Table 2.
Expression data for selected Hda1-regulated genes identified by modified gene ontology enrichment analysis.
| Gene ID | Gene name | Product Description | log2(fold change) |
|---|---|---|---|
| Chromatin/Histones | |||
| CNAG_00051 | SNT1 | Putative Set3c deacetylase complex subunit | −0.276468546 |
| CNAG_00063 | Histone H3 | −0.466103457 | |
| CNAG_00085 | ASF1 | Histone chaperone ASF1 | 0.224363607 |
| CNAG_00375 | GCN5 | Saga complex histone acetyltransferase | −0.338704771 |
| CNAG_00561 | Histone acetyltransferase type B catalytic subunit | −0.237158105 | |
| CNAG_00660 | HOS3 | Histone deacetylase HOS3 | −0.576126726 |
| CNAG_00718 | CAC2 | Chromatin assembly factor 1 subunit B | −0.137046165 |
| CNAG_00740 | SNF5 | Swi/Snf chromatin-remodeling complex subunit | −0.374848103 |
| CNAG_01013 | Chromatin binding protein | −0.66158404 | |
| CNAG_01018 | Histone-lysine N-methyltransferase Su(var)3–9 | −0.225072362 | |
| CNAG_01148 | FPR3 | Peptidyl-prolyl cis-trans isomerase | −0.664323021 |
| CNAG_01520 | Histone-arginine methyltransferase CARM1 | −0.507582078 | |
| CNAG_01563 | HDA1 | Histone deacetylase | −3.811428692 |
| CNAG_01648 | Histone H4 | −0.45507281 | |
| CNAG_01699 | CLR61 | Histone deacetylase | −0.160504318 |
| CNAG_01863 | SNF2 | Chromatin remodeling complex ATPase | −0.202397993 |
| CNAG_01972 | TAF10 | C2H2 zinc finger protein Zas1A | 0.151175426 |
| CNAG_02195 | Origin recognition complex subunit 1 | −0.746619743 | |
| CNAG_02215 | HAP3 | Transcriptional activator | −0.184025245 |
| CNAG_02536 | TAF6 | Transcription initiation factor TFIID subunit 6 | −0.1596263 |
| CNAG_02749 | Histone-lysine N-methyltransferase SUV420H | −0.450115461 | |
| CNAG_03188 | SET202 | Histone-lysine N-methyltransferase, H3 lysine-36 specific | −0.252801765 |
| CNAG_03203 | DNA polymerase epsilon p12 subunit | 0.371759788 | |
| CNAG_04168 | Histone H1/5 | −0.582447791 | |
| CNAG_05096 | HOS1 | Histone deacetylase | −0.123187881 |
| CNAG_05221 | Histone H2A.Z | −0.183930793 | |
| CNAG_05276 | CLR62 | Histone deacetylase | −0.176270846 |
| CNAG_05290 | SPT3 | Transcription initiation protein SPT3 | 0.159839958 |
| CNAG_05404 | Histone-lysine N-methyltransferase SUV39H | 0.135941792 | |
| CNAG_05428 | TAF5 | Transcription initiation factor TFIID subunit 5 | 0.16375121 |
| CNAG_06283 | LIV4 | Putative myb-like mRNA polymerase I termination factor | −0.479281412 |
| CNAG_06392 | SGF29 | Putative saga histone acetyltransferase complex component | −0.489834833 |
| CNAG_06544 | Non-histone chromosomal protein 6 | −0.61516928 | |
| CNAG_06597 | SPT8 | Transcriptional activator SPT8 | −0.224863088 |
| CNAG_06745 | Histone H3 | −0.576382711 | |
| CNAG_06746 | Histone H2B | −0.606684422 | |
| CNAG_06747 | Histone H2A | −0.53480499 | |
| CNAG_07027 | SPT2 | Protein SPT2 | 0.101538608 |
| CNAG_07565 | TAF9 | Transcription initiation factor TFIID subunit 9B | 0.194617264 |
| CNAG_07572 | ELP3 | Pol II transcription elongation factor | −0.32202168 |
| CNAG_07680 | HAP5 | Transcriptional activator HAP5 | 0.131411312 |
| CNAG_07807 | Histone H4 | −0.37405091 | |
| Capsule | |||
| CNAG_00600 | CAP60 | Capsule-associated protein | 0.472665779 |
| CNAG_00697 | UGE1 | UDP-glucose epimerase | 0.406541427 |
| CNAG_00701 | CAS31 | Protein involved in gxm O-acetylation | 0.195896704 |
| CNAG_00721 | CAP59 | Alpha-1,3-mannosyltransferase | −0.283339391 |
| CNAG_02581 | CAS33 | Hypothetical protein | −0.230488663 |
| CNAG_02805 | CAN1 | Carbonic anhydrase | 0.381708027 |
| CNAG_02885 | CAP64 | Capsule-associated protein | −0.411533956 |
| CNAG_03322 | UXS1 | UDP-glucuronic acid decarboxylase | −0.192984755 |
| CNAG_03426 | GMT2 | GDP-mannose transporter 2 | −1.301133952 |
| CNAG_03644 | CAS3 | Hypothetical protein | −0.680904969 |
| CNAG_03695 | CAS41 | Probable sugar phosphate/phosphate translocator; capsule biosynthetic protein | −0.289383393 |
| CNAG_03735 | CAP4 | Hypothetical protein | −0.583727866 |
| CNAG_03929 | CAS42 | Solute carrier family 35, member C2 | −0.140514137 |
| CNAG_04312 | MAN1 | Mannose-6-phosphate isomerase | −0.199177397 |
| CNAG_05023 | CAS91 | Putative maltose o-acetyltransferase | −0.396029552 |
| CNAG_05081 | PDE1 | Phosphodiesterase | −0.17141564 |
| CNAG_05139 | UGT1 | Solute carrier family 35 (UDP-sugar transporter), member A1/2/3 | 0.135099801 |
| CNAG_05144 | CAN2 | Carbonic anhydrase | −0.881416777 |
| CNAG_05222 | NRG1 | Transcriptional regulator Nrg1 | −0.265150815 |
| CNAG_05431 | RIM101 | pH-response transcription factor PacC/Rim101 | 0.181521283 |
| CNAG_05817 | GMT1 | GDP-mannose transporter 1 | −0.2343137 |
| CNAG_06016 | CAP6 | Hypothetical protein | 0.139069648 |
| CNAG_06524 | FRE3 | Ferric reductase | 4.348573694 |
| Melanin | |||
| CNAG_02434 | ATX1 | Putative copper ion transporter | −0.164690738 |
| CNAG_03464 | LAC2 | Laccase | −0.253171475 |
| CNAG_03465 | LAC1 | Laccase | −0.509427708 |
| CNAG_05081 | PDE1 | Phosphodiesterase, phosphodiesterase, variant | −0.17141564 |
| CNAG_05465 | GIB2 | Guanine nucleotide-binding protein subunit beta-like protein | −0.316312202 |
| CNAG_06415 | CCC2 | Cu2 -exporting ATPase | 0.152106422 |
| CNAG_06524 | FRE3 | Ferric reductase | 4.348573694 |
| CNAG_07701 | CTR2 | Putative copper ion transporter | 0.528660759 |
| Mating | |||
| CNAG_00293 | RAS1 | Ras-like protein | −0.198864829 |
| CNAG_01262 | GPB1 | Guanine nucleotide-binding protein subunit beta | −0.14439011 |
| CNAG_01452 | MAT3 | Mat3 pheromone repeat protein | −0.31601691 |
| CNAG_01730 | STE7 | MAP kinase kinase | −0.264935377 |
| CNAG_02756 | CDC43 | Geranylgeranyltransferase-I beta subunit | −0.21364078 |
| CNAG_02883 | RAC1 | Rho family protein | −0.428370761 |
| CNAG_03938 | CPR2 | Pheromone a factor receptor | 0.549162139 |
| CNAG_04119 | ROM2 | Rho guanyl-nucleotide exchange factor | 0.13250298 |
| CNAG_04761 | RAS2 | Ras family protein | −0.779751921 |
| CNAG_05465 | GIB2 | Guanine nucleotide-binding protein subunit beta-like protein | −0.316312202 |
| CNAG_05866 | PRM1 | Putative plasma membrane fusion protein | 1.12944946 |
| CNAG_05925 | CDC3 | Septin ring protein | −0.208014522 |
| CNAG_05970 | PAK1 | Ste/Ste20/PakA protein kinase | 0.070285615 |
| CNAG_06806 | ETF1alpha | Electron transfer flavoprotein alpha subunit | −0.523135543 |
| CNAG_06808 | STE3alpha | Pheromone a factor receptor | −0.657125254 |
| CNAG_06811 | RPL22alpha | Large subunit ribosomal protein L22e | −0.406283818 |
| CNAG_06812 | SPO14alpha | Phospholipase D1 | −0.323123919 |
| CNAG_06813 | CAP1alpha | Hypothetical protein | −0.701589794 |
| CNAG_06980 | STE11alpha | MAPKK kinase, Ste/Ste11 protein kinase | 0.317591405 |
| CNAG_07407 | MFalpha3 | Mating-type pheromone alpha | −0.974668369 |
| CNAG_07409 | RPO41alpha | DNA-directed mRNA polymerase, mitochondrial | −0.66659612 |
| CNAG_07410 | CID1alpha | Hypothetical protein | −0.197735218 |
| CNAG_07507 | STE50 | Protein kinase regulator | −0.274868604 |
| Protease | |||
| CNAG_00581 | Saccharopepsin | 0.406541427 | |
| CNAG_01343 | ATP-dependent Clp protease ATP-binding subunit ClpX | 0.397082268 | |
| CNAG_01688 | ATP-dependent metalloprotease | −0.454088763 | |
| CNAG_02239 | 26 S protease regulatory subunit 4 | 0.447325323 | |
| CNAG_02282 | Carboxypeptidase A4 | 0.450060236 | |
| CNAG_03904 | 26 S protease regulatory subunit 6B | 0.150163286 | |
| CNAG_04380 | Peptidase | −0.391189814 | |
| CNAG_04635 | Endopeptidase | 0.225975854 | |
| CNAG_04666 | 26 S protease regulatory subunit 8 | 0.186381652 | |
| CNAG_04906 | 26 S protease regulatory subunit 10B | 0.282517098 | |
| CNAG_05742 | STP1 | Putative site-2 protease | −0.354935589 |
| CNAG_05872 | Endopeptidase | 0.437070994 | |
| CNAG_06153 | 26 S protease regulatory subunit 6A-B | 0.401220915 | |
| CNAG_06410 | ATP-dependent Clp endopeptidase, proteolytic subunit ClpP | −0.20806081 | |
| CNAG_07520 | Endopeptidase | 0.661884424 | |
| HDA1 associated | |||
| CNAG_05333 | Hypothetical protein | 3.16455427 | |
| CNAG_06874 | HpcH/HpaI aldolase/citrate lyase | 0.721327† | |
| CNAG_07651 | DEAD-box ATP-dependent RNA helicase 26 | 0.924457338 | |
Log2(fold change) values for hda1∆ versus wild-type from DESeq2 analysis. Table amended from full list of differentially expressed genes in each category (Table S1). Negative changes represent genes positively regulated by Hda1; positive changes represent genes negatively regulated by Hda1.
†log2(fold change) value obtained from TopHat2/Cuffdiff analysis.