# Conservation of Nucleosome Positions in Duplicated and Orthologous Gene Pairs

Authors: Hiromi Nishida
Journal: The Scientific World Journal
 (2012)

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## 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 ascomyceteAspergillus 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.


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## Body

## 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 inA. 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 inA. fumigatus and S. cerevisiae.


## 2. Materials and Methods

### 2.1. Identification of Duplicated Gene Pairs inAspergillus 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 9630A. 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 inAspergillus fumigatus.
Gene pairChromosomeGene body regionGene directionFunctionAFUA1G0015012544227017+RING finger proteinAFUA6G09370622455492247121+RING finger proteinAFUA1G004201135528137781+Carboxypeptidase S1, putativeAFUA8G041208897824900076−Carboxypeptidase S1, putativeAFUA1G004401138359140093−DUF895 domain membrane proteinAFUA8G041108895512897246+DUF895 domain membrane proteinAFUA1G004501143117144466+N-acetylglucosamine-6-phosphate deacetylase(NagA), putativeAFUA8G041008891135892484−N-acetylglucosamine-6-phosphate deacetylase(NagA), putativeAFUA1G004701148615150219+Betaine aldehyde dehydrogenase, putativeAFUA8G040808885376886980−Betaine aldehyde dehydrogenase (BadH), putativeAFUA1G005301164101164771−Thermoresistant gluconokinase family proteinAFUA4G12050431637473164530−Thermoresistant gluconokinaseAFUA1G005501177114178593+Hypothetical proteinAFUA1G009101328785330274+Hypothetical proteinAFUA1G005801184790186873+Acid phosphatase (PhoG), putativeAFUA8G040508870757872487−Acid phosphatase (PhoG), putativeAFUA1G006501215584217006+Alpha-1,3-glucanase, putativeAFUA7G08510719733981974759+Alpha-1,3-glucanase, putativeAFUA1G009201331676332955−Hypothetical proteinAFUA3G06425315827481584037−Hypothetical proteinAFUA1G010501385302386244−Hypothetical proteinAFUA8G06160814656951466634+Hypothetical proteinAFUA1G025501744583746335−Tubulin alpha-1 subunitAFUA2G14990239470083948834−Tubulin alpha-2 subunitAFUA1G027301788249789373−Mitochondrial phosphate carrier protein (Ptp), putativeAFUA1G15140140702304071449−Mitochondrial phosphate carrier protein (Mir1), putativeAFUA1G05760116583821659697−Arsenite efflux transporterAFUA5G15010538824253883746+Arsenite permease (ArsB), putativeAFUA1G05760116583821659697−Arsenite efflux transporterAFUA1G16100143788984380216+Arsenite permease (ArsB), putativeAFUA1G10910128481552850137−Tubulin beta, putativeAFUA7G0025077022171948+Tubulin beta-2 subunitAFUA1G11260129715292971889−Conserved hypothetical proteinAFUA6G0027067954279886−Conserved hypothetical proteinAFUA1G11610130600583060510+3-Dehydroquinate dehydratase, type IIAFUA3G14850339297213930173+3-Dehydroquinate dehydratase, type IIAFUA1G11890131294473131489+Serine palmitoyltransferase 2, putativeAFUA6G0030068585187692−Serine palmitoyltransferase 1, putativeAFUA1G12850133988373400611+Nitrate transporter (nitrate permease)AFUA1G17470147823204783995+High-affinity nitrate transporter NrtBAFUA1G15970143384074339712+Aldo-keto reductase (AKR13), putativeAFUA8G015608401581402815−Aldo-keto reductase (YakC), putativeAFUA1G16030143588664360256−Conserved hypothetical proteinAFUA5G14930538632183864521−Conserved hypothetical proteinAFUA1G16040143634934365310+Metalloreductase, putativeAFUA5G14940538677973869542+Cell surface metalloreductase (FreA), putativeAFUA1G16050143665734368232+Hypothetical proteinAFUA5G14950538706353872465+Hypothetical proteinAFUA1G16070143703464373694+Conserved hypothetical proteinAFUA5G14980538745393877890+Conserved hypothetical proteinAFUA1G16080143745794375298−Hypothetical proteinAFUA5G14990538787973879579−Hypothetical proteinAFUA1G16090143778424378249−Arsenate reductase (ArsC), putativeAFUA5G15000538813863881835−Arsenate reductase (ArsC), putativeAFUA1G16100143788984380216+Arsenite permease (ArsB), putativeAFUA5G15010538824253883746+Arsenite permease (ArsB), putativeAFUA1G16110143804744381455−Arsenic methyltransferase (Cyt19), putativeAFUA5G15020538839293884993−Arsenic methyltransferase (Cyt19), putativeAFUA1G16120143856504386671−Arsenic resistance protein (ArsH), putativeAFUA8G07150817516931752688+ArsH proteinAFUA1G16120143856504386671−Arsenic resistance protein (ArsH), putativeAFUA5G15030538872873888230−Arsenic resistance protein (ArsH), putativeAFUA2G008002178081179459−PelA proteinAFUA5G10380526586562659968+Pectin lyase, putativeAFUA2G008002178081179459−PelA proteinAFUA7G05030711821041183794−Pectin lyase BAFUA2G04010210929731094679−Alpha, alpha-trehalose-phosphate synthase subunit, putativeAFUA6G12950632689583270783+Alpha, alpha-trehalose-phosphate Synthase subunitTPS1, putativeAFUA2G11270228972752904954−Alpha-1,3-glucan synthase, putativeAFUA3G009103210186217666+Alpha-1,3-glucan synthase, putativeAFUA3G0034037118672734+Glycosyl hydrolase, putativeAFUA4G027204751306752715−Glycosyl hydrolase, putativeAFUA3G006803151397153549−Copper amine oxidaseAFUA7G041807943893946136+Amine oxidaseAFUA3G015603393032394802−Aminoacid permease, putativeAFUA5G04260511409531142714+Arginine transporter, putativeAFUA3G024203597476598286+ThiJ/PfpI family proteinAFUA4G014004369123369944−ThiJ/PfpI family proteinAFUA3G030803824479825425+Endo-1,3(4)-beta-glucanase, putativeAFUA6G14540637024163703383−Endo-1,3(4)-beta-glucanase, putativeAFUA3G03980311346091136404+Cytochrome P450 monooxygenase, putativeAFUA5G10050525893012591081−Cytochrome P450 monooxygenase, putativeAFUA3G08160320942232095759−Eukaryotic translation initiation Factor eIF4A, putativeAFUA5G024105621886623486−DEAD/DEAH box helicase, putativeAFUA3G14420338318683834921+Chitin synthase GAFUA5G007605211013213795+Chitin synthase CAFUA4G005104133477135102−Hypothetical proteinAFUA7G08600720094362011052+Hypothetical proteinAFUA4G031104868474870249−Monosaccharide transporterAFUA5G10690527373482739178−Monosaccharide transporterAFUA4G03680410315861032539−Oxidoreductase, short-chain dehydrogenase/reductase familyAFUA6G035206764308765294−Short-chain dehydrogenase/reductase family protein, putativeAFUA4G09440424629202466158−Sodium P-type ATPase, putativeAFUA6G036906810027813362−Sodium transport ATPase, putativeAFUA4G14360437743073776166+Capsular associated protein, putativeAFUA5G07560518897911891689−Capsular associated protein, putativeAFUA5G0014551574916327−Hypothetical proteinAFUA6G11710629159032916483+Conserved hypothetical proteinAFUA5G0014551574916327−Hypothetical proteinAFUA7G08440719423191942804+Hypothetical proteinAFUA5G010305266294267439−Glyceraldehyde 3-phosphate dehydrogenase(Ccg-7), putativeAFUA5G019705503797505194+Glyceraldehyde 3-phosphate dehydrogenase GpdAAFUA5G06240514944551495619−Alcohol dehydrogenase, putativeAFUA7G010107270494271675−Alcohol dehydrogenase, putativeAFUA5G07980520190692020841+Hypothetical proteinAFUA5G14920538573503859167+Hypothetical proteinAFUA5G09130523456892346728−Polysaccharide deacetylase family proteinAFUA6G05030611958461196956+Polysaccharide deacetylase family proteinAFUA5G15030538872873888230−Arsenic resistance protein (ArsH), putativeAFUA8G07150817516931752688+ArsH proteinAFUA6G06750614752391476209+14-3-3 family proteinAFUA2G032902867203868250−14-3-3 family protein ArtA, putativeAFUA6G07070615876431589124+Cellobiohydrolase DAFUA6G11610628780782879676−1,4-beta-D-glucan-cellobiohydrolyase, putativeAFUA6G11430628371402839051+Aldehyde dehydrogenase, putativeAFUA7G010007267518269163−Aldehyde dehydrogenase, putativeAFUA6G11710629159032916483+Conserved hypothetical proteinAFUA7G08440719423191942804+Hypothetical proteinAFUA6G13490634319123433612−Glutamate decarboxylaseAFUA8G06020814288121430515+Glutamate decarboxylaseAFUA7G003607102030103064−UDP-galactose 4-epimerase, putativeAFUA8G008608203496204338+UDP-galactose 4-epimerase, putativeAFUA7G07050717256861726402−Hypothetical proteinAFUA7G08300718702441870960−Hypothetical proteinAFUA7G07060717288761732992−Hypothetical proteinAFUA7G08310718734371877817−Hypothetical proteinTable 2
Spearman's rank correlation coefficients of nucleosome position profiles in the promoter and body regions of 63 duplicated gene pairs inAspergillus fumigatus.
Gene pairGene promoterGene bodyAFUA1G00150AFUA6G093700.7501769130.215204254AFUA1G00420AFUA8G041200.803709740.723149072AFUA1G00440AFUA8G041100.8560485610.225149091AFUA1G00450AFUA8G041000.92136020.94633912AFUA1G00470AFUA8G040800.4331180450.818800395AFUA1G00530AFUA4G120500.326735006−0.199291887AFUA1G00550AFUA1G009100.6769103340.678763937AFUA1G00580AFUA8G040500.3052917930.312927993AFUA1G00650AFUA7G085100.4481715250.085599209AFUA1G00920AFUA3G064250.719748778−0.340001527AFUA1G01050AFUA8G061600.6351493080.176679577AFUA1G02550AFUA2G149900.139079116−0.036644732AFUA1G02730AFUA1G151400.4521932590.067186644AFUA1G05760AFUA5G150100.3958497110.117006666AFUA1G05760AFUA1G161000.127911436−0.397363108AFUA1G10910AFUA7G002500.3107185770.665906466AFUA1G11260AFUA6G002700.617303556−0.02397179AFUA1G11610AFUA3G148500.6362810690.869300724AFUA1G11890AFUA6G003000.2544875640.429087849AFUA1G12850AFUA1G174700.6444472870.008468365AFUA1G15970AFUA8G015600.373850536−0.106800689AFUA1G16030AFUA5G149300.6183497650.858488283AFUA1G16040AFUA5G149400.4810540050.017330056AFUA1G16050AFUA5G14950−0.345037268−0.392132138AFUA1G16070AFUA5G149800.9309221240.902581516AFUA1G16080AFUA5G149900.5599807870.136819379AFUA1G16090AFUA5G150000.7738679240.338119153AFUA1G16100AFUA5G150100.6811700980.70434823AFUA1G16110AFUA5G15020−0.2618649050.632982505AFUA1G16120AFUA8G071500.3568699150.074502754AFUA1G16120AFUA5G15030−0.135442129−0.239074416AFUA2G00800AFUA5G103800.3520639160.460712971AFUA2G00800AFUA7G05030−0.1141844430.457081245AFUA2G04010AFUA6G129500.134790545−0.14813806AFUA2G11270AFUA3G00910−0.0042078580.192024608AFUA3G00340AFUA4G02720−0.0502599870.055757479AFUA3G00680AFUA7G041800.399912713−0.044615588AFUA3G01560AFUA5G042600.1793950670.125177632AFUA3G02420AFUA4G014000.6627124810.646400554AFUA3G03080AFUA6G145400.3401707−0.021961056AFUA3G03980AFUA5G100500.4867265340.318475376AFUA3G08160AFUA5G024100.309645464−0.255654021AFUA3G14420AFUA5G007600.9176851340.415111431AFUA4G00510AFUA7G086000.5785827430.441363777AFUA4G03110AFUA5G106900.7215401930.176996881AFUA4G03680AFUA6G035200.662657833−0.320417166AFUA4G09440AFUA6G036900.2041591840.000609208AFUA4G14360AFUA5G075600.0380830730.515103795AFUA5G00145AFUA6G117100.809402393−0.741045496AFUA5G00145AFUA7G084400.019652845−0.575600966AFUA5G01030AFUA5G019700.5762111780.132479521AFUA5G06240AFUA7G010100.163674862−0.552899419AFUA5G07980AFUA5G149200.669562689−0.265207346AFUA5G09130AFUA6G050300.0924529380.729278817AFUA5G15030AFUA8G071500.337482368−0.502391454AFUA6G06750AFUA2G032900.333402926−0.538389013AFUA6G07070AFUA6G11610−0.048961745−0.239430043AFUA6G11430AFUA7G010000.01454920.476692417AFUA6G11710AFUA7G084400.2433626230.823124582AFUA6G13490AFUA8G060200.7681865330.174847009AFUA7G00360AFUA8G00860−0.1150502680.03815086AFUA7G07050AFUA7G083000.707568420.778653567AFUA7G07060AFUA7G083100.9068527250.919839072


### 2.2. Identification of Orthologous Gene Pairs inAspergillus fumigates and Saccharomyces cerevisiae

In a comparison of nucleosome positioning betweenA. fumigatusandS. cerevisiae, I focused on 466 genes (Table 3) that showed notably high conservation of nucleosome positioning in the promoters of the control and the ELP3andHOS2 deletion mutants from the previous study [10].Table 3
Genes ofSaccharomyces cerevisiae with highly conserved nucleosome positions in the promoters of the control and histone modification gene deletion mutants.
ChromosomeGeneCorrelation coefficient between the control and theELP3 deletionCorrelation coefficient between the control and theHOS2 deletionTranslational start siteTranscription directionchr01YAL064W-B0.9747199550.96581424312047+chr01YAL056W0.9898010030.98215732839260+chr01YAL047C0.9502436910.95312923256858−chr01YAR019C0.9701151620.960628643175133−chr01YAR033W0.9688078750.987221166188101+chr02YBL111C0.9958020650.994550655009−chr02YBL108C-A0.9594970130.9699665427733−chr02YBL101C0.9585171250.99132409628299−chr02YBL087C0.957191870.95727320360735−chr02YBL061C0.9849602120.992728731107408−chr02YBL060W0.9603302890.99357258107934+chr02YBL051C0.976537340.989165943124762−chr02YBL032W0.9568748540.980366627160187+chr02YBL005W-B0.9507813220.952679326221333+chr02YBL005W-A0.9507813220.952679326221333+chr02YBR023C0.9602384990.992906362287925−chr02YBR029C0.9592313890.987222377297742−chr02YBR047W0.9645645220.963289004331831+chr02YBR060C0.9592298710.974718825362512−chr02YBR084W0.9621728660.981530879411048+chr02YBR090C0.9676587850.971792497427052−chr02YBR091C0.9650378620.985960321427478−chr02YBR131W0.9533232490.969685452497157+chr02YBR136W0.9635468220.974854426505662+chr02YBR173C0.9785183910.961438459582167−chr02YBR179C0.9884891460.991754907589109−chr02YBR180W0.9871322120.975974209589736+chr02YBR204C0.9709589460.978433534633376−chr02YBR243C0.9722534670.961252065706788−chr02YBR244W0.9742023060.992702483707523+chr02YBR249C0.9557426820.976101912717989−chr02YBR250W0.9541491880.976352348719028+chr02YBR251W0.962732610.961120273721385+chr02YBR258C0.9666018990.955155711730157−chr02YBR260C0.9693460190.970918059734634−chr02YBR279W0.9560813870.964626558761253+chr02YBR290W0.9815868230.967935658782587+chr03YCL064C0.9571506980.9527051416880−chr03YCL058W-A0.9698953450.99239482923584+chr03YCL057C-A0.9908861920.98717057624325−chr03YCL057W0.9630623570.96180462324768+chr03YCL038C0.9782105370.95763354856527−chr03YCL035C0.9813607050.97356815161173−chr03YCL019W0.9532416640.97868845985102+chr03YCR026C0.968866650.97932414166335−chr03YCR043C0.9517648640.966166673206640−chr03YCR053W0.9897282410.992623598216693+chr03YCR087C-A0.9753989190.993232435264464−chr03YCR090C0.9656372940.95018878272860−chr03YCR108C0.9858030860.993860549316185−chr04YDL248W0.9647013650.9802173261802+chr04YDL247W0.9896861990.9979977415985+chr04YDL233W0.9576722520.9785748936798+chr04YDL232W0.9795926860.97041347738488+chr04YDL225W0.9500531330.97844134852446+chr04YDL208W0.9872648930.98789479487513+chr04YDL189W0.9658153560.98561241122217+chr04YDL174C0.9562155710.953787348147590−chr04YDL147W0.9717550590.950911485190925+chr04YDL116W0.9659361230.976379579251566+chr04YDL110C0.9742382540.97295169264964−chr04YDL102W0.9577865380.980122821276872+chr04YDL085W0.978879370.960150217303211+chr04YDL035C0.9755732120.977145228392054−chr04YDL025C0.961346730.972526893407203−chr04YDR019C0.952697720.953635877485362−chr04YDR028C0.9609374360.959981321500876−chr04YDR034C-C0.9672226360.9814374519353−chr04YDR034C-D0.9672226360.981437429519353−chr04YDR037W0.9513652920.956861294525437+chr04YDR054C0.9559288020.982048103562325−chr04YDR055W0.9503210120.952540035563525+chr04YDR062W0.9740218330.967688258576471+chr04YDR109C0.9543961630.952291074675664−chr04YDR110W0.9860819050.974555387676099+chr04YDR120C0.9602008450.969981962693258−chr04YDR162C0.9673017410.984347121781097−chr04YDR233C0.9670240580.967951444930353−chr04YDR234W0.9674151590.980945022931125+chr04YDR238C0.976026420.973622232940812−chr04YDR261C-D0.9848486460.993722663992345−chr04YDR261C-C0.9848486460.9937227992345−chr04YDR262W0.9909893970.995915841993130+chr04YDR270W0.9511398260.962635341005671+chr04YDR281C0.9846193290.9593929091022317−chr04YDR300C0.9758496440.9716779381062787−chr04YDR301W0.9529233410.9775152221063348+chr04YDR307W0.9519188860.9700336261075861+chr04YDR310C0.9517239310.9692731531084312−chr04YDR311W0.9536853570.9805957381085062+chr04YDR317W0.989692210.9915980491102181+chr04YDR322W0.9548432720.972043121110586+chr04YDR328C0.9574219930.9839578351126013−chr04YDR334W0.9530302880.9631555121135927+chr04YDR359C0.9774891720.9696060291194877−chr04YDR365C0.9850735440.9989266111206375−chr04YDR367W0.9900418050.9946892011212840+chr04YDR369C0.9576559190.969873051217572−chr04YDR379W0.9628990570.9749398211230159+chr04YDR397C0.9662989180.9751333371266890−chr04YDR420W0.9712171770.9918869411306259+chr04YDR424C0.9668818080.9898132331319833−chr04YDR432W0.9557287380.9821717181328775+chr04YDR438W0.9716269250.989040821338266+chr04YDR444W0.9735664330.9765024471350282+chr04YDR453C0.9526614920.9544810141365654−chr04YDR476C0.9699401590.9646792791411119−chr04YDR477W0.9547433430.9792437381412365+chr04YDR479C0.9774608250.9945017861416866−chr04YDR480W0.9677270740.9869534031417391+chr04YDR488C0.9831145120.9791871551430781−chr04YDR497C0.9558554120.9582365771445459−chr04YDR529C0.9662735760.9718120761496540−chr05YEL072W0.9681319130.97743553413720+chr05YEL043W0.9790798580.9622770670478+chr05YEL038W0.9815722210.98836915180462+chr05YEL021W0.9513154750.951565922116167+chr05YER004W0.9563486380.987671859159579+chr05YER026C0.9649528970.993875293208473−chr05YER076C0.9653982440.971982059313494−chr05YER083C0.9531850480.981521771327027−chr05YER094C0.9760270490.982595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total of 3339 ortholog clusters were identified (See table 1 in Supplementary Material available at doi: 10.1100/2012/298174) betweenA. fumigatusandS. 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 betweenAspergillus fumigatus and Saccharomyces cerevisiae.
S. cerevisiae geneA. fumigatus geneCorrelation coefficientYCR053WAFUA_3G089800.851750303YOL006CAFUA_1G035000.814728478YLR208WAFUA_4G060900.810778356YJR160CAFUA_8G072400.807607644YKL064WAFUA_2G080700.771984405YDL208WAFUA_1G135700.763687527YDL247WAFUA_8G072400.751799318YJL034WAFUA_2G046200.751475734YJL174WAFUA_2G075900.731359519YGL006WAFUA_1G108800.706118907YLR307WAFUA_6G104300.701428537YOR056CAFUA_5G040000.693624039YJR049CAFUA_5G128700.6873278YOR132WAFUA_5G071500.684358232YDR028CAFUA_8G027200.681519128YKL059CAFUA_2G062200.677236775YDR019CAFUA_1G107800.673590566YDR262WAFUA_8G053600.668577442YJR160CAFUA_3G017000.655149877YBL087CAFUA_2G033800.654275917YDR120CAFUA_3G042000.653965099YMR110CAFUA_4G135000.649573592YDR479CAFUA_2G015100.649340576YLR307WAFUA_4G099400.641152119YLL050CAFUA_5G105700.636927762YMR011WAFUA_2G115200.631877767YGR149WAFUA_3G082400.627253467YKL125WAFUA_1G025900.626251676YDL247WAFUA_3G017000.621782331YHR165CAFUA_2G030300.616638486YLR355CAFUA_3G144900.615946987YLR307WAFUA_3G072100.615345397YNL156CAFUA_4G076800.605449075YOL157CAFUA_8G070700.600254438YPL196WAFUA_3G087400.596649007YOL156WAFUA_2G115200.589475104YGL055WAFUA_7G059200.583471232YER094CAFUA_4G074200.580111415YER026CAFUA_4G136800.579632053YKR031CAFUA_3G056300.578947614YJR041CAFUA_1G132000.577042969YCL057C-AAFUA_1G131950.56703028YKL167CAFUA_6G126200.566497151YDR334WAFUA_7G023700.556810391YDL085WAFUA_1G119600.555058025YIR038CAFUA_8G025000.553657653YGL056CAFUA_1G066600.550891198YLR133WAFUA_1G159300.547961885YLR137WAFUA_2G099300.542448721YER095WAFUA_1G104100.540102076YCR090CAFUA_2G155100.540015424YIR022WAFUA_3G128400.539096148YJR048WAFUA_2G131100.537701308YDL247WAFUA_8G013400.536753536YGL119WAFUA_6G043800.528264148YDR054CAFUA_5G092000.520282879YNR036CAFUA_5G107500.51817226YJL050WAFUA_4G071600.517374235YKR036CAFUA_5G131400.515007541YML041CAFUA_2G050300.514819597YML080WAFUA_1G165500.512494533YJL093CAFUA_1G142500.5107227YDR238CAFUA_1G109700.509749906YJL197WAFUA_2G141300.501902821YER173WAFUA_8G028200.501581347YJR160CAFUA_8G013400.499250408YOL058WAFUA_2G043100.497155736YGR006WAFUA_1G169900.496383573YPR161CAFUA_5G055100.495551014YBR136WAFUA_4G047600.49434371YJR049CAFUA_2G013500.493221085YPR060CAFUA_5G131300.490832735YDR055WAFUA_4G068200.482973721YLR104WAFUA_5G040400.47610876YIL129CAFUA_6G110100.473123981YDR300CAFUA_2G075700.469287567YOL156WAFUA_7G009500.46726022YGL201CAFUA_5G108900.462753539YKR086WAFUA_1G038200.461061937YPL157WAFUA_6G086100.460257721YIL046WAFUA_2G141100.45798838YGL048CAFUA_4G046600.457664607YHR216WAFUA_2G036100.456902272YDR424CAFUA_1G048500.455530713YPR141CAFUA_2G142800.452133975YLR427WAFUA_1G071500.444534443YHL004WAFUA_1G065700.439699159YLL002WAFUA_5G095400.431520497YKR052CAFUA_6G125500.429429023YNL260CAFUA_1G090000.425937756YNL112WAFUA_2G107500.423331447YFL026WAFUA_3G143300.422540136YCL038CAFUA_2G153700.420548714YPR156CAFUA_4G011400.419838437YHL024WAFUA_3G062300.417835282YBR173CAFUA_5G107400.414366599YGR178CAFUA_1G096300.410618083YMR036CAFUA_6G082000.408252022YDL147WAFUA_3G066100.40670988YJR095WAFUA_2G169300.405617695YPL171CAFUA_2G179600.40043227YBL061CAFUA_8G056200.398124519YHL001WAFUA_6G038300.397471165YNL255CAFUA_1G076300.390527675YGL006WAFUA_3G106900.389206341YIL125WAFUA_4G116500.387564721YMR011WAFUA_5G011600.381368332YMR010WAFUA_5G035100.378223656YMR319CAFUA_4G146400.376638524YDL110CAFUA_1G091600.376540694YOL086CAFUA_5G062400.376281416YGR076CAFUA_4G090000.373900773YOR204WAFUA_4G076600.368301524YMR229CAFUA_2G160400.367246087YLR025WAFUA_1G064200.363738278YPL281CAFUA_6G067700.363265962YOR294WAFUA_7G044300.363077313YLR299WAFUA_7G047600.36169498YCL038CAFUA_2G061700.359699115YKL113CAFUA_3G060600.351986208YHL020CAFUA_5G094200.350312962YMR224CAFUA_6G114100.348946198YDR444WAFUA_3G042400.345942811YER107CAFUA_1G090200.34238252YDR162CAFUA_2G036800.342381673YNL212WAFUA_3G087500.341561675YNL097CAFUA_3G119400.339603963YKL191WAFUA_6G071000.337319743YPL030WAFUA_6G025700.336821966YNL224CAFUA_3G053300.336636223YKR024CAFUA_5G110500.328747023YPR020WAFUA_1G162800.323479927YPL171CAFUA_2G040600.322952534YOR393WAFUA_6G067700.321210691YPR088CAFUA_5G038800.31284654YGL058WAFUA_6G142100.312000165YFL059WAFUA_5G080900.309971957YBR243CAFUA_2G112400.307271969YJL048CAFUA_3G063600.306215007YNL055CAFUA_4G069100.305279025YOR058CAFUA_2G162600.305221634YGR240CAFUA_4G009600.304340045YBR279WAFUA_2G110000.303224YPL078CAFUA_8G054400.300712891YLR059CAFUA_3G118200.296403753YLR380WAFUA_6G126900.295562758YDL174CAFUA_1G175200.29517154YCL057WAFUA_7G059300.293762978YDR234WAFUA_5G088900.293096856YDR438WAFUA_5G121400.287954196YGL028CAFUA_8G056100.287899385YML004CAFUA_6G079400.285261452YOL045WAFUA_2G028500.284622252YLR429WAFUA_2G142700.283845667YDR397CAFUA_3G023400.283499213YBR260CAFUA_3G062800.282196097YCR087C-AAFUA_7G047000.281322207YMR011WAFUA_7G009500.280854319YOL148CAFUA_1G165800.274850272YDR379WAFUA_1G126800.273041289YJL151CAFUA_5G105900.272979399YML020WAFUA_5G120900.266526854YGR082WAFUA_6G113800.265129767YJR113CAFUA_1G042800.262789584YIL031WAFUA_5G032000.256820972YDR432WAFUA_3G101000.255963453YDR359CAFUA_4G075600.255317292YDR233CAFUA_6G136700.253861938YGR255CAFUA_4G129300.252312468YFR009WAFUA_4G060700.245534257YPL280WAFUA_3G084900.243781447YOR075WAFUA_2G096700.239487119YJL219WAFUA_7G009500.239124986YCR026CAFUA_2G147700.234276623YOR391CAFUA_3G084900.233098887YGL180WAFUA_4G090500.231299038YLR323CAFUA_5G077200.231114462YGL006WAFUA_7G010300.222088168YBR179CAFUA_5G133920.219453048YKR082WAFUA_4G058400.214144582YLR087CAFUA_2G135200.209434557YCL064CAFUA_4G078100.204494803YOL156WAFUA_5G011600.203744073YBR249CAFUA_7G040700.202306902YJL093CAFUA_3G075400.201465401YOL077CAFUA_1G022100.196710807YLR426WAFUA_1G062800.196041865YMR060CAFUA_2G038400.194299595YOR048CAFUA_1G137300.193994391YDL174CAFUA_7G025600.193117882YJL221CAFUA_8G070700.187015236YGR054WAFUA_3G059700.181434929YPR176CAFUA_7G044600.180215936YML003WAFUA_1G098700.173517378YKR084CAFUA_2G046300.171646807YDR270WAFUA_4G126200.171601357YOR336WAFUA_2G023600.164107564YFL058WAFUA_5G024700.160695353YNL301CAFUA_2G073800.151927636YJL221CAFUA_7G063800.150927464YGR280CAFUA_7G036900.150422383YOL089CAFUA_6G019600.149731857YGR193CAFUA_3G082700.14875632YDR328CAFUA_5G060600.143711765YPL254WAFUA_2G060600.143220591YPL206CAFUA_2G009900.138505935YEL021WAFUA_2G083600.13720587YOL068CAFUA_4G121200.134069861YJR160CAFUA_7G063900.131179873YNL310CAFUA_6G082300.130305791YIL061CAFUA_5G134800.126828721YGL163CAFUA_6G129100.12597657YGR173WAFUA_5G067700.123606414YJL092WAFUA_2G039100.122708164YJR065CAFUA_5G115600.121854722YBR023CAFUA_8G056300.120791924YBR084WAFUA_3G086500.118154138YMR197CAFUA_4G107100.114428905YMR241WAFUA_5G042200.114113659YNL097CAFUA_7G018700.109316946YGL171WAFUA_1G162900.103112508YOR365CAFUA_4G133400.094260129YHR215WAFUA_6G113300.092128581YKL013CAFUA_6G023700.088958318YOR043WAFUA_4G061300.087990985YPR062WAFUA_1G050500.087018417YDR497CAFUA_2G079100.078863767YDR477WAFUA_2G017000.074801159YLR378CAFUA_5G081300.074624328YBR060CAFUA_5G081100.073589072YGL120CAFUA_5G116200.069009268YIL063CAFUA_2G108100.06328373YOL157CAFUA_7G063800.06047767YGL043WAFUA_3G076700.059398891YMR027WAFUA_5G067100.058232831YHR215WAFUA_8G019100.05787337YDL247WAFUA_7G051900.05184022YPR048WAFUA_5G072900.049809159YBL051CAFUA_5G019400.048514144YHR148WAFUA_2G083200.047441878YJR160CAFUA_7G051900.045923723YJL039CAFUA_5G126700.042943521YNL029CAFUA_5G121600.031203315YGR267CAFUA_5G031400.029526621YNL027WAFUA_1G069000.02747405YDL247WAFUA_7G063900.023887472YHR107CAFUA_5G030800.020068991YKL165CAFUA_4G039700.01938034YNR012WAFUA_2G054300.019075112YLR085CAFUA_4G044200.018617278YPL082CAFUA_1G058300.017285628YCL064CAFUA_1G061500.014476469YNR039CAFUA_1G120900.011820922YOR216CAFUA_1G088300.008439713YOR148CAFUA_4G075500.006702846YDR420WAFUA_4G005000.006566287YPR018WAFUA_5G03720−0.000683184YDR322WAFUA_5G12810−0.002517201YNR015WAFUA_3G08390−0.013154917YBR251WAFUA_5G11540−0.01637247YHL028WAFUA_5G09020−0.020657813YPL146CAFUA_2G05550−0.023787247YKL127WAFUA_3G11830−0.026619404YJR160CAFUA_2G10910−0.029508087YIR038CAFUA_1G17010−0.030714781YDL247WAFUA_2G10910−0.033905332YBR204CAFUA_1G03540−0.038361835YJR010WAFUA_3G06530−0.038908707YMR210WAFUA_6G04640−0.046477426YPR187WAFUA_1G05160−0.048502572YDR037WAFUA_6G07640−0.052027721YIL134WAFUA_6G05170−0.053118026YLR286CAFUA_5G03760−0.062116003YKL179CAFUA_1G14240−0.062203351YDR109CAFUA_4G04680−0.063717983YOL157CAFUA_3G07380−0.064624439YIR038CAFUA_2G17300−0.068756542YDL102WAFUA_2G16600−0.088010728YOR389WAFUA_2G01940−0.09375584YBR244WAFUA_3G12270−0.097477745YJL219WAFUA_2G11520−0.098366126YPL126WAFUA_7G02610−0.101632712YDL189WAFUA_1G09400−0.104331651YHL016CAFUA_1G04870−0.106608293YLR380WAFUA_4G13930−0.111437921YPR165WAFUA_6G06900−0.117573203YOL062CAFUA_5G07930−0.122120003YGL248WAFUA_1G14890−0.124318908YLR029CAFUA_1G04660−0.129375946YMR214WAFUA_2G08300−0.130867913YOR124CAFUA_6G12270−0.136050424YOL023WAFUA_1G06520−0.136914472YPL280WAFUA_3G01210−0.13706189YLR380WAFUA_7G06760−0.141209958YNL241CAFUA_3G08470−0.153108798YOR391CAFUA_3G01210−0.154014157YOL089CAFUA_6G02330−0.161608796YGL215WAFUA_3G10040−0.170171082YMR137CAFUA_2G15220−0.174259735YER004WAFUA_6G08930−0.179730339YDR365CAFUA_2G05420−0.181946191YDR529CAFUA_4G06790−0.185927497YDR062WAFUA_6G00300−0.189190157YOL086CAFUA_7G01010−0.190813468YOL026CAFUA_5G03630−0.19138562YIL033CAFUA_3G10000−0.195925157YBR290WAFUA_4G13740−0.19955841YAR019CAFUA_4G06750−0.204744755YHL007CAFUA_2G04680−0.20737573YMR078CAFUA_7G05480−0.222707833YDR311WAFUA_4G11690−0.22686955YOL100WAFUA_3G12670−0.230714484YGR162WAFUA_2G09490−0.232235851YGL255WAFUA_1G01550−0.248116851YPL038WAFUA_6G01910−0.252388553YCL035CAFUA_1G06100−0.255759517YNL082WAFUA_2G13410−0.259394819YDR062WAFUA_1G11890−0.263523207YOR390WAFUA_2G16210−0.269616243YJR141WAFUA_3G07970−0.2738444YOR365CAFUA_2G17650−0.274036262YDL116WAFUA_1G10860−0.278315121YKL020CAFUA_1G12550−0.278379939YDL174CAFUA_3G06820−0.286419799YBR029CAFUA_1G07010−0.296926336YLR096WAFUA_1G11080−0.297540349YFL028CAFUA_6G05080−0.303502181YOR089CAFUA_3G10740−0.30892361YPR010CAFUA_2G13000−0.309890067YJL219WAFUA_5G01160−0.321415181YNL097CAFUA_4G11660−0.329160424YMR116CAFUA_4G13170−0.329415498YPL280WAFUA_5G01430−0.331554435YHR091CAFUA_2G14030−0.337931682YIL030CAFUA_2G08650−0.350942099YFR037CAFUA_7G05510−0.356342064YOR391CAFUA_5G01430−0.356843862YDL174CAFUA_1G00510−0.402217656YML121WAFUA_5G09650−0.410825283YFL060CAFUA_2G08580−0.411505108YDR301WAFUA_8G04040−0.413112754YJL221CAFUA_3G07380−0.413321446YLR326WAFUA_5G12410−0.458648708YBL108C-AAFUA_4G03360−0.487139446YGR165WAFUA_5G08380−0.519339895YKL157WAFUA_4G09030−0.604021491YNL334CAFUA_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/).


## 2.1. Identification of Duplicated Gene Pairs inAspergillus 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 9630A. 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 inAspergillus fumigatus.
Gene pairChromosomeGene body regionGene directionFunctionAFUA1G0015012544227017+RING finger proteinAFUA6G09370622455492247121+RING finger proteinAFUA1G004201135528137781+Carboxypeptidase S1, putativeAFUA8G041208897824900076−Carboxypeptidase S1, putativeAFUA1G004401138359140093−DUF895 domain membrane proteinAFUA8G041108895512897246+DUF895 domain membrane proteinAFUA1G004501143117144466+N-acetylglucosamine-6-phosphate deacetylase(NagA), putativeAFUA8G041008891135892484−N-acetylglucosamine-6-phosphate deacetylase(NagA), putativeAFUA1G004701148615150219+Betaine aldehyde dehydrogenase, putativeAFUA8G040808885376886980−Betaine aldehyde dehydrogenase (BadH), putativeAFUA1G005301164101164771−Thermoresistant gluconokinase family proteinAFUA4G12050431637473164530−Thermoresistant gluconokinaseAFUA1G005501177114178593+Hypothetical proteinAFUA1G009101328785330274+Hypothetical proteinAFUA1G005801184790186873+Acid phosphatase (PhoG), putativeAFUA8G040508870757872487−Acid phosphatase (PhoG), putativeAFUA1G006501215584217006+Alpha-1,3-glucanase, putativeAFUA7G08510719733981974759+Alpha-1,3-glucanase, putativeAFUA1G009201331676332955−Hypothetical proteinAFUA3G06425315827481584037−Hypothetical proteinAFUA1G010501385302386244−Hypothetical proteinAFUA8G06160814656951466634+Hypothetical proteinAFUA1G025501744583746335−Tubulin alpha-1 subunitAFUA2G14990239470083948834−Tubulin alpha-2 subunitAFUA1G027301788249789373−Mitochondrial phosphate carrier protein (Ptp), putativeAFUA1G15140140702304071449−Mitochondrial phosphate carrier protein (Mir1), putativeAFUA1G05760116583821659697−Arsenite efflux transporterAFUA5G15010538824253883746+Arsenite permease (ArsB), putativeAFUA1G05760116583821659697−Arsenite efflux transporterAFUA1G16100143788984380216+Arsenite permease (ArsB), putativeAFUA1G10910128481552850137−Tubulin beta, putativeAFUA7G0025077022171948+Tubulin beta-2 subunitAFUA1G11260129715292971889−Conserved hypothetical proteinAFUA6G0027067954279886−Conserved hypothetical proteinAFUA1G11610130600583060510+3-Dehydroquinate dehydratase, type IIAFUA3G14850339297213930173+3-Dehydroquinate dehydratase, type IIAFUA1G11890131294473131489+Serine palmitoyltransferase 2, putativeAFUA6G0030068585187692−Serine palmitoyltransferase 1, putativeAFUA1G12850133988373400611+Nitrate transporter (nitrate permease)AFUA1G17470147823204783995+High-affinity nitrate transporter NrtBAFUA1G15970143384074339712+Aldo-keto reductase (AKR13), putativeAFUA8G015608401581402815−Aldo-keto reductase (YakC), putativeAFUA1G16030143588664360256−Conserved hypothetical proteinAFUA5G14930538632183864521−Conserved hypothetical proteinAFUA1G16040143634934365310+Metalloreductase, putativeAFUA5G14940538677973869542+Cell surface metalloreductase (FreA), putativeAFUA1G16050143665734368232+Hypothetical proteinAFUA5G14950538706353872465+Hypothetical proteinAFUA1G16070143703464373694+Conserved hypothetical proteinAFUA5G14980538745393877890+Conserved hypothetical proteinAFUA1G16080143745794375298−Hypothetical proteinAFUA5G14990538787973879579−Hypothetical proteinAFUA1G16090143778424378249−Arsenate reductase (ArsC), putativeAFUA5G15000538813863881835−Arsenate reductase (ArsC), putativeAFUA1G16100143788984380216+Arsenite permease (ArsB), putativeAFUA5G15010538824253883746+Arsenite permease (ArsB), putativeAFUA1G16110143804744381455−Arsenic methyltransferase (Cyt19), putativeAFUA5G15020538839293884993−Arsenic methyltransferase (Cyt19), putativeAFUA1G16120143856504386671−Arsenic resistance protein (ArsH), putativeAFUA8G07150817516931752688+ArsH proteinAFUA1G16120143856504386671−Arsenic resistance protein (ArsH), putativeAFUA5G15030538872873888230−Arsenic resistance protein (ArsH), putativeAFUA2G008002178081179459−PelA proteinAFUA5G10380526586562659968+Pectin lyase, putativeAFUA2G008002178081179459−PelA proteinAFUA7G05030711821041183794−Pectin lyase BAFUA2G04010210929731094679−Alpha, alpha-trehalose-phosphate synthase subunit, putativeAFUA6G12950632689583270783+Alpha, alpha-trehalose-phosphate Synthase subunitTPS1, putativeAFUA2G11270228972752904954−Alpha-1,3-glucan synthase, putativeAFUA3G009103210186217666+Alpha-1,3-glucan synthase, putativeAFUA3G0034037118672734+Glycosyl hydrolase, putativeAFUA4G027204751306752715−Glycosyl hydrolase, putativeAFUA3G006803151397153549−Copper amine oxidaseAFUA7G041807943893946136+Amine oxidaseAFUA3G015603393032394802−Aminoacid permease, putativeAFUA5G04260511409531142714+Arginine transporter, putativeAFUA3G024203597476598286+ThiJ/PfpI family proteinAFUA4G014004369123369944−ThiJ/PfpI family proteinAFUA3G030803824479825425+Endo-1,3(4)-beta-glucanase, putativeAFUA6G14540637024163703383−Endo-1,3(4)-beta-glucanase, putativeAFUA3G03980311346091136404+Cytochrome P450 monooxygenase, putativeAFUA5G10050525893012591081−Cytochrome P450 monooxygenase, putativeAFUA3G08160320942232095759−Eukaryotic translation initiation Factor eIF4A, putativeAFUA5G024105621886623486−DEAD/DEAH box helicase, putativeAFUA3G14420338318683834921+Chitin synthase GAFUA5G007605211013213795+Chitin synthase CAFUA4G005104133477135102−Hypothetical proteinAFUA7G08600720094362011052+Hypothetical proteinAFUA4G031104868474870249−Monosaccharide transporterAFUA5G10690527373482739178−Monosaccharide transporterAFUA4G03680410315861032539−Oxidoreductase, short-chain dehydrogenase/reductase familyAFUA6G035206764308765294−Short-chain dehydrogenase/reductase family protein, putativeAFUA4G09440424629202466158−Sodium P-type ATPase, putativeAFUA6G036906810027813362−Sodium transport ATPase, putativeAFUA4G14360437743073776166+Capsular associated protein, putativeAFUA5G07560518897911891689−Capsular associated protein, putativeAFUA5G0014551574916327−Hypothetical proteinAFUA6G11710629159032916483+Conserved hypothetical proteinAFUA5G0014551574916327−Hypothetical proteinAFUA7G08440719423191942804+Hypothetical proteinAFUA5G010305266294267439−Glyceraldehyde 3-phosphate dehydrogenase(Ccg-7), putativeAFUA5G019705503797505194+Glyceraldehyde 3-phosphate dehydrogenase GpdAAFUA5G06240514944551495619−Alcohol dehydrogenase, putativeAFUA7G010107270494271675−Alcohol dehydrogenase, putativeAFUA5G07980520190692020841+Hypothetical proteinAFUA5G14920538573503859167+Hypothetical proteinAFUA5G09130523456892346728−Polysaccharide deacetylase family proteinAFUA6G05030611958461196956+Polysaccharide deacetylase family proteinAFUA5G15030538872873888230−Arsenic resistance protein (ArsH), putativeAFUA8G07150817516931752688+ArsH proteinAFUA6G06750614752391476209+14-3-3 family proteinAFUA2G032902867203868250−14-3-3 family protein ArtA, putativeAFUA6G07070615876431589124+Cellobiohydrolase DAFUA6G11610628780782879676−1,4-beta-D-glucan-cellobiohydrolyase, putativeAFUA6G11430628371402839051+Aldehyde dehydrogenase, putativeAFUA7G010007267518269163−Aldehyde dehydrogenase, putativeAFUA6G11710629159032916483+Conserved hypothetical proteinAFUA7G08440719423191942804+Hypothetical proteinAFUA6G13490634319123433612−Glutamate decarboxylaseAFUA8G06020814288121430515+Glutamate decarboxylaseAFUA7G003607102030103064−UDP-galactose 4-epimerase, putativeAFUA8G008608203496204338+UDP-galactose 4-epimerase, putativeAFUA7G07050717256861726402−Hypothetical proteinAFUA7G08300718702441870960−Hypothetical proteinAFUA7G07060717288761732992−Hypothetical proteinAFUA7G08310718734371877817−Hypothetical proteinTable 2
Spearman's rank correlation coefficients of nucleosome position profiles in the promoter and body regions of 63 duplicated gene pairs inAspergillus fumigatus.
Gene pairGene promoterGene bodyAFUA1G00150AFUA6G093700.7501769130.215204254AFUA1G00420AFUA8G041200.803709740.723149072AFUA1G00440AFUA8G041100.8560485610.225149091AFUA1G00450AFUA8G041000.92136020.94633912AFUA1G00470AFUA8G040800.4331180450.818800395AFUA1G00530AFUA4G120500.326735006−0.199291887AFUA1G00550AFUA1G009100.6769103340.678763937AFUA1G00580AFUA8G040500.3052917930.312927993AFUA1G00650AFUA7G085100.4481715250.085599209AFUA1G00920AFUA3G064250.719748778−0.340001527AFUA1G01050AFUA8G061600.6351493080.176679577AFUA1G02550AFUA2G149900.139079116−0.036644732AFUA1G02730AFUA1G151400.4521932590.067186644AFUA1G05760AFUA5G150100.3958497110.117006666AFUA1G05760AFUA1G161000.127911436−0.397363108AFUA1G10910AFUA7G002500.3107185770.665906466AFUA1G11260AFUA6G002700.617303556−0.02397179AFUA1G11610AFUA3G148500.6362810690.869300724AFUA1G11890AFUA6G003000.2544875640.429087849AFUA1G12850AFUA1G174700.6444472870.008468365AFUA1G15970AFUA8G015600.373850536−0.106800689AFUA1G16030AFUA5G149300.6183497650.858488283AFUA1G16040AFUA5G149400.4810540050.017330056AFUA1G16050AFUA5G14950−0.345037268−0.392132138AFUA1G16070AFUA5G149800.9309221240.902581516AFUA1G16080AFUA5G149900.5599807870.136819379AFUA1G16090AFUA5G150000.7738679240.338119153AFUA1G16100AFUA5G150100.6811700980.70434823AFUA1G16110AFUA5G15020−0.2618649050.632982505AFUA1G16120AFUA8G071500.3568699150.074502754AFUA1G16120AFUA5G15030−0.135442129−0.239074416AFUA2G00800AFUA5G103800.3520639160.460712971AFUA2G00800AFUA7G05030−0.1141844430.457081245AFUA2G04010AFUA6G129500.134790545−0.14813806AFUA2G11270AFUA3G00910−0.0042078580.192024608AFUA3G00340AFUA4G02720−0.0502599870.055757479AFUA3G00680AFUA7G041800.399912713−0.044615588AFUA3G01560AFUA5G042600.1793950670.125177632AFUA3G02420AFUA4G014000.6627124810.646400554AFUA3G03080AFUA6G145400.3401707−0.021961056AFUA3G03980AFUA5G100500.4867265340.318475376AFUA3G08160AFUA5G024100.309645464−0.255654021AFUA3G14420AFUA5G007600.9176851340.415111431AFUA4G00510AFUA7G086000.5785827430.441363777AFUA4G03110AFUA5G106900.7215401930.176996881AFUA4G03680AFUA6G035200.662657833−0.320417166AFUA4G09440AFUA6G036900.2041591840.000609208AFUA4G14360AFUA5G075600.0380830730.515103795AFUA5G00145AFUA6G117100.809402393−0.741045496AFUA5G00145AFUA7G084400.019652845−0.575600966AFUA5G01030AFUA5G019700.5762111780.132479521AFUA5G06240AFUA7G010100.163674862−0.552899419AFUA5G07980AFUA5G149200.669562689−0.265207346AFUA5G09130AFUA6G050300.0924529380.729278817AFUA5G15030AFUA8G071500.337482368−0.502391454AFUA6G06750AFUA2G032900.333402926−0.538389013AFUA6G07070AFUA6G11610−0.048961745−0.239430043AFUA6G11430AFUA7G010000.01454920.476692417AFUA6G11710AFUA7G084400.2433626230.823124582AFUA6G13490AFUA8G060200.7681865330.174847009AFUA7G00360AFUA8G00860−0.1150502680.03815086AFUA7G07050AFUA7G083000.707568420.778653567AFUA7G07060AFUA7G083100.9068527250.919839072


## 2.2. Identification of Orthologous Gene Pairs inAspergillus fumigates and Saccharomyces cerevisiae

In a comparison of nucleosome positioning betweenA. fumigatusandS. cerevisiae, I focused on 466 genes (Table 3) that showed notably high conservation of nucleosome positioning in the promoters of the control and the ELP3andHOS2 deletion mutants from the previous study [10].Table 3
Genes ofSaccharomyces cerevisiae with highly conserved nucleosome positions in the promoters of the control and histone modification gene deletion mutants.
ChromosomeGeneCorrelation coefficient between the control and theELP3 deletionCorrelation coefficient between the control and theHOS2 deletionTranslational start siteTranscription directionchr01YAL064W-B0.9747199550.96581424312047+chr01YAL056W0.9898010030.98215732839260+chr01YAL047C0.9502436910.95312923256858−chr01YAR019C0.9701151620.960628643175133−chr01YAR033W0.9688078750.987221166188101+chr02YBL111C0.9958020650.994550655009−chr02YBL108C-A0.9594970130.9699665427733−chr02YBL101C0.9585171250.99132409628299−chr02YBL087C0.957191870.95727320360735−chr02YBL061C0.9849602120.992728731107408−chr02YBL060W0.9603302890.99357258107934+chr02YBL051C0.976537340.989165943124762−chr02YBL032W0.9568748540.980366627160187+chr02YBL005W-B0.9507813220.952679326221333+chr02YBL005W-A0.9507813220.952679326221333+chr02YBR023C0.9602384990.992906362287925−chr02YBR029C0.9592313890.987222377297742−chr02YBR047W0.9645645220.963289004331831+chr02YBR060C0.9592298710.974718825362512−chr02YBR084W0.9621728660.981530879411048+chr02YBR090C0.9676587850.971792497427052−chr02YBR091C0.9650378620.985960321427478−chr02YBR131W0.9533232490.969685452497157+chr02YBR136W0.9635468220.974854426505662+chr02YBR173C0.9785183910.961438459582167−chr02YBR179C0.9884891460.991754907589109−chr02YBR180W0.9871322120.975974209589736+chr02YBR204C0.9709589460.978433534633376−chr02YBR243C0.9722534670.961252065706788−chr02YBR244W0.9742023060.992702483707523+chr02YBR249C0.9557426820.976101912717989−chr02YBR250W0.9541491880.976352348719028+chr02YBR251W0.962732610.961120273721385+chr02YBR258C0.9666018990.955155711730157−chr02YBR260C0.9693460190.970918059734634−chr02YBR279W0.9560813870.964626558761253+chr02YBR290W0.9815868230.967935658782587+chr03YCL064C0.9571506980.9527051416880−chr03YCL058W-A0.9698953450.99239482923584+chr03YCL057C-A0.9908861920.98717057624325−chr03YCL057W0.9630623570.96180462324768+chr03YCL038C0.9782105370.95763354856527−chr03YCL035C0.9813607050.97356815161173−chr03YCL019W0.9532416640.97868845985102+chr03YCR026C0.968866650.97932414166335−chr03YCR043C0.9517648640.966166673206640−chr03YCR053W0.9897282410.992623598216693+chr03YCR087C-A0.9753989190.993232435264464−chr03YCR090C0.9656372940.95018878272860−chr03YCR108C0.9858030860.993860549316185−chr04YDL248W0.9647013650.9802173261802+chr04YDL247W0.9896861990.9979977415985+chr04YDL233W0.9576722520.9785748936798+chr04YDL232W0.9795926860.97041347738488+chr04YDL225W0.9500531330.97844134852446+chr04YDL208W0.9872648930.98789479487513+chr04YDL189W0.9658153560.98561241122217+chr04YDL174C0.9562155710.953787348147590−chr04YDL147W0.9717550590.950911485190925+chr04YDL116W0.9659361230.976379579251566+chr04YDL110C0.9742382540.97295169264964−chr04YDL102W0.9577865380.980122821276872+chr04YDL085W0.978879370.960150217303211+chr04YDL035C0.9755732120.977145228392054−chr04YDL025C0.961346730.972526893407203−chr04YDR019C0.952697720.953635877485362−chr04YDR028C0.9609374360.959981321500876−chr04YDR034C-C0.9672226360.9814374519353−chr04YDR034C-D0.9672226360.981437429519353−chr04YDR037W0.9513652920.956861294525437+chr04YDR054C0.9559288020.982048103562325−chr04YDR055W0.9503210120.952540035563525+chr04YDR062W0.9740218330.967688258576471+chr04YDR109C0.9543961630.952291074675664−chr04YDR110W0.9860819050.974555387676099+chr04YDR120C0.9602008450.969981962693258−chr04YDR162C0.9673017410.984347121781097−chr04YDR233C0.9670240580.967951444930353−chr04YDR234W0.9674151590.980945022931125+chr04YDR238C0.976026420.973622232940812−chr04YDR261C-D0.9848486460.993722663992345−chr04YDR261C-C0.9848486460.9937227992345−chr04YDR262W0.9909893970.995915841993130+chr04YDR270W0.9511398260.962635341005671+chr04YDR281C0.9846193290.9593929091022317−chr04YDR300C0.9758496440.9716779381062787−chr04YDR301W0.9529233410.9775152221063348+chr04YDR307W0.9519188860.9700336261075861+chr04YDR310C0.9517239310.9692731531084312−chr04YDR311W0.9536853570.9805957381085062+chr04YDR317W0.989692210.9915980491102181+chr04YDR322W0.9548432720.972043121110586+chr04YDR328C0.9574219930.9839578351126013−chr04YDR334W0.9530302880.9631555121135927+chr04YDR359C0.9774891720.9696060291194877−chr04YDR365C0.9850735440.9989266111206375−chr04YDR367W0.9900418050.9946892011212840+chr04YDR369C0.9576559190.969873051217572−chr04YDR379W0.9628990570.9749398211230159+chr04YDR397C0.9662989180.9751333371266890−chr04YDR420W0.9712171770.9918869411306259+chr04YDR424C0.9668818080.9898132331319833−chr04YDR432W0.9557287380.9821717181328775+chr04YDR438W0.9716269250.989040821338266+chr04YDR444W0.9735664330.9765024471350282+chr04YDR453C0.9526614920.9544810141365654−chr04YDR476C0.9699401590.9646792791411119−chr04YDR477W0.9547433430.9792437381412365+chr04YDR479C0.9774608250.9945017861416866−chr04YDR480W0.9677270740.9869534031417391+chr04YDR488C0.9831145120.9791871551430781−chr04YDR497C0.9558554120.9582365771445459−chr04YDR529C0.9662735760.9718120761496540−chr05YEL072W0.9681319130.97743553413720+chr05YEL043W0.9790798580.9622770670478+chr05YEL038W0.9815722210.98836915180462+chr05YEL021W0.9513154750.951565922116167+chr05YER004W0.9563486380.987671859159579+chr05YER026C0.9649528970.993875293208473−chr05YER076C0.9653982440.971982059313494−chr05YER083C0.9531850480.981521771327027−chr05YER094C0.9760270490.982595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total of 3339 ortholog clusters were identified (See table 1 in Supplementary Material available at doi: 10.1100/2012/298174) betweenA. fumigatusandS. 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 betweenAspergillus fumigatus and Saccharomyces cerevisiae.
S. cerevisiae geneA. fumigatus geneCorrelation coefficientYCR053WAFUA_3G089800.851750303YOL006CAFUA_1G035000.814728478YLR208WAFUA_4G060900.810778356YJR160CAFUA_8G072400.807607644YKL064WAFUA_2G080700.771984405YDL208WAFUA_1G135700.763687527YDL247WAFUA_8G072400.751799318YJL034WAFUA_2G046200.751475734YJL174WAFUA_2G075900.731359519YGL006WAFUA_1G108800.706118907YLR307WAFUA_6G104300.701428537YOR056CAFUA_5G040000.693624039YJR049CAFUA_5G128700.6873278YOR132WAFUA_5G071500.684358232YDR028CAFUA_8G027200.681519128YKL059CAFUA_2G062200.677236775YDR019CAFUA_1G107800.673590566YDR262WAFUA_8G053600.668577442YJR160CAFUA_3G017000.655149877YBL087CAFUA_2G033800.654275917YDR120CAFUA_3G042000.653965099YMR110CAFUA_4G135000.649573592YDR479CAFUA_2G015100.649340576YLR307WAFUA_4G099400.641152119YLL050CAFUA_5G105700.636927762YMR011WAFUA_2G115200.631877767YGR149WAFUA_3G082400.627253467YKL125WAFUA_1G025900.626251676YDL247WAFUA_3G017000.621782331YHR165CAFUA_2G030300.616638486YLR355CAFUA_3G144900.615946987YLR307WAFUA_3G072100.615345397YNL156CAFUA_4G076800.605449075YOL157CAFUA_8G070700.600254438YPL196WAFUA_3G087400.596649007YOL156WAFUA_2G115200.589475104YGL055WAFUA_7G059200.583471232YER094CAFUA_4G074200.580111415YER026CAFUA_4G136800.579632053YKR031CAFUA_3G056300.578947614YJR041CAFUA_1G132000.577042969YCL057C-AAFUA_1G131950.56703028YKL167CAFUA_6G126200.566497151YDR334WAFUA_7G023700.556810391YDL085WAFUA_1G119600.555058025YIR038CAFUA_8G025000.553657653YGL056CAFUA_1G066600.550891198YLR133WAFUA_1G159300.547961885YLR137WAFUA_2G099300.542448721YER095WAFUA_1G104100.540102076YCR090CAFUA_2G155100.540015424YIR022WAFUA_3G128400.539096148YJR048WAFUA_2G131100.537701308YDL247WAFUA_8G013400.536753536YGL119WAFUA_6G043800.528264148YDR054CAFUA_5G092000.520282879YNR036CAFUA_5G107500.51817226YJL050WAFUA_4G071600.517374235YKR036CAFUA_5G131400.515007541YML041CAFUA_2G050300.514819597YML080WAFUA_1G165500.512494533YJL093CAFUA_1G142500.5107227YDR238CAFUA_1G109700.509749906YJL197WAFUA_2G141300.501902821YER173WAFUA_8G028200.501581347YJR160CAFUA_8G013400.499250408YOL058WAFUA_2G043100.497155736YGR006WAFUA_1G169900.496383573YPR161CAFUA_5G055100.495551014YBR136WAFUA_4G047600.49434371YJR049CAFUA_2G013500.493221085YPR060CAFUA_5G131300.490832735YDR055WAFUA_4G068200.482973721YLR104WAFUA_5G040400.47610876YIL129CAFUA_6G110100.473123981YDR300CAFUA_2G075700.469287567YOL156WAFUA_7G009500.46726022YGL201CAFUA_5G108900.462753539YKR086WAFUA_1G038200.461061937YPL157WAFUA_6G086100.460257721YIL046WAFUA_2G141100.45798838YGL048CAFUA_4G046600.457664607YHR216WAFUA_2G036100.456902272YDR424CAFUA_1G048500.455530713YPR141CAFUA_2G142800.452133975YLR427WAFUA_1G071500.444534443YHL004WAFUA_1G065700.439699159YLL002WAFUA_5G095400.431520497YKR052CAFUA_6G125500.429429023YNL260CAFUA_1G090000.425937756YNL112WAFUA_2G107500.423331447YFL026WAFUA_3G143300.422540136YCL038CAFUA_2G153700.420548714YPR156CAFUA_4G011400.419838437YHL024WAFUA_3G062300.417835282YBR173CAFUA_5G107400.414366599YGR178CAFUA_1G096300.410618083YMR036CAFUA_6G082000.408252022YDL147WAFUA_3G066100.40670988YJR095WAFUA_2G169300.405617695YPL171CAFUA_2G179600.40043227YBL061CAFUA_8G056200.398124519YHL001WAFUA_6G038300.397471165YNL255CAFUA_1G076300.390527675YGL006WAFUA_3G106900.389206341YIL125WAFUA_4G116500.387564721YMR011WAFUA_5G011600.381368332YMR010WAFUA_5G035100.378223656YMR319CAFUA_4G146400.376638524YDL110CAFUA_1G091600.376540694YOL086CAFUA_5G062400.376281416YGR076CAFUA_4G090000.373900773YOR204WAFUA_4G076600.368301524YMR229CAFUA_2G160400.367246087YLR025WAFUA_1G064200.363738278YPL281CAFUA_6G067700.363265962YOR294WAFUA_7G044300.363077313YLR299WAFUA_7G047600.36169498YCL038CAFUA_2G061700.359699115YKL113CAFUA_3G060600.351986208YHL020CAFUA_5G094200.350312962YMR224CAFUA_6G114100.348946198YDR444WAFUA_3G042400.345942811YER107CAFUA_1G090200.34238252YDR162CAFUA_2G036800.342381673YNL212WAFUA_3G087500.341561675YNL097CAFUA_3G119400.339603963YKL191WAFUA_6G071000.337319743YPL030WAFUA_6G025700.336821966YNL224CAFUA_3G053300.336636223YKR024CAFUA_5G110500.328747023YPR020WAFUA_1G162800.323479927YPL171CAFUA_2G040600.322952534YOR393WAFUA_6G067700.321210691YPR088CAFUA_5G038800.31284654YGL058WAFUA_6G142100.312000165YFL059WAFUA_5G080900.309971957YBR243CAFUA_2G112400.307271969YJL048CAFUA_3G063600.306215007YNL055CAFUA_4G069100.305279025YOR058CAFUA_2G162600.305221634YGR240CAFUA_4G009600.304340045YBR279WAFUA_2G110000.303224YPL078CAFUA_8G054400.300712891YLR059CAFUA_3G118200.296403753YLR380WAFUA_6G126900.295562758YDL174CAFUA_1G175200.29517154YCL057WAFUA_7G059300.293762978YDR234WAFUA_5G088900.293096856YDR438WAFUA_5G121400.287954196YGL028CAFUA_8G056100.287899385YML004CAFUA_6G079400.285261452YOL045WAFUA_2G028500.284622252YLR429WAFUA_2G142700.283845667YDR397CAFUA_3G023400.283499213YBR260CAFUA_3G062800.282196097YCR087C-AAFUA_7G047000.281322207YMR011WAFUA_7G009500.280854319YOL148CAFUA_1G165800.274850272YDR379WAFUA_1G126800.273041289YJL151CAFUA_5G105900.272979399YML020WAFUA_5G120900.266526854YGR082WAFUA_6G113800.265129767YJR113CAFUA_1G042800.262789584YIL031WAFUA_5G032000.256820972YDR432WAFUA_3G101000.255963453YDR359CAFUA_4G075600.255317292YDR233CAFUA_6G136700.253861938YGR255CAFUA_4G129300.252312468YFR009WAFUA_4G060700.245534257YPL280WAFUA_3G084900.243781447YOR075WAFUA_2G096700.239487119YJL219WAFUA_7G009500.239124986YCR026CAFUA_2G147700.234276623YOR391CAFUA_3G084900.233098887YGL180WAFUA_4G090500.231299038YLR323CAFUA_5G077200.231114462YGL006WAFUA_7G010300.222088168YBR179CAFUA_5G133920.219453048YKR082WAFUA_4G058400.214144582YLR087CAFUA_2G135200.209434557YCL064CAFUA_4G078100.204494803YOL156WAFUA_5G011600.203744073YBR249CAFUA_7G040700.202306902YJL093CAFUA_3G075400.201465401YOL077CAFUA_1G022100.196710807YLR426WAFUA_1G062800.196041865YMR060CAFUA_2G038400.194299595YOR048CAFUA_1G137300.193994391YDL174CAFUA_7G025600.193117882YJL221CAFUA_8G070700.187015236YGR054WAFUA_3G059700.181434929YPR176CAFUA_7G044600.180215936YML003WAFUA_1G098700.173517378YKR084CAFUA_2G046300.171646807YDR270WAFUA_4G126200.171601357YOR336WAFUA_2G023600.164107564YFL058WAFUA_5G024700.160695353YNL301CAFUA_2G073800.151927636YJL221CAFUA_7G063800.150927464YGR280CAFUA_7G036900.150422383YOL089CAFUA_6G019600.149731857YGR193CAFUA_3G082700.14875632YDR328CAFUA_5G060600.143711765YPL254WAFUA_2G060600.143220591YPL206CAFUA_2G009900.138505935YEL021WAFUA_2G083600.13720587YOL068CAFUA_4G121200.134069861YJR160CAFUA_7G063900.131179873YNL310CAFUA_6G082300.130305791YIL061CAFUA_5G134800.126828721YGL163CAFUA_6G129100.12597657YGR173WAFUA_5G067700.123606414YJL092WAFUA_2G039100.122708164YJR065CAFUA_5G115600.121854722YBR023CAFUA_8G056300.120791924YBR084WAFUA_3G086500.118154138YMR197CAFUA_4G107100.114428905YMR241WAFUA_5G042200.114113659YNL097CAFUA_7G018700.109316946YGL171WAFUA_1G162900.103112508YOR365CAFUA_4G133400.094260129YHR215WAFUA_6G113300.092128581YKL013CAFUA_6G023700.088958318YOR043WAFUA_4G061300.087990985YPR062WAFUA_1G050500.087018417YDR497CAFUA_2G079100.078863767YDR477WAFUA_2G017000.074801159YLR378CAFUA_5G081300.074624328YBR060CAFUA_5G081100.073589072YGL120CAFUA_5G116200.069009268YIL063CAFUA_2G108100.06328373YOL157CAFUA_7G063800.06047767YGL043WAFUA_3G076700.059398891YMR027WAFUA_5G067100.058232831YHR215WAFUA_8G019100.05787337YDL247WAFUA_7G051900.05184022YPR048WAFUA_5G072900.049809159YBL051CAFUA_5G019400.048514144YHR148WAFUA_2G083200.047441878YJR160CAFUA_7G051900.045923723YJL039CAFUA_5G126700.042943521YNL029CAFUA_5G121600.031203315YGR267CAFUA_5G031400.029526621YNL027WAFUA_1G069000.02747405YDL247WAFUA_7G063900.023887472YHR107CAFUA_5G030800.020068991YKL165CAFUA_4G039700.01938034YNR012WAFUA_2G054300.019075112YLR085CAFUA_4G044200.018617278YPL082CAFUA_1G058300.017285628YCL064CAFUA_1G061500.014476469YNR039CAFUA_1G120900.011820922YOR216CAFUA_1G088300.008439713YOR148CAFUA_4G075500.006702846YDR420WAFUA_4G005000.006566287YPR018WAFUA_5G03720−0.000683184YDR322WAFUA_5G12810−0.002517201YNR015WAFUA_3G08390−0.013154917YBR251WAFUA_5G11540−0.01637247YHL028WAFUA_5G09020−0.020657813YPL146CAFUA_2G05550−0.023787247YKL127WAFUA_3G11830−0.026619404YJR160CAFUA_2G10910−0.029508087YIR038CAFUA_1G17010−0.030714781YDL247WAFUA_2G10910−0.033905332YBR204CAFUA_1G03540−0.038361835YJR010WAFUA_3G06530−0.038908707YMR210WAFUA_6G04640−0.046477426YPR187WAFUA_1G05160−0.048502572YDR037WAFUA_6G07640−0.052027721YIL134WAFUA_6G05170−0.053118026YLR286CAFUA_5G03760−0.062116003YKL179CAFUA_1G14240−0.062203351YDR109CAFUA_4G04680−0.063717983YOL157CAFUA_3G07380−0.064624439YIR038CAFUA_2G17300−0.068756542YDL102WAFUA_2G16600−0.088010728YOR389WAFUA_2G01940−0.09375584YBR244WAFUA_3G12270−0.097477745YJL219WAFUA_2G11520−0.098366126YPL126WAFUA_7G02610−0.101632712YDL189WAFUA_1G09400−0.104331651YHL016CAFUA_1G04870−0.106608293YLR380WAFUA_4G13930−0.111437921YPR165WAFUA_6G06900−0.117573203YOL062CAFUA_5G07930−0.122120003YGL248WAFUA_1G14890−0.124318908YLR029CAFUA_1G04660−0.129375946YMR214WAFUA_2G08300−0.130867913YOR124CAFUA_6G12270−0.136050424YOL023WAFUA_1G06520−0.136914472YPL280WAFUA_3G01210−0.13706189YLR380WAFUA_7G06760−0.141209958YNL241CAFUA_3G08470−0.153108798YOR391CAFUA_3G01210−0.154014157YOL089CAFUA_6G02330−0.161608796YGL215WAFUA_3G10040−0.170171082YMR137CAFUA_2G15220−0.174259735YER004WAFUA_6G08930−0.179730339YDR365CAFUA_2G05420−0.181946191YDR529CAFUA_4G06790−0.185927497YDR062WAFUA_6G00300−0.189190157YOL086CAFUA_7G01010−0.190813468YOL026CAFUA_5G03630−0.19138562YIL033CAFUA_3G10000−0.195925157YBR290WAFUA_4G13740−0.19955841YAR019CAFUA_4G06750−0.204744755YHL007CAFUA_2G04680−0.20737573YMR078CAFUA_7G05480−0.222707833YDR311WAFUA_4G11690−0.22686955YOL100WAFUA_3G12670−0.230714484YGR162WAFUA_2G09490−0.232235851YGL255WAFUA_1G01550−0.248116851YPL038WAFUA_6G01910−0.252388553YCL035CAFUA_1G06100−0.255759517YNL082WAFUA_2G13410−0.259394819YDR062WAFUA_1G11890−0.263523207YOR390WAFUA_2G16210−0.269616243YJR141WAFUA_3G07970−0.2738444YOR365CAFUA_2G17650−0.274036262YDL116WAFUA_1G10860−0.278315121YKL020CAFUA_1G12550−0.278379939YDL174CAFUA_3G06820−0.286419799YBR029CAFUA_1G07010−0.296926336YLR096WAFUA_1G11080−0.297540349YFL028CAFUA_6G05080−0.303502181YOR089CAFUA_3G10740−0.30892361YPR010CAFUA_2G13000−0.309890067YJL219WAFUA_5G01160−0.321415181YNL097CAFUA_4G11660−0.329160424YMR116CAFUA_4G13170−0.329415498YPL280WAFUA_5G01430−0.331554435YHR091CAFUA_2G14030−0.337931682YIL030CAFUA_2G08650−0.350942099YFR037CAFUA_7G05510−0.356342064YOR391CAFUA_5G01430−0.356843862YDL174CAFUA_1G00510−0.402217656YML121WAFUA_5G09650−0.410825283YFL060CAFUA_2G08580−0.411505108YDR301WAFUA_8G04040−0.413112754YJL221CAFUA_3G07380−0.413321446YLR326WAFUA_5G12410−0.458648708YBL108C-AAFUA_4G03360−0.487139446YGR165WAFUA_5G08380−0.519339895YKL157WAFUA_4G09030−0.604021491YNL334CAFUA_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 inAspergillus 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 (Figure1), 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 inAspergillus 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 duplicatedA. 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 betweenAspergillus 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).Mapping numbers of nucleosomes and transcription start sites in the promoter regions ofYIR038C, AFUA_8G02500, AFUA_1G17010, and AFUA_2G17300. Position 0 indicates the translational start site.
(a)(b)(c)(d)(e)(f)(g)(h)Interestingly, although the nucleosome position profile ofAFUA_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.


## 3.1. Nucleosome Position Profiles of Duplicated Genes inAspergillus 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 (Figure1), 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 inAspergillus 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 duplicatedA. 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 betweenAspergillus 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).Mapping numbers of nucleosomes and transcription start sites in the promoter regions ofYIR038C, AFUA_8G02500, AFUA_1G17010, and AFUA_2G17300. Position 0 indicates the translational start site.
(a)(b)(c)(d)(e)(f)(g)(h)Interestingly, although the nucleosome position profile ofAFUA_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.



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*Source: 298174-2012-02-15.xml*