Table IX.
Fold-changes in expression of epigenetic-related genes
T87, Calli derived from the T87 habituated cell line; FC, freshly derived nonhabituated calli; BA, the cytokinin benzyl adenine.
| Gene Familya | Locus Identifier | T87 − BA/FC + BAb | FC + BA/FC − BAc |
|---|---|---|---|
| Histone deacetylases | |||
| HDT1 | At3g44750 | 2.82 | 0.71 |
| HDT2 | At5g22650 | 3.43 | 0.66 |
| HDT2 | At5g22650 | 3.18 | 0.74 |
| HDT3 | At5g03740 | 1.31 | 0.78 |
| HDT4 | At2g27840 | 1.14 | 0.67 |
| HDT4 | At2g27840 | 1.02 | 0.82 |
| HDA2 | At5g26040 | 0.81 | 0.88 |
| HDA5 | At5g61060 | 0.79 | 1.26 |
| HDA6 | At5g63110 | 1.19 | 0.89 |
| HDA7 | At5g35600 | 1.05 | 0.79 |
| HDA8 | At1g08460 | 0.69 | 1.04 |
| HDA9 | At3g44680 | 2.16 | 0.94 |
| HDA10 | At3g44660 | 1.74 | 1.10 |
| HDA14 | At4g33470 | 0.86 | 1.40 |
| HDA15 | At3g18520 | 0.84 | 1.01 |
| HDA15 | At3g18520 | 0.91 | 0.88 |
| HDA17 | At3g44490 | 2.25 | 0.95 |
| HDA18 | At5g61070 | 2.79 | 0.70 |
| HDA19 | At4g38130 | 1.51 | 0.76 |
| SRT1 | At5g55760 | 0.79 | 0.90 |
| SRT2 | At5g09230 | 1.22 | 0.86 |
| SRT2 | At5g09230 | 1.08 | 1.21 |
| SRT2 | At5g09230 | 1.11 | 1.20 |
| SRT2 | At5g09230 | 1.02 | 1.11 |
| SNT1 | At1g24190 | 0.78 | 0.80 |
| SNT2 | At1g70060 | 1.04 | 0.88 |
| SNT3 | At3g01320 | 1.12 | 0.96 |
| SNT4 | At5g15020 | 0.65 | 1.14 |
| HCP1 | At2g45640 | 0.97 | 0.82 |
| Histone acetyltransferases | |||
| HAC1 | At1g79000 | 0.77 | 1.16 |
| HAC2 | At1g67220 | 3.84 | 0.57 |
| HAC4 | At1g55970 | 0.91 | 0.97 |
| HAC5 | At3g12980 | 1.40 | 0.87 |
| HAC12 | At1g16710 | 0.72 | 0.98 |
| HAG1 | At3g54610 | 0.94 | 1.22 |
| HAG2 | At5g56740 | 1.18 | 0.91 |
| HAG3 | At5g50320 | 0.95 | 0.85 |
| HAM1 | At5g64610 | 1.58 | 1.21 |
| HAM2 | At5g09740 | 1.09 | 0.90 |
| HAF1 | At1g32750 | 1.67 | 0.86 |
| HAF2 | At3g19040 | 1.18 | 0.67 |
| HXA1 | At4g16420 | 0.84 | 0.98 |
| HXA2 | At3g07740 | 0.98 | 0.95 |
| Histone methyltransferases | |||
| SDG1/SET1 | At2g23380 | 1.03 | 0.95 |
| SDG2/SET2/ATXR3 | At4g15180 | 1.26 | 0.88 |
| SDG3/SET3/SUVH2 | At2g33290 | 1.12 | 1.13 |
| SDG4/SET4/ASHR3 | At4g30860 | 1.25 | 1.08 |
| SDG5/SET5/FIS1/MEA | At1g02580 | 0.96 | 0.74 |
| SDG6/SET6/SUVR5 | At2g23750 | 1.14 | 0.93 |
| SDG7/SET7/ASHH3 | At2g44150 | 0.50 | 0.97 |
| SDG8/SET8/ASHH2 | At1g77300 | 1.18 | 0.78 |
| SDG9/SET9/SUVH5 | At2g35160 | 0.76 | 0.85 |
| SDG10/SET10/EZA1 | At4g02020 | 1.88 | 1.08 |
| SDG11/SET11/SUVH10 | At2g05900 | 1.06 | 1.10 |
| SDG13/SET13/SUVR1 | At1g04050 | 1.34 | 1.09 |
| SDG14/SET14/ATX3 | At3g61740 | 1.47 | 0.82 |
| SDG15/SET15/ATXR5 | At5g09790 | 1.17 | 0.91 |
| SDG16/SET16/ATX4 | At4g27910 | 1.28 | 1.00 |
| SDG17/SET17/SUVH7 | At1g17770 | 0.98 | 0.86 |
| SDG18/SET18/SUVR2 | At5g43990 | 2.11 | 1.11 |
| SDG19/SET19/SUVH3 | At1g73100 | 0.99 | 1.21 |
| SDG20/SET20/SUVR3 | At3g03750 | 1.29 | 0.98 |
| SDG21/SET21/SUVH8 | At2g24740 | 1.09 | 0.90 |
| SDG22/SET22/SUVH9 | At4g13460 | 1.32 | 1.04 |
| SDG23/SET23/SUVH6 | At2g22740 | 1.37 | 0.94 |
| SDG24/SET24/ASHH4 | At3g59960 | 0.97 | 0.72 |
| SDG25/SET25/ATXR7 | At5g42400 | 0.94 | 1.03 |
| SDG26/SET26/ASHH1 | At1g76710 | 0.70 | 1.19 |
| SDG27/SET27/TRX1 | At2g31650 | 1.84 | 0.81 |
| SDG29/SET29/ATX5 | At5g53430 | 1.24 | 1.04 |
| SDG30/SET30/ATX2 | At1g05830 | 0.94 | 1.45 |
| SDG31/SET31/SUVR4 | At3g04380 | 1.46 | 0.82 |
| SDG32/SET32/SUVH1 | At5g04940 | 1.28 | 0.99 |
| SDG32/SET32/SUVH1 | At5g04940 | 1.40 | 0.86 |
| SDG33/SET33/SUVH4/KYP | At5g13960 | 1.79 | 1.30 |
| SDG34/SET34/ATXR6 | At5g24330 | 2.08 | 0.91 |
| SDG35/SET35/ATXR1 | At1g26760 | 1.10 | 1.02 |
| SDG36/SET36/ATXR2 | At3g21820 | 1.05 | 0.86 |
| SDG37/SET37/ASHR1 | At2g17900 | 1.45 | 0.89 |
| SDG38/SET38/ATXR4 | At5g06620 | 1.16 | 1.18 |
| SDG39/SET39/ASHR2 | At2g19640 | 1.72 | 0.61 |
| SDG39/SET39/ASHR2 | At2g19640 | 1.35 | 0.65 |
| SDG40 | At5g17240 | 1.30 | 0.98 |
| SDG41 | At1g43245 | 0.64 | 1.01 |
| Chromatin remodeling | |||
| CHB1 | At2g47620 | 0.95 | 1.10 |
| CHB2 | At2g33610 | 0.59 | 1.74 |
| CHB3 | At4g34430 | 1.06 | 0.96 |
| CHB3 | At4g34430 | 1.09 | 1.01 |
| CHB3 | At4g34430 | 1.12 | 1.03 |
| CHB4 | At1g21700 | 0.63 | 0.95 |
| CHC1 | At5g14170 | 1.03 | 1.08 |
| CHC2 | At3g01890 | 3.12 | 0.85 |
| CHE1 | At3g17590 | 1.10 | 1.32 |
| CHR1/DDM1 | At5g66750 | 2.31 | 0.81 |
| CHR2 | At2g46020 | 0.78 | 1.26 |
| CHR3/SYD | At2g28290 | 0.94 | 0.79 |
| CHR3/SYD | At2g28290 | 0.81 | 0.77 |
| CHR4 | At5g44800 | 1.14 | 1.05 |
| CHR5 | At2g13370 | 0.96 | 0.90 |
| CHR6/PKL | At2g25170 | 1.07 | 0.94 |
| CHR7 | At4g31900 | 7.82 | 0.76 |
| CHR8 | At2g18760 | 0.99 | 0.71 |
| CHR9 | At1g03750 | 0.78 | 1.01 |
| CHR10 | At2g44980 | 0.83 | 1.33 |
| CHR11 | At3g06400 | 0.60 | 1.12 |
| CHR12 | At3g06010 | 0.80 | 0.87 |
| CHR13 | At3g12810 | 1.12 | 0.98 |
| CHR14 | At5g07810 | 1.77 | 0.79 |
| CHR15/MOM | At1g08060 | 1.08 | 0.85 |
| CHR15/MOM | At1g08060 | 1.23 | 0.84 |
| CHR16 | At3g54280 | 1.20 | 0.95 |
| CHR17 | At5g18620 | 1.18 | 0.86 |
| CHR17 | At5g18620 | 1.13 | 0.95 |
| CHR18 | At1g48310 | 1.20 | 0.95 |
| CHR19 | At2g02090 | 0.78 | 0.93 |
| CHR20 | At1g08600 | 1.05 | 0.79 |
| CHR21 | At3g57300 | 0.77 | 1.10 |
| CHR22 | At5g05130 | 1.49 | 1.18 |
| CHR23 | At5g19310 | 1.45 | 0.69 |
| CHR24 | At5g63950 | 2.08 | 1.08 |
| CHR25 | At3g19210 | 1.42 | 0.75 |
| CHR26 | At3g16600 | 1.34 | 0.73 |
| CHR27 | At3g20010 | 1.52 | 0.75 |
| CHR28 | At1g50410 | 1.16 | 1.20 |
| CHR29 | At5g22750 | 1.92 | 0.93 |
| CHR30 | At1g11100 | 1.24 | 0.53 |
| CHR31 | At1g05490 | 2.00 | 0.89 |
| CHR32 | At5g43530 | 1.22 | 0.78 |
| CHR33 | At1g61140 | 1.05 | 0.93 |
| CHR34 | At2g21450 | 1.85 | 0.84 |
| CHR35/DRD1 | At2g16390 | 1.28 | 1.15 |
| CHR36 | At2g40770 | 0.78 | 1.02 |
| CHR37 | At1g05120 | 1.00 | 1.11 |
| CHR38 | At3g42670 | 2.44 | 1.16 |
| CHR39 | At3g54460 | 0.94 | 1.36 |
| CHR40 | At3g24340 | 2.62 | 0.85 |
| CHR41 | At1g02670 | 2.74 | 0.87 |
| CHR42 | At5g20420 | 1.10 | 0.89 |
| DNA methyltransferases | |||
| MET1/DDM2/DMT1 | At5g49160 | 3.51 | 1.33 |
| MET2/DMT2 | At4g14140 | 0.95 | 0.92 |
| MET3/DMT3 | At4g13610 | 1.24 | 0.97 |
| METIIb/DMT8 | At4g08990 | 1.22 | 0.94 |
| CMT1/DMT4 | At1g80740 | 5.48 | 1.03 |
| CMT2/DMT5 | At4g19020 | 0.93 | 1.52 |
| CMT3/DMT3 | At1g69770 | 3.16 | 1.48 |
| DRM1/DMT9 | At5g15380 | 2.05 | 0.73 |
| DRM2/DMT7 | At5g14620 | 0.77 | 1.05 |
| DRM3/DMT10 | At3g17310 | 1.44 | 1.33 |
| DRM3/DMT10 | At3g17310 | 1.34 | 1.34 |
| DMT11/DNMT2 | At5g25480 | 1.09 | 1.07 |
| DNA glycosylases | |||
| DNG1 | At2g36490 | 0.50 | 1.43 |
| DNG2 | At3g10010 | 1.28 | 0.83 |
| DNG3/DEMETER | AT5G04560 | 0.99 | 1.05 |
| DNG4 | At4g34060 | 1.01 | 0.94 |
| Dicer-like proteins | |||
| DCL1 | At1g01040 | 0.71 | 0.93 |
| DCL2 | At3g03300 | 0.95 | 1.03 |
| DCL3 | At3g43920 | 2.48 | 1.33 |
| DCL4 | At5g20320 | 0.67 | 1.03 |
| Histone demethylases | |||
| HDMA1 | At3g10390 | 0.99 | 0.83 |
| HDMA3 | At1g62830 | 0.80 | 1.00 |
| HDMA2 | At3g13682 | 1.60 | 0.75 |
| HDMA4 | At4g16310 | 1.30 | 0.81 |
a
The signal intensities for genes represented more than once on the microarray are presented separately.
b
The fold-change for the expression of each gene in habituated calli maintained in the absence of cytokinin is presented relative to the expression of the gene in nonhabituated calli maintained in the presence of cytokinin.
c
The fold-change for the expression of each gene in nonhabituated calli maintained in the presence of cytokinin is presented relative to the expression of the gene in nonhabituated calli maintained in the absence of cytokinin.