Table III. List of putative MtABI3 regulons according to our GRN analysis.
The 2-kb promoter sequence analysis was performed to reveal the presence and number of RYL and GBL cis-regulatory motifs known to bind ABI3 for each predicted M. truncatula regulon. Promoter sequences used for the analysis are provided in Supplemental Table S9. Loss-of-function data from expression in Mtabi3 mutant seeds compared with wild-type seeds at 32 DAP and gain-of-function data from hairy roots transformed with MtABI3 compared with control lines are expressed as log2 ratios and are from probe sets present on the Nimblegen gene chip with their corresponding P values. Arabidopsis orthologs of the putative MtABI3 regulons identified in our network are indicated, and the methods used by Mönke et al. (2012) to validate them as targets of ABI3 in Arabidopsis are specified as follows: A, transient promoter activation assay; C, chromatin immunoprecipitation chip analysis; P, quantitative reverse transcription-PCR; T, array-based transcriptome analysis. Affymetrix identifiers in boldface represent genes displaying significant changes in expression in both gain- and loss-of function experiments.
| Probe Set Identifier of Putative ABI3 Regulons According to the GRN |
Promoter Analysis (2-kb Sequence) |
Ectopic Expression (Hairy Roots) |
abi3 Mutants 32 DAP | Targets of ABI3 in Arabidopsis (Mönke et al., 2012) |
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|---|---|---|---|---|---|---|---|---|---|---|---|
| 32 DAP |
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| Affymetrix Identifier | Tentative Annotation | IMGAG Mt3.5.1 | No. of RYL Motifs (CATGCA) | No. of GBL Motifs (ACGTGTC) | Nimblegen Identifier | Log2 ABI3/Control | P | Log2 abi3/Wild Type | P | Arabidopsis Orthologs | Methods Used to Identify Regulons |
| Mtr.37233.1.S1_at | Oleosin | – | – | – | – | – | – | – | – | AT5G40420 | CTPA |
| Mtr.24397.1.S1_at | Cupin | Medtr1g071710 | 1 | 1 | Medtr_v1_006027 | 3.05 | 2.29E-03 | −2.86 | 6.92E-08 | AT3G22640 | CT |
| Mtr.43017.1.S1_at | Cupin | Medtr1g071710 | 1 | 1 | Medtr_v1_006027 | 3.05 | 2.29E-03 | −2.86 | 6.92E-08 | AT3G22640 | CT |
| Mtr.31203.1.S1_s_at | Legumin A | – | – | – | Medtr_v1_006092 | 2.81 | 2.61E-03 | −1.43 | 7.09E-06 | AT5G44120 | CTP |
| Mtr.21257.1.S1_at | LEA | Medtr2g014040 | 2 | 0 | Medtr_v1_009629 | 2.98 | 0.002341 | −0.93 | 0.000896 | AT4G21020 | CT |
| Mtr.21376.1.S1_at | Mitochondrial translocase | Medtr2g034550 | 1 | 0 | Medtr_v1_010795 | 3.85 | 0.000438 | −1.16 | 4.95E-05 | AT4G16160 | CTPA |
| Mtr.17433.1.S1_at | Unknown | Medtr3g096890 | 0 | 0 | Medtr_v1_019345 | 1.23 | 0.103578 | −1.94 | 1.07E-05 | AT1G27990 | TP |
| Mtr.17102.1.S1_at | Dehydrin | Medtr3g117190 | 5 | 0 | Medtr_v1_020579 | 3.67 | 0.001524 | −0.98 | 0.000286 | AT2G21490 | CTP |
| Mtr.8682.1.S1_s_at | Cupin | Medtr4g060780 | 3 | 1 | Medtr_v1_021810 | 3.08 | 9.30E-03 | −0.24 | 0.094514 | AT2G28490 | CTP |
| Mtr.37595.1.S1_s_at | Cupin | Medtr4g060780 | 3 | 1 | Medtr_v1_024309 | 3.08 | 0.009303 | −1.01 | 9.35E-05 | AT2G28490 | CTP |
| Mtr.37595.1.S1_at | Allergen Gly | Medtr4g060780 | 3 | 1 | Medtr_v1_024309 | 3.08 | 0.009303 | −1.01 | 9.35E-05 | AT2G28490 | CTP |
| Mtr.41721.1.S1_at | Oleosin | Medtr6g005040 | 1 | 0 | Medtr_v1_038147 | 3.3 | 0.030741 | −2.89 | 1.12E-07 | AT3G27660 | CP |
| Mtr.18309.1.S1_at | Tonoplast intrinsic protein | Medtr6g069040 | 2 | 1 | Medtr_v1_039779 | 2.51 | 0.009378 | −0.63 | 0.001548 | AT1G73190 | CTPA |
| Mtr.198.1.S1_s_at | Tonoplast intrinsic protein | Medtr6g069040 | 2 | 1 | Medtr_v1_039779 | 2.51 | 9.38E-03 | −0.63 | 0.001548 | AT1G17810 | CTA |
| Mtr.23887.1.S1_at | Unknown | Medtr7g080030 | 6 | 1 | Medtr_v1_044786 | 3.96 | 2.92E-05 | −2.13 | 4.87E-07 | AT5G16460 | TP |
| Mtr.12358.1.S1_at | LEA | Medtr7g093160 | 6 | 0 | Medtr_v1_045825 | 4.35 | 8.92E-05 | −1.89 | 1.82E-06 | AT5G06760 | CPA |
| Mtr.12942.1.S1_at | LEA4, LEA5 | Medtr7g093170 | 0 | 2 | Medtr_v1_045825 | 4.35 | 8.92E-05 | −1.89 | 1.82E-06 | AT5G06760 | CPA |
| Mtr.5956.1.S1_s_at | LEA | Medtr7g093170 | 0 | 2 | Medtr_v1_045826 | 4.59 | 7.89E-07 | −0.98 | 0.000197 | AT5G06760 | CPA |
| Mtr.9420.1.S1_s_at | Calcium-binding protein | – | – | – | Medtr_v1_068117 | 4.03 | 1.35E-05 | −2.51 | 2.44E-07 | AT4G26740 | CTPA |
| Mtr.43091.1.S1_s_at | LEA | Medtr7g093160 | 6 | 0 | Medtr_v1_074975 | 2.95 | 4.31E-03 | −0.97 | 0.000130 | AT5G06760 | CPA |
| Mtr.9049.1.S1_at | SBP65 | – | – | – | Medtr_v1_083614 | 4.18 | 0.003071 | −2.26 | 4.25E-06 | AT2G42560 | TP |
| Mtr.37679.1.S1_at | Tonoplast intrinsic protein | – | – | – | Medtr_v1_086805 | 3.51 | 0.007926 | −1.44 | 7.73E-06 | AT1G73190 | CTPA |
| Mtr.35625.1.S1_s_at | Unknown | – | – | – | Medtr_v1_088080 | 3.66 | 5.45E-05 | −0.78 | 0.002302 | AT5G07330 | CT |
| Mtr.37272.1.S1_at | Legumin A | – | – | – | Medtr_v1_088220 | 0.02 | 0.833278 | −1.03 | 6.69E-05 | AT5G44120 | CTP |
| Mtr.37270.1.S1_at | Legumin | – | – | – | Medtr_v1_091453 | 2.13 | 0.094826 | −1.33 | 0.000107 | AT5G44120 | CTP |
| Mtr.31204.1.S1_s_at | Oleosin | – | – | – | Medtr_v1_093522 | 3.61 | 0.000696 | −1.45 | 6.43E-06 | AT3G01570 | CTA |
| Mtr.12327.1.S1_s_at | LEA | – | – | – | Medtr_v1_085905 | 1.06 | 0.069602 | −0.87 | 0.000219 | AT1G52690 | – |
| Mtr.7496.1.S1_at | Unknown | – | – | – | Medtr_v1_083970 | 4.79 | 0.000158 | −0.87 | 0.001075 | AT5G36100 | – |
| Mtr.10877.1.S1_at | Aldehyde dehydogenase | – | – | – | Medtr_v1_072305 | 2.86 | 0.034275 | −0.61 | 0.002170 | AT1G23800 | – |
| Mtr.8651.1.S1_a_at | Dehydrin | – | – | – | Medtr_v1_066754 | 3.32 | 1.10E-05 | −0.79 | 0.000374 | AT3G50970 | – |
| Mtr.7231.1.S1_at | Defensin | Medtr8g095370 | 7 | 0 | Medtr_v1_051884 | 0.46 | 0.200574 | −0.55 | 0.004721 | AT2G02130 | – |
| Mtr.50543.1.S1_at | Unknown | Medtr8g020560 | 3 | 1 | Medtr_v1_048842 | 0.61 | 0.352299 | −0.07 | 0.720525 | AT3G13960 | – |
| Mtr.50542.1.S1_at | Unknown | Medtr8g020550 | 0 | 0 | Medtr_v1_048841 | 0.45 | 0.399151 | 0.16 | 0.247374 | AT3G13960 | – |
| Mtr.11561.1.S1_at | Unknown | Medtr5g025800 | 3 | 0 | Medtr_v1_031191 | 2.56 | 0.007446 | −0.93 | 0.000140 | AT5G45310 | – |
| Msa.3093.1.S1_at | Desiccation-induced protein | Medtr4g063500 | 2 | 0 | Medtr_v1_024482 | 2.69 | 0.000739 | −2.28 | 3.44E-07 | AT1G07645 | – |
| Mtr.17894.1.S1_at | Unknown | Medtr1g014110 | 0 | 1 | Medtr_v1_004332 | 3.53 | 0.000135 | −1.09 | 0.001158 | AT4G31830 | – |
| Mtr.38008.1.S1_at | Phosphofructokinase | AC233669_8 | 2 | 0 | Medtr_v1_002457 | 1.35 | 0.048458 | −1.09 | 5.32E-05 | AT5G47810 | – |
| Msa.1254.1.S1_at | Unknown | – | – | – | – | – | – | – | – | – | – |
| Msa.900.1.S1_s_at | Unknown | – | – | – | – | – | – | – | – | – | – |
| Mtr.8651.1.S1_at | Dehydrin | – | – | – | – | – | – | – | – | – | – |