+
chr02	YBL111C	0.995802065	0.99455065	5009	−
chr02	YBL108C-A	0.959497013	0.969966542	7733	−
chr02	YBL101C	0.958517125	0.991324096	28299	−
chr02	YBL087C	0.95719187	0.957273203	60735	−
chr02	YBL061C	0.984960212	0.992728731	107408	−
chr02	YBL060W	0.960330289	0.99357258	107934	+
chr02	YBL051C	0.97653734	0.989165943	124762	−
chr02	YBL032W	0.956874854	0.980366627	160187	+
chr02	YBL005W-B	0.950781322	0.952679326	221333	+
chr02	YBL005W-A	0.950781322	0.952679326	221333	+
chr02	YBR023C	0.960238499	0.992906362	287925	−
chr02	YBR029C	0.959231389	0.987222377	297742	−
chr02	YBR047W	0.964564522	0.963289004	331831	+
chr02	YBR060C	0.959229871	0.974718825	362512	−
chr02	YBR084W	0.962172866	0.981530879	411048	+
chr02	YBR090C	0.967658785	0.971792497	427052	−
chr02	YBR091C	0.965037862	0.985960321	427478	−
chr02	YBR131W	0.953323249	0.969685452	497157	+
chr02	YBR136W	0.963546822	0.974854426	505662	+
chr02	YBR173C	0.978518391	0.961438459	582167	−
chr02	YBR179C	0.988489146	0.991754907	589109	−
chr02	YBR180W	0.987132212	0.975974209	589736	+
chr02	YBR204C	0.970958946	0.978433534	633376	−
chr02	YBR243C	0.972253467	0.961252065	706788	−
chr02	YBR244W	0.974202306	0.992702483	707523	+
chr02	YBR249C	0.955742682	0.976101912	717989	−
chr02	YBR250W	0.954149188	0.976352348	719028	+
chr02	YBR251W	0.96273261	0.961120273	721385	+
chr02	YBR258C	0.966601899	0.955155711	730157	−
chr02	YBR260C	0.969346019	0.970918059	734634	−
chr02	YBR279W	0.956081387	0.964626558	761253	+
chr02	YBR290W	0.981586823	0.967935658	782587	+
chr03	YCL064C	0.957150698	0.95270514	16880	−
chr03	YCL058W-A	0.969895345	0.992394829	23584	+
chr03	YCL057C-A	0.990886192	0.987170576	24325	−
chr03	YCL057W	0.963062357	0.961804623	24768	+
chr03	YCL038C	0.978210537	0.957633548	56527	−
chr03	YCL035C	0.981360705	0.973568151	61173	−
chr03	YCL019W	0.953241664	0.978688459	85102	+
chr03	YCR026C	0.96886665	0.97932414	166335	−
chr03	YCR043C	0.951764864	0.966166673	206640	−
chr03	YCR053W	0.989728241	0.992623598	216693	+
chr03	YCR087C-A	0.975398919	0.993232435	264464	−
chr03	YCR090C	0.965637294	0.95018878	272860	−
chr03	YCR108C	0.985803086	0.993860549	316185	−
chr04	YDL248W	0.964701365	0.980217326	1802	+
chr04	YDL247W	0.989686199	0.997997741	5985	+
chr04	YDL233W	0.957672252	0.97857489	36798	+
chr04	YDL232W	0.979592686	0.970413477	38488	+
chr04	YDL225W	0.950053133	0.978441348	52446	+
chr04	YDL208W	0.987264893	0.987894794	87513	+
chr04	YDL189W	0.965815356	0.98561241	122217	+
chr04	YDL174C	0.956215571	0.953787348	147590	−
chr04	YDL147W	0.971755059	0.950911485	190925	+
chr04	YDL116W	0.965936123	0.976379579	251566	+
chr04	YDL110C	0.974238254	0.97295169	264964	−
chr04	YDL102W	0.957786538	0.980122821	276872	+
chr04	YDL085W	0.97887937	0.960150217	303211	+
chr04	YDL035C	0.975573212	0.977145228	392054	−
chr04	YDL025C	0.96134673	0.972526893	407203	−
chr04	YDR019C	0.95269772	0.953635877	485362	−
chr04	YDR028C	0.960937436	0.959981321	500876	−
chr04	YDR034C-C	0.967222636	0.9814374	519353	−
chr04	YDR034C-D	0.967222636	0.981437429	519353	−
chr04	YDR037W	0.951365292	0.956861294	525437	+
chr04	YDR054C	0.955928802	0.982048103	562325	−
chr04	YDR055W	0.950321012	0.952540035	563525	+
chr04	YDR062W	0.974021833	0.967688258	576471	+
chr04	YDR109C	0.954396163	0.952291074	675664	−
chr04	YDR110W	0.986081905	0.974555387	676099	+
chr04	YDR120C	0.960200845	0.969981962	693258	−
chr04	YDR162C	0.967301741	0.984347121	781097	−
chr04	YDR233C	0.967024058	0.967951444	930353	−
chr04	YDR234W	0.967415159	0.980945022	931125	+
chr04	YDR238C	0.97602642	0.973622232	940812	−
chr04	YDR261C-D	0.984848646	0.993722663	992345	−
chr04	YDR261C-C	0.984848646	0.9937227	992345	−
chr04	YDR262W	0.990989397	0.995915841	993130	+
chr04	YDR270W	0.951139826	0.96263534	1005671	+
chr04	YDR281C	0.984619329	0.959392909	1022317	−
chr04	YDR300C	0.975849644	0.971677938	1062787	−
chr04	YDR301W	0.952923341	0.977515222	1063348	+
chr04	YDR307W	0.951918886	0.970033626	1075861	+
chr04	YDR310C	0.951723931	0.969273153	1084312	−
chr04	YDR311W	0.953685357	0.980595738	1085062	+
chr04	YDR317W	0.98969221	0.991598049	1102181	+
chr04	YDR322W	0.954843272	0.97204312	1110586	+
chr04	YDR328C	0.957421993	0.983957835	1126013	−
chr04	YDR334W	0.953030288	0.963155512	1135927	+
chr04	YDR359C	0.977489172	0.969606029	1194877	−
chr04	YDR365C	0.985073544	0.998926611	1206375	−
chr04	YDR367W	0.990041805	0.994689201	1212840	+
chr04	YDR369C	0.957655919	0.96987305	1217572	−
chr04	YDR379W	0.962899057	0.974939821	1230159	+
chr04	YDR397C	0.966298918	0.975133337	1266890	−
chr04	YDR420W	0.971217177	0.991886941	1306259	+
chr04	YDR424C	0.966881808	0.989813233	1319833	−
chr04	YDR432W	0.955728738	0.982171718	1328775	+
chr04	YDR438W	0.971626925	0.98904082	1338266	+
chr04	YDR444W	0.973566433	0.976502447	1350282	+
chr04	YDR453C	0.952661492	0.954481014	1365654	−
chr04	YDR476C	0.969940159	0.964679279	1411119	−
chr04	YDR477W	0.954743343	0.979243738	1412365	+
chr04	YDR479C	0.977460825	0.994501786	1416866	−
chr04	YDR480W	0.967727074	0.986953403	1417391	+
chr04	YDR488C	0.983114512	0.979187155	1430781	−
chr04	YDR497C	0.955855412	0.958236577	1445459	−
chr04	YDR529C	0.966273576	0.971812076	1496540	−
chr05	YEL072W	0.968131913	0.977435534	13720	+
chr05	YEL043W	0.979079858	0.96227706	70478	+
chr05	YEL038W	0.981572221	0.988369151	80462	+
chr05	YEL021W	0.951315475	0.951565922	116167	+
chr05	YER004W	0.956348638	0.987671859	159579	+
chr05	YER026C	0.964952897	0.993875293	208473	−
chr05	YER076C	0.965398244	0.971982059	313494	−
chr05	YER083C	0.953185048	0.981521771	327027	−
chr05	YER094C	0.976027049	0.982595427	349342	−
chr05	YER095W	0.963423619	0.988752501	349976	+
chr05	YER107C	0.982024941	0.98488468	374541	−
chr05	YER109C	0.969371754	0.986034001	377610	−
chr05	YER173W	0.960496827	0.952930419	536295	+
chr05	YER188C-A	0.991489293	0.996538184	569902	−
chr05	YER189W	0.997057108	0.998333831	571150	+
chr06	YFL066C	0.970012372	0.993098415	2615	−
chr06	YFL065C	0.957034943	0.97004682	3338	−
chr06	YFL060C	0.987757312	0.995138274	10969	−
chr06	YFL059W	0.976205235	0.962195117	11363	+
chr06	YFL058W	0.9750941	0.994474768	12929	+
chr06	YFL028C	0.966244522	0.959308346	80211	−
chr06	YFL026W	0.957755207	0.952711873	82578	+
chr06	YFR009W	0.979200258	0.985708335	162482	+
chr06	YFR013W	0.972958971	0.986214291	169914	+
chr06	YFR037C	0.965415915	0.972070667	229173	−
chr07	YGL255W	0.961366208	0.972062316	20978	+
chr07	YGL248W	0.971369747	0.971756841	35653	+
chr07	YGL223C	0.956215218	0.984994924	80364	−
chr07	YGL215W	0.965861339	0.95181154	87980	+
chr07	YGL201C	0.954296336	0.979120204	120911	−
chr07	YGL180W	0.982084299	0.994334205	160071	+
chr07	YGL171W	0.969321982	0.974163208	182396	+
chr07	YGL163C	0.975825825	0.968348392	196409	−
chr07	YGL138C	0.971247145	0.983410766	249536	−
chr07	YGL120C	0.981452639	0.964320425	283943	−
chr07	YGL119W	0.986610225	0.981525372	284448	+
chr07	YGL108C	0.961840326	0.985939242	304074	−
chr07	YGL058W	0.977732494	0.975176081	393992	+
chr07	YGL056C	0.960426378	0.969119302	397624	−
chr07	YGL055W	0.964044825	0.969447792	398631	+
chr07	YGL048C	0.971402915	0.953304338	411289	−
chr07	YGL043W	0.964287661	0.976335397	417487	+
chr07	YGL028C	0.960077919	0.965512687	442914	−
chr07	YGL006W	0.950151816	0.968357705	485925	+
chr07	YGR001C	0.958621356	0.990717019	498038	−
chr07	YGR006W	0.980877592	0.97721459	506074	+
chr07	YGR027W-B	0.973585999	0.969942324	536061	+
chr07	YGR027W-A	0.973585999	0.969942324	536061	+
chr07	YGR054W	0.964434273	0.980689617	596697	+
chr07	YGR076C	0.981588154	0.958402031	637581	−
chr07	YGR082W	0.986433799	0.977608093	644048	+
chr07	YGR084C	0.952879595	0.959716787	648146	−
chr07	YGR109C	0.967037071	0.989224447	706505	−
chr07	YGR109W-B	0.964433838	0.990506548	707614	+
chr07	YGR109W-A	0.964433838	0.990506548	707614	+
chr07	YGR149W	0.957244122	0.960107682	789036	+
chr07	YGR161W-B	0.958455297	0.972873884	811743	+
chr07	YGR161W-A	0.958455297	0.9728739	811743	+
chr07	YGR161C-D	0.9711882	0.974318881	823020	−
chr07	YGR161C-C	0.9711882	0.9743189	823020	−
chr07	YGR162W	0.967152562	0.972476532	824064	+
chr07	YGR165W	0.959888658	0.951709091	829121	+
chr07	YGR166W	0.978481923	0.950610672	830520	+
chr07	YGR173W	0.978946749	0.974220242	843859	+
chr07	YGR178C	0.97338186	0.951056442	853220	−
chr07	YGR193C	0.977703185	0.9816188	885746	−
chr07	YGR198W	0.954889766	0.972754857	894698	+
chr07	YGR239C	0.968888325	0.989258725	970058	−
chr07	YGR240C	0.966313371	0.971843468	973739	−
chr07	YGR255C	0.966583058	0.991666026	1003967	−
chr07	YGR267C	0.960278778	0.969707488	1025741	−
chr07	YGR280C	0.961084505	0.952670993	1051732	−
chr07	YGR295C	0.967286944	0.964457386	1082736	−
chr07	YGR296W	0.971130914	0.991185295	1084871	+
chr08	YHL044W	0.958725508	0.965538017	13563	+
chr08	YHL029C	0.988947037	0.966760586	47966	−
chr08	YHL028W	0.983034685	0.977043411	48761	+
chr08	YHL024W	0.961645582	0.966633627	56647	+
chr08	YHL020C	0.978013871	0.986901259	67453	−
chr08	YHL016C	0.976082816	0.988408432	74241	−
chr08	YHL007C	0.973847748	0.981293306	97933	−
chr08	YHL004W	0.97418766	0.993677693	99215	+
chr08	YHL001W	0.959021584	0.965334128	104272	+
chr08	YHR001W-A	0.991644256	0.988918444	107821	+
chr08	YHR056C	0.972836967	0.982728846	217836	−
chr08	YHR081W	0.961720079	0.960688905	267540	+
chr08	YHR091C	0.955695121	0.987437891	286772	−
chr08	YHR101C	0.984820398	0.996893941	315971	−
chr08	YHR102W	0.96127201	0.995534701	316575	+
chr08	YHR107C	0.950250496	0.982165489	328039	−
chr08	YHR118C	0.973725305	0.961118169	345631	−
chr08	YHR127W	0.95014104	0.981438554	360916	+
chr08	YHR136C	0.953476026	0.965665058	375103	−
chr08	YHR148W	0.978585198	0.950179497	393537	+
chr08	YHR153C	0.959414518	0.982780385	402685	−
chr08	YHR165C	0.958747068	0.984253541	436950	−
chr08	YHR214C-D	0.987951207	0.966688891	550941	−
chr08	YHR215W	0.987951207	0.966688891	552099	+
chr08	YHR216W	0.972948554	0.975124764	554396	+
chr09	YIL158W	0.961579117	0.957386446	46201	+
chr09	YIL154C	0.954401073	0.971892535	55021	−
chr09	YIL137C	0.976010283	0.976810775	92788	−
chr09	YIL135C	0.976089791	0.979613921	96375	−
chr09	YIL134W	0.974541094	0.979148771	97395	+
chr09	YIL129C	0.958227819	0.99048832	113237	−
chr09	YIL125W	0.963070211	0.960333013	122689	+
chr09	YIL063C	0.970956253	0.957414461	243741	−
chr09	YIL061C	0.95394965	0.989156182	245556	−
chr09	YIL046W	0.967209958	0.952996831	268650	+
chr09	YIL033C	0.989017477	0.989306501	291668	−
chr09	YIL031W	0.985799922	0.98683422	292632	+
chr09	YIL030C	0.957449018	0.97109633	300008	−
chr09	YIR022W	0.960636707	0.971998311	398730	+
chr09	YIR024C	0.961569219	0.970038905	403488	−
chr09	YIR038C	0.973108358	0.975735046	424510	−
chr10	YJL221C	0.992889333	0.995409763	18536	−
chr10	YJL219W	0.992889333	0.995409763	19497	+
chr10	YJL197W	0.963017116	0.967339021	63804	+
chr10	YJL181W	0.971567753	0.971225117	85658	+
chr10	YJL176C	0.979890865	0.967535459	94528	−
chr10	YJL174W	0.983474082	0.9822043	95090	+
chr10	YJL173C	0.986867668	0.989398406	96527	−
chr10	YJL151C	0.952976229	0.987631587	136770	−
chr10	YJL149W	0.975756648	0.990848833	137376	+
chr10	YJL118W	0.953268112	0.959468203	191638	+
chr10	YJL113W	0.982940363	0.963188993	197913	+
chr10	YJL114W	0.982940363	0.963188993	197913	+
chr10	YJL093C	0.967675882	0.964352732	256807	−
chr10	YJL092W	0.963240719	0.958166876	257418	+
chr10	YJL066C	0.953982678	0.974252054	314867	−
chr10	YJL050W	0.950677364	0.95235067	342517	+
chr10	YJL048C	0.96132641	0.958967756	348632	−
chr10	YJL039C	0.950918953	0.970557445	373794	−
chr10	YJL034W	0.963347804	0.980266739	381322	+
chr10	YJR010W	0.971667854	0.97428271	456232	+
chr10	YJR021C	0.956762721	0.994264722	469572	−
chr10	YJR029W	0.958070547	0.974229894	478337	+
chr10	YJR028W	0.958070547	0.9742299	478337	+
chr10	YJR041C	0.976618081	0.981063923	513756	−
chr10	YJR048W	0.960606245	0.975055837	526328	+
chr10	YJR049C	0.954983464	0.986149168	528469	−
chr10	YJR055W	0.976932113	0.992763445	538765	+
chr10	YJR065C	0.975569729	0.987649101	559151	−
chr10	YJR095W	0.97047495	0.971814385	609769	+
chr10	YJR113C	0.969228269	0.954716018	638969	−
chr10	YJR115W	0.952485858	0.960980837	639936	+
chr10	YJR141W	0.957349189	0.956946497	695900	+
chr10	YJR160C	0.978268521	0.997490962	739810	−
chr10	YJR161C	0.965251269	0.976575544	743993	−
chr11	YKL191W	0.950933251	0.978993764	81040	+
chr11	YKL179C	0.975707433	0.967918905	112508	−
chr11	YKL167C	0.956085616	0.955561088	134139	−
chr11	YKL165C	0.960609423	0.966621061	140696	−
chr11	YKL157W	0.95635277	0.9813363	154996	+
chr11	YKL127W	0.955985661	0.982208081	203185	+
chr11	YKL125W	0.976449752	0.960074911	207891	+
chr11	YKL113C	0.971544612	0.954413703	225519	−
chr11	YKL065C	0.96005541	0.969818928	316701	−
chr11	YKL064W	0.974644257	0.972632809	317408	+
chr11	YKL059C	0.957153957	0.961241915	329087	−
chr11	YKL020C	0.955860253	0.977812511	401723	−
chr11	YKL013C	0.972958978	0.953444609	417666	−
chr11	YKR007W	0.981387104	0.972277081	451077	+
chr11	YKR024C	0.971944038	0.981215773	487015	−
chr11	YKR031C	0.952123552	0.969614994	506037	−
chr11	YKR036C	0.959340192	0.988104612	510275	−
chr11	YKR041W	0.982786597	0.957524998	517840	+
chr11	YKR052C	0.954392373	0.96688713	533106	−
chr11	YKR082W	0.962931616	0.991018501	592467	+
chr11	YKR084C	0.953228662	0.976903834	598532	−
chr11	YKR086W	0.952006608	0.976533657	599499	+
chr12	YLL050C	0.976179673	0.990695339	40413	−
chr12	YLL002W	0.972688874	0.981122544	146290	+
chr12	YLR001C	0.966206724	0.98012374	153976	−
chr12	YLR012C	0.956516633	0.962463803	170280	−
chr12	YLR013W	0.978873849	0.985557204	171338	+
chr12	YLR024C	0.953442868	0.956160837	193282	−
chr12	YLR025W	0.971468039	0.96202948	194453	+
chr12	YLR029C	0.961637928	0.991619508	202591	−
chr12	YLR059C	0.963450626	0.974770886	260548	−
chr12	YLR085C	0.9560163	0.984640913	301990	−
chr12	YLR087C	0.953704478	0.990085627	315732	−
chr12	YLR096W	0.977966477	0.979318401	332591	+
chr12	YLR104W	0.966174553	0.97921157	346586	+
chr12	YLR133W	0.961307333	0.951823465	408446	+
chr12	YLR135W	0.977560494	0.977991425	413282	+
chr12	YLR137W	0.967174193	0.983596278	417007	+
chr12	YLR162W-A	0.968123219	0.962766706	490407	+
chr12	YLR208W	0.96802684	0.969296393	559553	+
chr12	YLR223C	0.966783974	0.974989936	585492	−
chr12	YLR224W	0.974582795	0.978003757	586466	+
chr12	YLR286C	0.972231318	0.978358686	710138	−
chr12	YLR299W	0.962625418	0.970226227	726071	+
chr12	YLR307W	0.962710223	0.990591743	745622	+
chr12	YLR323C	0.953205594	0.975247431	778952	−
chr12	YLR326W	0.979769576	0.991583861	782174	+
chr12	YLR355C	0.967858474	0.973834311	839252	−
chr12	YLR356W	0.968277882	0.974767083	840320	+
chr12	YLR378C	0.974122358	0.977246394	877177	−
chr12	YLR380W	0.973258508	0.97821865	878282	+
chr12	YLR410W-A	0.951545011	0.9529714	941481	+
chr12	YLR410W-B	0.951545011	0.952971407	941481	+
chr12	YLR426W	0.9668981	0.990317101	987059	+
chr12	YLR427W	0.968631588	0.972538491	988425	+
chr12	YLR429W	0.950464544	0.951528134	990774	+
chr12	YLR443W	0.964525656	0.991440098	1022622	+
chr13	YML121W	0.974659011	0.985969584	26930	+
chr13	YML115C	0.97337994	0.996063492	41794	−
chr13	YML080W	0.989302036	0.986381735	108806	+
chr13	YML078W	0.975873108	0.974136336	111002	+
chr13	YML045W	0.993016416	0.993250991	184461	+
chr13	YML045W-A	0.993016416	0.993251	184461	+
chr13	YML041C	0.969801821	0.979224272	195755	−
chr13	YML020W	0.975260683	0.95439232	231149	+
chr13	YML004C	0.966616377	0.98388072	262685	−
chr13	YML003W	0.968338912	0.981828638	263483	+
chr13	YMR010W	0.985774326	0.979191015	285099	+
chr13	YMR011W	0.963732981	0.981283867	288078	+
chr13	YMR027W	0.961041993	0.957831173	325876	+
chr13	YMR036C	0.969260192	0.963784402	343519	−
chr13	YMR060C	0.990018805	0.990517987	392514	−
chr13	YMR066W	0.98321165	0.95995151	401540	+
chr13	YMR078C	0.969392941	0.976546196	424727	−
chr13	YMR081C	0.981254312	0.956294421	431094	−
chr13	YMR110C	0.961424621	0.983151943	491991	−
chr13	YMR116C	0.977129849	0.989254306	500687	−
chr13	YMR137C	0.971971845	0.978526214	544962	−
chr13	YMR138W	0.978634859	0.963362392	545154	+
chr13	YMR152W	0.958913422	0.961601086	563095	+
chr13	YMR197C	0.960464224	0.981756931	659197	−
chr13	YMR210W	0.974579381	0.983178959	687515	+
chr13	YMR214W	0.977906077	0.988639434	695349	+
chr13	YMR219W	0.964555974	0.962486321	707132	+
chr13	YMR224C	0.975063127	0.950620617	720652	−
chr13	YMR229C	0.960514554	0.957025636	731122	−
chr13	YMR241W	0.956225901	0.967912184	751960	+
chr13	YMR319C	0.950340769	0.968043162	914536	−
chr14	YNL339C	0.975221324	0.997373072	6098	−
chr14	YNL334C	0.968865734	0.991228175	12876	−
chr14	YNL322C	0.954706246	0.977799203	34234	−
chr14	YNL311C	0.986814003	0.993782307	51687	−
chr14	YNL310C	0.956852702	0.980516471	52430	−
chr14	YNL309W	0.988062215	0.993825499	52661	+
chr14	YNL301C	0.968107997	0.966680876	64562	−
chr14	YNL295W	0.952849161	0.964836983	76946	+
chr14	YNL261W	0.950477134	0.976226949	155101	+
chr14	YNL260C	0.968893453	0.965562883	157456	−
chr14	YNL255C	0.959418743	0.961868386	167791	−
chr14	YNL248C	0.959305496	0.962132738	182609	−
chr14	YNL241C	0.952591706	0.968306617	197944	−
chr14	YNL234W	0.975005906	0.964281927	210234	+
chr14	YNL224C	0.973438019	0.985601741	227100	−
chr14	YNL212W	0.967303893	0.964441355	247462	+
chr14	YNL166C	0.973079673	0.979903307	323567	−
chr14	YNL156C	0.961076874	0.96913283	341970	−
chr14	YNL112W	0.953769466	0.987266001	413641	+
chr14	YNL099C	0.959678116	0.95727388	439285	−
chr14	YNL097C	0.978605808	0.986440434	442360	−
chr14	YNL082W	0.955790378	0.980457797	473392	+
chr14	YNL055C	0.982685169	0.981068004	518846	−
chr14	YNL042W-B	0.956836355	0.979900708	547114	+
chr14	YNL029C	0.976101029	0.988675718	578774	−
chr14	YNL027W	0.96462873	0.978413199	579581	+
chr14	YNR012W	0.958400399	0.977490746	647434	+
chr14	YNR015W	0.967843094	0.979265652	653389	+
chr14	YNR023W	0.975180387	0.972628935	670420	+
chr14	YNR026C	0.966267575	0.984095961	674691	−
chr14	YNR036C	0.955455936	0.956914254	694824	−
chr14	YNR039C	0.97056523	0.9708253	699433	−
chr14	YNR075W	0.950188074	0.953766447	779916	+
chr14	YNR075C-A	0.986389631	0.991000914	781603	−
chr15	YOL166W-A	0.969218719	0.964760148	585	+
chr15	YOL157C	0.977029388	0.98945557	24293	−
chr15	YOL156W	0.979765672	0.992685071	25272	+
chr15	YOL148C	0.957761501	0.971157209	47573	−
chr15	YOL104C	0.976917372	0.981386975	117454	−
chr15	YOL100W	0.961328138	0.959394148	129237	+
chr15	YOL089C	0.971692903	0.984860678	153490	−
chr15	YOL086C	0.976082094	0.966862518	160594	−
chr15	YOL077C	0.956963602	0.983941333	186723	−
chr15	YOL068C	0.959180595	0.953847182	201879	−
chr15	YOL062C	0.954102242	0.967526899	211995	−
chr15	YOL058W	0.969401099	0.978364009	219210	+
chr15	YOL045W	0.966108727	0.955785397	243496	+
chr15	YOL031C	0.971563515	0.959211572	267530	−
chr15	YOL026C	0.954115513	0.976281121	274354	−
chr15	YOL023W	0.960879668	0.960550998	278057	+
chr15	YOL006C	0.971429281	0.978082289	315388	−
chr15	YOR043W	0.970409112	0.977199399	410870	+
chr15	YOR048C	0.95240535	0.972598244	421651	−
chr15	YOR056C	0.95552512	0.980531823	431628	−
chr15	YOR058C	0.977288174	0.978577416	436347	−
chr15	YOR071C	0.980341941	0.989920087	461278	−
chr15	YOR075W	0.983591979	0.981471486	468214	+
chr15	YOR089C	0.978934603	0.984066065	490830	−
chr15	YOR104W	0.965107091	0.973591736	517643	+
chr15	YOR124C	0.97179062	0.983946384	558643	−
chr15	YOR129C	0.979558976	0.983142651	569559	−
chr15	YOR132W	0.955282168	0.965555781	573176	+
chr15	YOR148C	0.987044445	0.98569999	609198	−
chr15	YOR192C-C	0.980704362	0.966062169	704225	−
chr15	YOR193W	0.973179583	0.992657727	710447	+
chr15	YOR204W	0.985619071	0.960639074	722912	+
chr15	YOR216C	0.971045967	0.970515948	748980	−
chr15	YOR247W	0.959336754	0.957210052	797677	+
chr15	YOR294W	0.972999786	0.97236413	868339	+
chr15	YOR336W	0.973501735	0.969442343	949770	+
chr15	YOR365C	0.981766719	0.98630012	1025570	−
chr15	YOR372C	0.955936893	0.971693401	1036469	−
chr15	YOR389W	0.964833697	0.976852438	1074211	+
chr15	YOR390W	0.98673199	0.997343789	1076782	+
chr15	YOR391C	0.952090431	0.990889663	1079256	−
chr15	YOR393W	0.952090431	0.990889663	1080274	+
chr16	YPL283C	0.990485958	0.9953985	6007	−
chr16	YPL281C	0.961921468	0.977623026	10870	−
chr16	YPL280W	0.961921468	0.977623026	11887	+
chr16	YPL278C	0.965633274	0.959753752	15355	−
chr16	YPL257W-B	0.976897418	0.976806903	56748	+
chr16	YPL257W-A	0.976897418	0.976807	56748	+
chr16	YPL255W	0.96664841	0.970266728	67725	+
chr16	YPL254W	0.95123182	0.962107221	69485	+
chr16	YPL206C	0.975807996	0.972912432	163596	−
chr16	YPL196W	0.978338347	0.984467392	175042	+
chr16	YPL180W	0.976152618	0.987674239	205247	+
chr16	YPL171C	0.96524809	0.961521166	227370	−
chr16	YPL158C	0.980225654	0.985491741	254309	−
chr16	YPL157W	0.98638216	0.988124386	254813	+
chr16	YPL146C	0.98509812	0.956540524	277528	−
chr16	YPL139C	0.981115598	0.987215069	291050	−
chr16	YPL126W	0.988937478	0.982334739	310209	+
chr16	YPL082C	0.980458525	0.992300343	404080	−
chr16	YPL078C	0.957476311	0.95576197	408741	−
chr16	YPL038W	0.953416137	0.966495031	480532	+
chr16	YPL030W	0.973101156	0.975002429	493541	+
chr16	YPL007C	0.954338314	0.983931954	543845	−
chr16	YPR010C	0.983770387	0.983449754	581193	−
chr16	YPR017C	0.986325514	0.989002388	593914	−
chr16	YPR018W	0.981145288	0.96510122	594473	+
chr16	YPR020W	0.950323294	0.983815562	599867	+
chr16	YPR048W	0.980910651	0.976100682	659179	+
chr16	YPR060C	0.960902075	0.969265445	675628	−
chr16	YPR062W	0.96911875	0.967204709	677162	+
chr16	YPR088C	0.957617837	0.976321629	713026	−
chr16	YPR141C	0.978516693	0.973377917	817919	−
chr16	YPR145C-A	0.961127516	0.965220022	824922	−
chr16	YPR156C	0.966866802	0.956230015	839773	−
chr16	YPR158C-D	0.981640164	0.971311933	856253	−
chr16	YPR158C-C	0.981640164	0.971311933	856253	−
chr16	YPR161C	0.969622155	0.984283791	866418	−
chr16	YPR165W	0.959239007	0.967322323	875364	+
chr16	YPR176C	0.986542093	0.977514778	892074	−
chr16	YPR187W	0.964480751	0.98804279	911253	+
chr16	YPR203W	0.968955474	0.985644074	943876	+

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.

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.

S. cerevisiae gene	A. fumigatus gene	Correlation coefficient
YCR053W	AFUA_3G08980	0.851750303
YOL006C	AFUA_1G03500	0.814728478
YLR208W	AFUA_4G06090	0.810778356
YJR160C	AFUA_8G07240	0.807607644
YKL064W	AFUA_2G08070	0.771984405
YDL208W	AFUA_1G13570	0.763687527
YDL247W	AFUA_8G07240	0.751799318
YJL034W	AFUA_2G04620	0.751475734
YJL174W	AFUA_2G07590	0.731359519
YGL006W	AFUA_1G10880	0.706118907
YLR307W	AFUA_6G10430	0.701428537
YOR056C	AFUA_5G04000	0.693624039
YJR049C	AFUA_5G12870	0.6873278
YOR132W	AFUA_5G07150	0.684358232
YDR028C	AFUA_8G02720	0.681519128
YKL059C	AFUA_2G06220	0.677236775
YDR019C	AFUA_1G10780	0.673590566
YDR262W	AFUA_8G05360	0.668577442
YJR160C	AFUA_3G01700	0.655149877
YBL087C	AFUA_2G03380	0.654275917
YDR120C	AFUA_3G04200	0.653965099
YMR110C	AFUA_4G13500	0.649573592
YDR479C	AFUA_2G01510	0.649340576
YLR307W	AFUA_4G09940	0.641152119
YLL050C	AFUA_5G10570	0.636927762
YMR011W	AFUA_2G11520	0.631877767
YGR149W	AFUA_3G08240	0.627253467
YKL125W	AFUA_1G02590	0.626251676
YDL247W	AFUA_3G01700	0.621782331
YHR165C	AFUA_2G03030	0.616638486
YLR355C	AFUA_3G14490	0.615946987
YLR307W	AFUA_3G07210	0.615345397
YNL156C	AFUA_4G07680	0.605449075
YOL157C	AFUA_8G07070	0.600254438
YPL196W	AFUA_3G08740	0.596649007
YOL156W	AFUA_2G11520	0.589475104
YGL055W	AFUA_7G05920	0.583471232
YER094C	AFUA_4G07420	0.580111415
YER026C	AFUA_4G13680	0.579632053
YKR031C	AFUA_3G05630	0.578947614
YJR041C	AFUA_1G13200	0.577042969
YCL057C-A	AFUA_1G13195	0.56703028
YKL167C	AFUA_6G12620	0.566497151
YDR334W	AFUA_7G02370	0.556810391
YDL085W	AFUA_1G11960	0.555058025
YIR038C	AFUA_8G02500	0.553657653
YGL056C	AFUA_1G06660	0.550891198
YLR133W	AFUA_1G15930	0.547961885
YLR137W	AFUA_2G09930	0.542448721
YER095W	AFUA_1G10410	0.540102076
YCR090C	AFUA_2G15510	0.540015424
YIR022W	AFUA_3G12840	0.539096148
YJR048W	AFUA_2G13110	0.537701308
YDL247W	AFUA_8G01340	0.536753536
YGL119W	AFUA_6G04380	0.528264148
YDR054C	AFUA_5G09200	0.520282879
YNR036C	AFUA_5G10750	0.51817226
YJL050W	AFUA_4G07160	0.517374235
YKR036C	AFUA_5G13140	0.515007541
YML041C	AFUA_2G05030	0.514819597
YML080W	AFUA_1G16550	0.512494533
YJL093C	AFUA_1G14250	0.5107227
YDR238C	AFUA_1G10970	0.509749906
YJL197W	AFUA_2G14130	0.501902821
YER173W	AFUA_8G02820	0.501581347
YJR160C	AFUA_8G01340	0.499250408
YOL058W	AFUA_2G04310	0.497155736
YGR006W	AFUA_1G16990	0.496383573
YPR161C	AFUA_5G05510	0.495551014
YBR136W	AFUA_4G04760	0.49434371
YJR049C	AFUA_2G01350	0.493221085
YPR060C	AFUA_5G13130	0.490832735
YDR055W	AFUA_4G06820	0.482973721
YLR104W	AFUA_5G04040	0.47610876
YIL129C	AFUA_6G11010	0.473123981
YDR300C	AFUA_2G07570	0.469287567
YOL156W	AFUA_7G00950	0.46726022
YGL201C	AFUA_5G10890	0.462753539
YKR086W	AFUA_1G03820	0.461061937
YPL157W	AFUA_6G08610	0.460257721
YIL046W	AFUA_2G14110	0.45798838
YGL048C	AFUA_4G04660	0.457664607
YHR216W	AFUA_2G03610	0.456902272
YDR424C	AFUA_1G04850	0.455530713
YPR141C	AFUA_2G14280	0.452133975
YLR427W	AFUA_1G07150	0.444534443
YHL004W	AFUA_1G06570	0.439699159
YLL002W	AFUA_5G09540	0.431520497
YKR052C	AFUA_6G12550	0.429429023
YNL260C	AFUA_1G09000	0.425937756
YNL112W	AFUA_2G10750	0.423331447
YFL026W	AFUA_3G14330	0.422540136
YCL038C	AFUA_2G15370	0.420548714
YPR156C	AFUA_4G01140	0.419838437
YHL024W	AFUA_3G06230	0.417835282
YBR173C	AFUA_5G10740	0.414366599
YGR178C	AFUA_1G09630	0.410618083
YMR036C	AFUA_6G08200	0.408252022
YDL147W	AFUA_3G06610	0.40670988
YJR095W	AFUA_2G16930	0.405617695
YPL171C	AFUA_2G17960	0.40043227
YBL061C	AFUA_8G05620	0.398124519
YHL001W	AFUA_6G03830	0.397471165
YNL255C	AFUA_1G07630	0.390527675
YGL006W	AFUA_3G10690	0.389206341
YIL125W	AFUA_4G11650	0.387564721
YMR011W	AFUA_5G01160	0.381368332
YMR010W	AFUA_5G03510	0.378223656
YMR319C	AFUA_4G14640	0.376638524
YDL110C	AFUA_1G09160	0.376540694
YOL086C	AFUA_5G06240	0.376281416
YGR076C	AFUA_4G09000	0.373900773
YOR204W	AFUA_4G07660	0.368301524
YMR229C	AFUA_2G16040	0.367246087
YLR025W	AFUA_1G06420	0.363738278
YPL281C	AFUA_6G06770	0.363265962
YOR294W	AFUA_7G04430	0.363077313
YLR299W	AFUA_7G04760	0.36169498
YCL038C	AFUA_2G06170	0.359699115
YKL113C	AFUA_3G06060	0.351986208
YHL020C	AFUA_5G09420	0.350312962
YMR224C	AFUA_6G11410	0.348946198
YDR444W	AFUA_3G04240	0.345942811
YER107C	AFUA_1G09020	0.34238252
YDR162C	AFUA_2G03680	0.342381673
YNL212W	AFUA_3G08750	0.341561675
YNL097C	AFUA_3G11940	0.339603963
YKL191W	AFUA_6G07100	0.337319743
YPL030W	AFUA_6G02570	0.336821966
YNL224C	AFUA_3G05330	0.336636223
YKR024C	AFUA_5G11050	0.328747023
YPR020W	AFUA_1G16280	0.323479927
YPL171C	AFUA_2G04060	0.322952534
YOR393W	AFUA_6G06770	0.321210691
YPR088C	AFUA_5G03880	0.31284654
YGL058W	AFUA_6G14210	0.312000165
YFL059W	AFUA_5G08090	0.309971957
YBR243C	AFUA_2G11240	0.307271969
YJL048C	AFUA_3G06360	0.306215007
YNL055C	AFUA_4G06910	0.305279025
YOR058C	AFUA_2G16260	0.305221634
YGR240C	AFUA_4G00960	0.304340045
YBR279W	AFUA_2G11000	0.303224
YPL078C	AFUA_8G05440	0.300712891
YLR059C	AFUA_3G11820	0.296403753
YLR380W	AFUA_6G12690	0.295562758
YDL174C	AFUA_1G17520	0.29517154
YCL057W	AFUA_7G05930	0.293762978
YDR234W	AFUA_5G08890	0.293096856
YDR438W	AFUA_5G12140	0.287954196
YGL028C	AFUA_8G05610	0.287899385
YML004C	AFUA_6G07940	0.285261452
YOL045W	AFUA_2G02850	0.284622252
YLR429W	AFUA_2G14270	0.283845667
YDR397C	AFUA_3G02340	0.283499213
YBR260C	AFUA_3G06280	0.282196097
YCR087C-A	AFUA_7G04700	0.281322207
YMR011W	AFUA_7G00950	0.280854319
YOL148C	AFUA_1G16580	0.274850272
YDR379W	AFUA_1G12680	0.273041289
YJL151C	AFUA_5G10590	0.272979399
YML020W	AFUA_5G12090	0.266526854
YGR082W	AFUA_6G11380	0.265129767
YJR113C	AFUA_1G04280	0.262789584
YIL031W	AFUA_5G03200	0.256820972
YDR432W	AFUA_3G10100	0.255963453
YDR359C	AFUA_4G07560	0.255317292
YDR233C	AFUA_6G13670	0.253861938
YGR255C	AFUA_4G12930	0.252312468
YFR009W	AFUA_4G06070	0.245534257
YPL280W	AFUA_3G08490	0.243781447
YOR075W	AFUA_2G09670	0.239487119
YJL219W	AFUA_7G00950	0.239124986
YCR026C	AFUA_2G14770	0.234276623
YOR391C	AFUA_3G08490	0.233098887
YGL180W	AFUA_4G09050	0.231299038
YLR323C	AFUA_5G07720	0.231114462
YGL006W	AFUA_7G01030	0.222088168
YBR179C	AFUA_5G13392	0.219453048
YKR082W	AFUA_4G05840	0.214144582
YLR087C	AFUA_2G13520	0.209434557
YCL064C	AFUA_4G07810	0.204494803
YOL156W	AFUA_5G01160	0.203744073
YBR249C	AFUA_7G04070	0.202306902
YJL093C	AFUA_3G07540	0.201465401
YOL077C	AFUA_1G02210	0.196710807
YLR426W	AFUA_1G06280	0.196041865
YMR060C	AFUA_2G03840	0.194299595
YOR048C	AFUA_1G13730	0.193994391
YDL174C	AFUA_7G02560	0.193117882
YJL221C	AFUA_8G07070	0.187015236
YGR054W	AFUA_3G05970	0.181434929
YPR176C	AFUA_7G04460	0.180215936
YML003W	AFUA_1G09870	0.173517378
YKR084C	AFUA_2G04630	0.171646807
YDR270W	AFUA_4G12620	0.171601357
YOR336W	AFUA_2G02360	0.164107564
YFL058W	AFUA_5G02470	0.160695353
YNL301C	AFUA_2G07380	0.151927636
YJL221C	AFUA_7G06380	0.150927464
YGR280C	AFUA_7G03690	0.150422383
YOL089C	AFUA_6G01960	0.149731857
YGR193C	AFUA_3G08270	0.14875632
YDR328C	AFUA_5G06060	0.143711765
YPL254W	AFUA_2G06060	0.143220591
YPL206C	AFUA_2G00990	0.138505935
YEL021W	AFUA_2G08360	0.13720587
YOL068C	AFUA_4G12120	0.134069861
YJR160C	AFUA_7G06390	0.131179873
YNL310C	AFUA_6G08230	0.130305791
YIL061C	AFUA_5G13480	0.126828721
YGL163C	AFUA_6G12910	0.12597657
YGR173W	AFUA_5G06770	0.123606414
YJL092W	AFUA_2G03910	0.122708164
YJR065C	AFUA_5G11560	0.121854722
YBR023C	AFUA_8G05630	0.120791924
YBR084W	AFUA_3G08650	0.118154138
YMR197C	AFUA_4G10710	0.114428905
YMR241W	AFUA_5G04220	0.114113659
YNL097C	AFUA_7G01870	0.109316946
YGL171W	AFUA_1G16290	0.103112508
YOR365C	AFUA_4G13340	0.094260129
YHR215W	AFUA_6G11330	0.092128581
YKL013C	AFUA_6G02370	0.088958318
YOR043W	AFUA_4G06130	0.087990985
YPR062W	AFUA_1G05050	0.087018417
YDR497C	AFUA_2G07910	0.078863767
YDR477W	AFUA_2G01700	0.074801159
YLR378C	AFUA_5G08130	0.074624328
YBR060C	AFUA_5G08110	0.073589072
YGL120C	AFUA_5G11620	0.069009268
YIL063C	AFUA_2G10810	0.06328373
YOL157C	AFUA_7G06380	0.06047767
YGL043W	AFUA_3G07670	0.059398891
YMR027W	AFUA_5G06710	0.058232831
YHR215W	AFUA_8G01910	0.05787337
YDL247W	AFUA_7G05190	0.05184022
YPR048W	AFUA_5G07290	0.049809159
YBL051C	AFUA_5G01940	0.048514144
YHR148W	AFUA_2G08320	0.047441878
YJR160C	AFUA_7G05190	0.045923723
YJL039C	AFUA_5G12670	0.042943521
YNL029C	AFUA_5G12160	0.031203315
YGR267C	AFUA_5G03140	0.029526621
YNL027W	AFUA_1G06900	0.02747405
YDL247W	AFUA_7G06390	0.023887472
YHR107C	AFUA_5G03080	0.020068991
YKL165C	AFUA_4G03970	0.01938034
YNR012W	AFUA_2G05430	0.019075112
YLR085C	AFUA_4G04420	0.018617278
YPL082C	AFUA_1G05830	0.017285628
YCL064C	AFUA_1G06150	0.014476469
YNR039C	AFUA_1G12090	0.011820922
YOR216C	AFUA_1G08830	0.008439713
YOR148C	AFUA_4G07550	0.006702846
YDR420W	AFUA_4G00500	0.006566287
YPR018W	AFUA_5G03720	−0.000683184
YDR322W	AFUA_5G12810	−0.002517201
YNR015W	AFUA_3G08390	−0.013154917
YBR251W	AFUA_5G11540	−0.01637247
YHL028W	AFUA_5G09020	−0.020657813
YPL146C	AFUA_2G05550	−0.023787247
YKL127W	AFUA_3G11830	−0.026619404
YJR160C	AFUA_2G10910	−0.029508087
YIR038C	AFUA_1G17010	−0.030714781
YDL247W	AFUA_2G10910	−0.033905332
YBR204C	AFUA_1G03540	−0.038361835
YJR010W	AFUA_3G06530	−0.038908707
YMR210W	AFUA_6G04640	−0.046477426
YPR187W	AFUA_1G05160	−0.048502572
YDR037W	AFUA_6G07640	−0.052027721
YIL134W	AFUA_6G05170	−0.053118026
YLR286C	AFUA_5G03760	−0.062116003
YKL179C	AFUA_1G14240	−0.062203351
YDR109C	AFUA_4G04680	−0.063717983
YOL157C	AFUA_3G07380	−0.064624439
YIR038C	AFUA_2G17300	−0.068756542
YDL102W	AFUA_2G16600	−0.088010728
YOR389W	AFUA_2G01940	−0.09375584
YBR244W	AFUA_3G12270	−0.097477745
YJL219W	AFUA_2G11520	−0.098366126
YPL126W	AFUA_7G02610	−0.101632712
YDL189W	AFUA_1G09400	−0.104331651
YHL016C	AFUA_1G04870	−0.106608293
YLR380W	AFUA_4G13930	−0.111437921
YPR165W	AFUA_6G06900	−0.117573203
YOL062C	AFUA_5G07930	−0.122120003
YGL248W	AFUA_1G14890	−0.124318908
YLR029C	AFUA_1G04660	−0.129375946
YMR214W	AFUA_2G08300	−0.130867913
YOR124C	AFUA_6G12270	−0.136050424
YOL023W	AFUA_1G06520	−0.136914472
YPL280W	AFUA_3G01210	−0.13706189
YLR380W	AFUA_7G06760	−0.141209958
YNL241C	AFUA_3G08470	−0.153108798
YOR391C	AFUA_3G01210	−0.154014157
YOL089C	AFUA_6G02330	−0.161608796
YGL215W	AFUA_3G10040	−0.170171082
YMR137C	AFUA_2G15220	−0.174259735
YER004W	AFUA_6G08930	−0.179730339
YDR365C	AFUA_2G05420	−0.181946191
YDR529C	AFUA_4G06790	−0.185927497
YDR062W	AFUA_6G00300	−0.189190157
YOL086C	AFUA_7G01010	−0.190813468
YOL026C	AFUA_5G03630	−0.19138562
YIL033C	AFUA_3G10000	−0.195925157
YBR290W	AFUA_4G13740	−0.19955841
YAR019C	AFUA_4G06750	−0.204744755
YHL007C	AFUA_2G04680	−0.20737573
YMR078C	AFUA_7G05480	−0.222707833
YDR311W	AFUA_4G11690	−0.22686955
YOL100W	AFUA_3G12670	−0.230714484
YGR162W	AFUA_2G09490	−0.232235851
YGL255W	AFUA_1G01550	−0.248116851
YPL038W	AFUA_6G01910	−0.252388553
YCL035C	AFUA_1G06100	−0.255759517
YNL082W	AFUA_2G13410	−0.259394819
YDR062W	AFUA_1G11890	−0.263523207
YOR390W	AFUA_2G16210	−0.269616243
YJR141W	AFUA_3G07970	−0.2738444
YOR365C	AFUA_2G17650	−0.274036262
YDL116W	AFUA_1G10860	−0.278315121
YKL020C	AFUA_1G12550	−0.278379939
YDL174C	AFUA_3G06820	−0.286419799
YBR029C	AFUA_1G07010	−0.296926336
YLR096W	AFUA_1G11080	−0.297540349
YFL028C	AFUA_6G05080	−0.303502181
YOR089C	AFUA_3G10740	−0.30892361
YPR010C	AFUA_2G13000	−0.309890067
YJL219W	AFUA_5G01160	−0.321415181
YNL097C	AFUA_4G11660	−0.329160424
YMR116C	AFUA_4G13170	−0.329415498
YPL280W	AFUA_5G01430	−0.331554435
YHR091C	AFUA_2G14030	−0.337931682
YIL030C	AFUA_2G08650	−0.350942099
YFR037C	AFUA_7G05510	−0.356342064
YOR391C	AFUA_5G01430	−0.356843862
YDL174C	AFUA_1G00510	−0.402217656
YML121W	AFUA_5G09650	−0.410825283
YFL060C	AFUA_2G08580	−0.411505108
YDR301W	AFUA_8G04040	−0.413112754
YJL221C	AFUA_3G07380	−0.413321446
YLR326W	AFUA_5G12410	−0.458648708
YBL108C-A	AFUA_4G03360	−0.487139446
YGR165W	AFUA_5G08380	−0.519339895
YKL157W	AFUA_4G09030	−0.604021491
YNL334C	AFUA_2G08580	−0.720610634

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].

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].

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).

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.

Ortholog cluster between Aspergillus fumigatus and Saccharomyces cerevisiae genes.

Click here for additional data file.