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Table 4 Pollen development-related genes covalently modified by H3K4me3 and H3K27me3

From: Comparative transcriptome analysis and ChIP-sequencing reveals stage-specific gene expression and regulation profiles associated with pollen wall formation in Brassica rapa

Classification Brassica rapa Type Arabidopsis
Locus Fold enrichment FDR (%) Locus Gene name Description References
Meiosis process Bra015676 6.35 2.19 H3K4 AT1G77320 MEI1 BRCT-domain-containing protein [38]
Bra029127 7.58 2.16 H3K4 AT5G52290 SHOC1 protein with similarity to XPF endonucleases [39]
Bra017718 6.02 4.73 H3K4 AT4G35520 MLH3 DNA mismatch repair protein [40]
Bra000955 9.92 1.61 H3K4 AT4G01370 MAPK4 MAP kinase [41]
Bra019444 2.27 11.76 H3K27 AT3G43210 TES ATP binding microtubule motor family protein [42]
Bra023796 9.7 44.54 H3K27 AT3G22880 DMC1 DNA repair (Rad51) family protein [43]
Bra001890 7.24 23.26 H3K27 AT3G22880    
Tapetum development Bra009277 10.25 1.91 H3K4 AT5G07280 EMS1 leucine-rich repeat receptor protein kinase [44]
Bra002401 5.8 11.36 H3K27 AT5G22260 MS1 PHD-finger motif transcription factor [17]
Bra000615 4.68 12.43 H3K27 AT5G50260 CEP1 papain-like cysteine protease [45]
Bra013041 6.24 11.48 H3K27 AT2G16910 AMS basic helix-loop helix transcription factor [16]
Pollen exine formation Bra014776 10.36 1.52 H3K4 AT3G55090 ABCG16 ABCG half-transporter [22]
Bra024796 9.47 1.76 H3K4 AT2G02970 APY6 putative apyrase [46]
Bra017147 7.5 1.52 H3K4 AT1G02050 LAP6 chalcone and stilbene synthase family [25]
Bra008832 15.49 12.07 H3K4 AT5G13390 NEF1 membrane protein [47]
Bra023407 15.38 5.03 H3K4 AT5G13390    
Bra034054 6.58 2.42 H3K4 AT3G09090 DEX1 membrane associated protein [48]
Bra029746 6.58 2.09 H3K4 AT3G09090    
Bra038909 6.69 2.54 H3K4 AT3G51610 NPU membrane protein [49]
Bra014776 8.58 11.76 H3K27 AT3G55090 ABCG16 ABCG half-transporter [22]
Bra025595 7.8 11.49 H3K27 AT5G40260 RPG1 a member of the MtN3/saliva gene family [50]
Bra013442 4.12 15.6 H3K27 AT4G20050 QRT3 polygalacturonase [51]
Pollen maturation Bra029700 9.92 1.51 H3K4 AT3G08590 IPGAM2 phosphoglycerate mutase [52]
Bra022067 7.76 1.59 H3K4 AT3G01780 TPLATE cytokinesis protein [53]
Bra037331 6.58 1.55 H3K4 AT4G00330 CRCK2 calmodulin-binding receptor-like cytoplasmtic kinase [54]
Bra001510 5.46 2.32 H3K4 AT3G13530 MAP3KE1 epsilon protein kinase [55]
Bra001358 4.9 3.06 H3K4 AT3G10405 vacuolar acid trehalase [54]
Bra026579 4.57 5.65 H3K4 AT2G02810 UTR1 multitransmembrane hydrophobic protein [56]
Bra008037 5.02 2.43 H3K4 AT1G72520 LOX4 PLAT/LH2 domain-containing lipoxygenase family protein [57]
Bra024316 5.02 3.98 H3K4 AT5G64630 FAS2 chromatin assembly factor-1 p60 subunit [58]
Bra029541 8.88 1.64 H3K4 AT4G04970 GSL1 callose synthase [59]
Bra008722 3.01 17.63 H3K27 AT5G15100 PIN8 auxin transporter [60]
Bra008615 9.47 14.76 H3K27 AT5G16530 PIN5 an atypical member of the PIN family [61]
Bra039940 7.91 11.59 H3K27 AT2G22950 ACA7 putative auto-regulated Ca2+-ATPase [62]
Bra033961 3.57 15.97 H3K27 AT1G68090 ANN5 calcium-binding protein [63]
Bra007536 6.69 11.27 H3K27 AT3G60460 DUO1 R2R3 MYB transcription factor [64]
Bra003413 5.57 14.1 H3K27 AT3G60460    
Pollen maturation and anther dehiscence Bra002816 11.48 1.82 H3K4 AT5G56450 PM-ANT mitochondrial substrate carrier family protein [65]
Bra004869 6.8 11.27 H3K27 AT2G44810 DAD1 alpha/beta hydrolases superfamily protein [66]
Pollen development and tube growth Bra040162 5.35 2.09 H3K4 AT4G17530 RAB1C Rab GTPase [67]
Bra009268 5.35 2.74 H3K27 AT5G07370 IPK2A inositol polyphosphate kinase [68]
Bra015643 3.68 14.95 H3K27 AT1G77980 AGL66 MADS transcription factor [69]
Pollen germination and tube growth Bra004738 5.24 4.14 H3K4 AT2G43040 NPG1 calmodulin-binding protein [70]
  Bra010936 4.9 5.3 H3K4 AT1G27460 NPGR1 calmodulin-binding protein [70]
  Bra011041 4.79 3.81 H3K4 AT4G28600 NPGR2 calmodulin-binding protein [70]
  Bra010358 4.57 5.02 H3K4 AT4G28600    
  Bra032785 4.57 5.35 H3K4 AT1G24620 CML25 EF-hand calcium-binding protein [71]
  Bra011622 10.36 1.5 H3K4 AT4G35540 PTF2 TFIIB-related protein [72]
  Bra039141 6.46 1.52 H3K4 AT3G01150 PTB1 polypyrimidine tract-binding protein [73]
  Bra003466 6.35 2.47 H3K4 AT3G61710 ATG6 autophagy protein [74]
  Bra005376 7.91 1.49 H3K4 AT2G34980 SETH1 phosphatidylinositol-glycan synthase subunit [75]
  Bra031332 4.57 5.25 H3K4 AT3G22200 POP2 gamma-aminobutyrate transaminase [76]
  Bra009450 10.59 1.52 H3K4 AT5G04480 BUP putative glycosyltransferase [77]
  Bra000950 9.81 1.43 H3K4 AT4G01220 MGP4 Rhamnogalacturonan II xylosyltransferase [78]
  Bra015010 8.92 1.51 H3K4 AT4G38430 ROPGEF1 guanine nucleotide exchange factor [79]
  Bra023489 6.24 2.66 H3K4 AT5G14850 APTG1 mannosyltransferase [80]
  Bra008404 5.91 1.53 H3K4 AT1G79250 AGC1.7 AGC kinase [81]
  Bra014529 5.46 2.83 H3K4 AT3G59760 ATCS-C O-acetylserine lyase [82]
  Bra008733 10.81 11.6 H3K27 AT5G14870 CNGC18 a member of the cyclic nucleotide gated channel family [83]
  Bra007785 7.91 14.93 H3K27 AT2G25600 SPIK member of the Shaker family potassium ion (K+) channel [84]
  Bra000105 8.69 11.79 H3K27 AT2G38910 CPK20 calcium dependent protein kinase [85]
  Bra015442 6.91 11.81 H3K27 AT1G05580 CHX23 member of putative Na+/H+ antiporter family [86]
  Bra025052 4.79 14.1 H3K27 AT5G45810 CIPK19 CBL-interacting protein kinase [87]
  Bra022172 4.35 15.47 H3K27 AT3G16640 TCTP1 a protein homologous to translationally controlled tumor protein [88]
  Bra027968 4.01 17.49 H3K27 AT1G54560 XIE myosin family protein with DIL domain-containing protein [89]
  Bra008656 4.01 14.78 H3K27 AT5G16020 GEX3 plasma membrane localized protein [90]
  1. Genes were selected on the basis of previous reports of Arabidopsis mutants affecting anther or pollen development as well as pollen germination or pollen tube growth. The Brassica ID in bold means the gene showed differential expressional levels between the fertile and sterile floral buds at mature pollen development in our RNA-seq analysis