Table 1.
Differentially regulated transcripts in DRNL::GFP-positive protoplasts (fold change ≥ 1.5; p ≤ 0.01) compared to DRNL::GFP− protoplasts that have functions associated with meristem maintenance and identity, polarity, boundary formation, hormones, vasculature, epigenetic changes and that generate miRNAs
| Gene | Alias | Locus | Fold change |
|---|---|---|---|
| Meristem maintenance and identity/floral markers | |||
| ASYMMETRIC LEAVES2 | AS2 | At1g65620 | +2.55 |
| FLOWERING PROMOTING FACTOR1 | FPF1 | At5g24860 | +2.38 |
| SHORT VEGETATIVE PHASE | SVP | At2g22540 | +2.16 |
| REPRODUCTIVE MERISTEM1 | REM1 | At3g19184 | +2.10 |
| AINTEGMUMENTA | ANT | At4g37750 | +2.08 |
| LEAFY | LFY | At5g61850 | +1.98 |
| AINTEGUMENTA-LIKE6 | AIL6 | At5g10510 | +1.96 |
| PISTILLATA | PI | At5g20240 | +1.93 |
| REGULATOR OF AXILLARY MERISTEMS1/MYB37 | RAX1 | At5g23000 | +1.86 |
| BASIC PENTACYSTEINE 3 | BPC3 | At1g68120 | +1.85 |
| UNUSUAL FLORAL ORGANS | UFO | At1g30950 | +1.85 |
| BRCA1-ASSOCIATED RING DOMAIN1 | BARD1 | At1g04020 | +1.83 |
| CAULIFLOWER | CAL | At1g26310 | +1.82 |
| REPRODUCTIVE MERISTEM3 | REM3 | At5g58280 | +1.82 |
| LATERAL MERISTEM IDENTITY1 | LMI1 | At5g03790 | +1.79 |
| ULTRAPETALA1 | ULT1 | At4g28190 | +1.77 |
| APETALA1 | AP1 | At1g69120 | +1.60 |
| LATERAL MERISTEM IDENTITY2 | LMI2 | At3g61250 | + 1.55 |
| TUBBY8 | TUB8 | At1g16070 | +1.52 |
| SHOOTMERISTEMLESS | STM | At1g62360 | −1.54 |
| BARELY ANY MERISTEM3 | BAM3 | At4g20270 | −2.89 |
| BREVIPEDICELLUS/KNAT1 | BP | At4g08150 | −3.57 |
| Polarity | |||
| YABBY5 | YAB5 | At2g26580 | +14.01 |
| NUBBIN | NUB | At1g13400 | +5.81 |
| BLADE-ON-PETIOLE2 | BOP2 | At2g41370 | + 5.44 |
| BLADE-ON-PETIOLE1 | BOP1 | At3g57130 | + 5.19 |
| FILAMENTOUS FLOWER (YABBY1) | FIL | At2g45190 | +4.37 |
| JAGGED | JAG | At1g68480 | + 3.32 |
| PUCHI | PUCHI | At5g18560 | + 3.25 |
| KNOX ARABIDOPSIS THALIANA MEINOX | KNATM | At1g14760 | +3.17 |
| HOMEOBOX GENE1 | ATH1 | At4g32980 | +2.90 |
| PRESSED FLOWER | PRS | At2g28610 | +2.40 |
| YABBY3 | YAB3 | At4g00180 | +2.14 |
| ETTIN | ETT | At2g33860 | +1.87 |
| KANADI3 | KAN3 | At4g17695 | −3.52 |
| Boundary genes | |||
| SUPERMAN | SUP | At3g23130 | +3.07 |
| JAGGED LATERAL ORGANS (LBD30) | JLO | At4g00220 | +2.38 |
| LATERAL BOUNDARY DOMAIN18 | LBD18 | At2g45420 | +2.21 |
| GROWTH REGULATING FACTOR2 | GRF2 | At4g37740 | +1.95 |
| GROWTH REGULATING FACTOR5 | GRF5 | At3g13960 | +1.86 |
| LATERAL ORGAN JUNCTION | LOJ | At2g39230 | +1.68 |
| GROWTH REGULATING FACTOR1 | GRF1 | At2g22840 | +1.63 |
| CUP-SHAPED COTYLEDON1 | CUC1 | At3g15170 | +1.54 |
| PETAL LOSS | PTL | At5g03680 | −1.63 |
| LATERAL ORGAN BOUNDARY | LOB | At5g63090 | −8.87 |
| Auxin | |||
| MONOPTEROS | MP | At1g19850 | +1.67 |
| IAA CARBOXYLMETHYLTRANSFERASE1 | IAMT 1 | At5g55250 | −4.64 |
| Brassinosteroids | |||
| BRI1-LIKE1 | BRL1 | At1g55610 | +1.59 |
| BR ENHANCED EXPRESSION2 | BEE2 | At4g36540 | −3.97 |
| BR ENHANCED EXPRESSION1 | BEE1 | At1g18400 | −8.15 |
| Cytokinins | |||
| HISTIDINE PHOSPHOTRANSFER PROTEIN6 | AHP6 | At1g80100 | +18.08 |
| ISOPENTENYLTRANSFERASE7 | IPT7 | At3g23630 | −7.25 |
| ISOPENTENYLTRANSFERASE3 | IPT3 | At3g63110 | −13.47 |
| Gibberellins | |||
| GIBBERELLIN OXIDASE3 | GA3ox3 | At4g21690 | +4.13 |
| GIBBERELLIN 2-OXIDASE4 | GA2ox4 | At1g47990 | +3.24 |
| GIBBERELLIN 20-OXIDASE2 | GA20ox2 | At5g51810 | +2.16 |
| GIBBERELLIN 3-OXIDASE1 | GA3ox1 | At1g15550 | +1.97 |
| GIBBERELLIN 2-OXIDASE2 | GA2ox2 | At1g30040 | +1.58 |
| Other transcription factors | |||
| SHI-RELATED SEQUENCE4 | SRS4 | At2g18120 | +3.61 |
| STYLISH1 | STY1 | At3g51060 | +2.74 |
| SHI-RELATED SEQUENCE7 | SRS7 | At1g19790 | +2.21 |
| INFLORESCENCE DEFICIENT IN ABSCISSION (IDA)-LIKE 2 | IDL2 | At5g64667 | +1.93 |
| SHORT INTERNODES | SHI | At5g66350 | +1.92 |
| MiRNAs and the siRNA precursor TAS3A | |||
| TAS3A | At3g17185 | −2.21 | |
| MiR390A | At2g38325 | −2.73 | |
| MiR159/159B | At1g18075 | −2.86 | |
| MiR172D | At3g55512 | −3.06 | |
| MiR156E | At5g11977 | −3.20 | |
| MiR172/172B | At5g04275 | −5.55 | |
| MiR164/164B | At5g01747 | −5.88 | |
| MiR319/319B | At5g41663 | −6.29 | |
| MiR160/160C | At5g46845 | −8.44 | |
| MiR156C | At4g31877 | −11.49 | |
| MiR172/172A | At2g28056 | −21.01 | |
| Vascular development | |||
| EPIDERMALPATTERNING LIKE FACTOR-LIKE 6 | EPFL6 | At2g30370 | −2.26 |
| REDUCED IN LATERAL GROWTH1 | RUL1 | At5g05160 | −2.44 |
| TDIF-RECEPTOR/PHLOEM INTERCALATED WITH XYLEM | TDR/PXY | At5g61480 | −2.81 |
| CLAVATA3/EMBRYO SURROUNDING REGION41 | CLE41 | At3g24770 | −2.84 |
| XYLEM CYSTEINE PEPTIDASE1 | XCP1 | At4g35350 | −3.02 |
| CLAVATA3/EMBRYO SURROUNDING REGION44 | CLE44 | At4g13195 | −3.24 |
| HIGH CAMBIAL ACTIVITY2 | HCA2 | At5g62940 | −6.05 |
| NAC SECONDARY WALL THICKENING PROMOTING FACTOR1 | NST1 | At2g46770 | −6.45 |
| VASCULAR RELATED NAC DOMAIN6 | VND6 | At5g62380 | −7.53 |
| VASCULAR RELATED NAC DOMAIN7 | VND7 | At1g71930 | −7.76 |
| XYLEM CYSTEINE PEPTIDASE2 | XCP2 | At1g20850 | −7.86 |
| WUSCHEL-RELATED HOMEOBOX4 | WOX4 | At1g46480 | −23.91 |
| Epigenetic regulation | |||
| DECREASED DNA METHYLATION1 | DDM1 | At5g66750 | +1.91 |
| SET DOMAIN GROUP4 | SDG4 | At4g30860 | +1.82 |
| VARIANT IN METHYLATION2 | VIM2 | At1g66050 | +1.78 |
| VARIANT IN METHYLATION6 | VIM6 | At4g08590 | +1.77 |
| VARIANT IN METHYLATION1 | VIM1 | At1g57820 | +1.75 |
| VARIANT IN METHYLATION3 | VIM3 | At5g39550 | +1.73 |
| DNA METHYLTRANSFERASE1 | MET1 | At5g49160 | +1.71 |
| CHROMOMETHYLASE3 | CMT3 | At1g69770 | +1.63 |
| KRYPTONITE | KYP | At5g13960 | +1.53 |
| SET DOMAIN PROTEIN35 | SDG35 | At1g26760 | +1.52 |
| DEMETER-LIKE PROTEIN3 | DML3 | At4g34060 | −4.58 |
Loci in bold represent genes used for the network in Fig. 5