Table 1. Genes Significantly Up- and Downregulated after Short (24 h) 20 μM Zebularine Treatment
AGI LocusGene AnnotationMockZebLog2 Fold ChangeAdjusted P ValueDDR
RPKM±sdRPKM±sd
Upregulated genes
At1g11580METHYLESTERASE PCR A (PMEPCRA)8.30.115.10.40.840.008
At1g20750RAD3-like0.00.00.40.1Infinite0.004+
At1g48460Unknown protein12.50.520.21.20.680.049
At1g63660GMP synthase16.11.726.71.80.720.049+
At1g65310XYLOGLUCAN ENDOTRANSGLUCOSYLASE/HYDROLASE17 (XTH17)0.80.13.20.11.950.043
At1g70260USUALLY MULTIPLE ACIDS MOVE IN AND OUT TRANSPORTERS36 (UMAMIT36)2.70.46.50.41.230.009
At1g72440SLOW WALKER2 (SWA2)10.01.516.50.20.700.048
At1g75780TUBULIN β-1 CHAIN (TUB1)8.50.214.30.80.730.037
At1g78370GLUTATHIONE S-TRANSFERASE TAU 20 (GSTU20)368.012.6721.374.70.950.000
At2g21790RIBONUCLEOTIDE REDUCTASE1 (RNR1)23.72.340.51.40.760.001+
At2g40360ARABIDOPSIS THALIANA PESCADILLO ORTHOLOG1 (ATPEP1)18.92.731.90.40.740.021
At2g43100ISOPROPYLMALATE ISOMERASE2 (IPMI2)60.86.7113.812.40.880.000
At3g03780METHIONINE SYNTHASE2 (MS2)77.310.3137.30.90.810.011
At3g07800THYMIDINE KINASE 1A (TK1A)13.92.629.74.11.070.000+
At3g13470CHAPERONIN-60BETA2 (CPN60BETA2)99.18.3158.816.10.670.005
At3g15950NAI232.21.449.12.00.590.009
At3g16150ASPARAGINASE B1 (ASPGB1)2.90.18.30.31.480.007
At3g19680Protein of unknown function (DUF1005)14.02.830.13.11.070.008
At3g27060TSO263.23.7127.29.70.990.005+
At3g27630SIAMESE-RELATED7 (SMR7)0.60.55.00.13.080.049+
At3g54810BLUE MICROPYLAR END3 (BME3)19.60.830.51.00.620.024
At3g59670Unknown protein4.40.59.90.51.170.000+
At4g21070BREAST CANCER SUSCEPTIBILITY1 (BRCA1)3.40.59.31.11.430.000+
At4g22410Ubiquitin C-terminal hydrolase protein0.00.01.80.1Infinite0.048
At4g22880LEUCOANTHOCYANIDIN DIOXYGENASE (LDOX)7.20.215.72.31.100.003
At4g31210DNA topoisomerase10.70.916.40.20.610.035+
At5g14200ISOPROPYLMALATE DEHYDROGENASE1 (IMD1)76.12.0146.923.20.920.000
At5g20850RAS ASSOCIATED WITH DIABETES51 (RAD51)3.30.37.30.81.110.043+
At5g42800DIHYDROFLAVONOL 4-REDUCTASE (DFR)5.30.411.80.91.140.000
At5g52470FIBRILLARIN1 (FIB1)83.81.4128.84.70.600.049
At5g55920OLIGOCELLULA2 (OLI2)12.02.822.90.10.920.011
Downregulated genes
At1g28330DORMANCY-ASSOCIATED PROTEIN1 (DYL1)170.65.9106.314.3−0.710.022
At1g35612Transposable element gene40.91.326.74.8−0.640.037
At1g68050FLAVIN-BINDING, KELCH REPEAT, F BOX1 (FKF1)4.80.71.80.6−1.460.003
At2g21210SMALL AUXIN UPREGULATED RNA6 (SAUR6)63.10.331.85.7−1.020.049
At2g33830DORMANCY ASSOCIATED GENE2 (DRM2)317.462.190.613.0−1.830.000
At2g42530COLD REGULATED 15B (COR15B)50.72.616.92.7−1.590.005
At3g05880RARE-COLD-INDUCIBLE 2A (RCI2A)144.04.089.79.6−0.710.005
At3g62550Adenine nucleotide α-hydrolase-like80.32.348.15.6−0.750.003
At4g04330HOMOLOG OF CYANOBACTERIAL RBCX1 (RBCX1)55.24.933.85.1−0.720.049
At4g39090RESPONSIVE TO DEHYDRATION19 (RD19)241.81.9163.87.4−0.580.008
At5g14780FORMATE DEHYDROGENASE (FDH)84.43.557.93.5−0.560.010
At5g54190PROTOCHLOROPHYLLIDE OXIDOREDUCTASE A (PORA)10.40.25.30.2−1.000.009
  • Reads per kilobase per million reads (RPKM) are an average of two biological replicates ± sd. Adjusted P values were calculated using DESeq statistics in R. DNA damage repair (DDR) genes (TAIR10) are marked with a “+.” Genes in bold were significantly up- or downregulated after a long (5 d) zebularine treatment.