Table I. Expression of region-specific and developmentally important genes in wild-type and dcl1 embryos.
Gene names in boldface indicate miRNA targets. Fold change represents log2(dcl1 expression/wild-type expression). Values that were significantly different from the wild type are in boldface, with those down-regulated underlined. The criteria for significance are as follows: for dcl1-15, an adjusted P < 0.05; for dcl1-5, at least a 1-fold change (no replicates were done for dcl1-5, and no P values are reported). For dcl1-5, genes with fewer than 20 raw reads in both the wild-type and mutant embryos were considered not expressed (Nodine and Bartel, 2010). If the gene had fewer than 20 raw reads in one genotype but more than 20 in the other, it was designated as not detected (nd) in that first genotype, and no ratio was reported.
| Name | Locus Identifier | dcl1-15 Torpedo Stage | dcl1-5 Globular Stage |
|---|---|---|---|
| fold change | |||
| Transcripts enriched in the suspensor | |||
| ARABIDOPSIS SHAGGY-RELATED PROTEIN KINASE η/BRASSINOID INSENSITIVE2 (ASKη/BIN2) | At4g18710 | 1.18 | 0.11 |
| SUCROSE TRANSPORTER3 (SUC3) | At2g02860 | 1.70 | 1.06 |
| WUSCHEL-LIKE HOMEOBOX8 (WOX8) | At5g45980 | 2.40 | 1.92 |
| WRKY2 | At5g56270 | −1.22 | 0.65 |
| Transcripts enriched in the protoderm | |||
| ARABIDOPSIS THALIANA MERISTEM LAYER1 (ATML1) | At4g21750 | 1.03 | 0.53 |
| CAPRICE (CPC) | At2g46410 | −1.85 | Not expressed |
| FIDDLEHEAD (FDH) | At2g26250 | −1.10 | 0.6 |
| GLABRA2 (GL2) | At1g79840 | 2.60 | 2.23 |
| LIPID TRANSFER PROTEIN1 (LTP1) | At2g38540 | −1.13 | 0.72 |
| PROTODERMAL FACTOR1 (PDF1) | At2G42840 | −1.18 | −0.44 |
| PROTODERMAL FACTOR2 (PDF2) | At4g04890 | 1.39 | −0.08 |
| Transcripts enriched at or around the SAM | |||
| CLAVATA1 (CLV1) | At1g75820 | −2.55 | nd wild type |
| CLAVATA3 (CLV3) | At2g27250 | −2.71 | Not expressed |
| CUP-SHAPED COTYLEDON1 (CUC1) | At3g15170 | 1.69 | nd dcl1-5 |
| CUP-SHAPED COTYLEDON2 (CUC2) | At5g53950 | −1.71 | Not expressed |
| CUP-SHAPED COTYLEDON3 (CUC3) | At1g76420 | −4.43 | nd dcl1-5 |
| KNOTTED-LIKE HOMEOBOX PROTEIN2 (KNAT2) | At1g70510 | −2.03 | Not expressed |
| PINOID (PID) | At2g34650 | −1.25 | 0.48 |
| SHOOTMERISTEMLESS (STM) | At1g62360 | −8.28 | Not expressed |
| UNUSUAL FLORAL ORGANS (UFO) | At1g30950 | −2.05 | Not expressed |
| WUSCHEL (WUS) | At2g17950 | −1.36 | Not expressed |
| Transcripts enriched in cotyledons | |||
| AINTEGUMENTA (ANT) | At4g37750 | −27.40 | Not expressed |
| ARABIDOPSIS HISTIDINE PHOSPHOTRANSFER PROTEIN6 (AHP6) | At1g80100 | −1.25 | nd dcl1-5 |
| ARABIDOPSIS THALIANA HOMEOBOX3 (HAT3) | At3g60390 | −2.09 | −1.05 |
| ARABIDOPSIS THALIANA HOMEOBOX4 (ATHB4) | At2g44910 | −2.12 | Not expressed |
| ASYMMETRIC LEAVES1 (AS1) | At2g37630 | −7.14 | 1.83 |
| BES-INTERACTING MYC-LIKE PROTEIN1 (BIM1) | At5G08130 | −1.27 | 2.00 |
| PHAVOLUTA (PHV) | At1g30490 | −1.28 | 2.95 |
| TCP4 | At3g15030 | 1.19 | 3.60 |
| YABBY3 (YAB3) | At4g00180 | −14.96 | Not expressed |
| Transcripts enriched in the RAM or initials | |||
| ARABIDOPSIS RESPONSE REGULATOR7 (ARR7) | At1g19050 | −12.47 | nd wild type |
| ARABIDOPSIS RESPONSE REGULATOR15 (ARR15) | At1g74890 | 1.14 | Not expressed |
| AUXIN RESPONSE FACTOR16 (ARF16) | At4g30080 | 2.27 | nd dcl1-5 |
| PIN-FORMED4 (PIN4) | At2g01420 | −4.20 | −1.58 |
| PIN-FORMED7 (PIN7) | At1g23080 | 3.80 | Not expressed |
| PLETHORA1 (PLT1) | At3g20840 | −7.77 | −1.27 |
| PLETHORA2 (PLT2) | At1g51190 | −4.15 | −1.30 |
| SCHIZORIZA | At1g46264 | −5.09 | Not expressed |
| TARGET OF MONOPTEROS7 (TMO7) | At1g74500 | −8.55 | Not expressed |
| WUSCHEL-LIKE HOMEOBOX5 (WOX5) | At3g11260 | Not on array | |
| Transcripts enriched in the central/adaxial domain | |||
| ARABIDOPSIS THALIANA HOMEOBOX2 (ATHB2) | At4g16780 | 2.04 | Not expressed |
| ARABIDOPSIS THALIANA HOMEOBOX8 (ATHB8) | At4g32880 | −1.18 | nd wild type |
| ARABIDOPSIS THALIANA HOMEOBOX15/CORONA (ATHB15/CNA) | At1g52150 | −7.04 | 5.28 |
| BODENLOS (BDL) | At1g04550 | −1.70 | −0.19 |
| CENTER CITY (CCT) | At4g00450 | −1.25 | −0.69 |
| COTYLEDON VASCULAR PATTERN2 (CVP2) | At1G05470 | −8.02 | Not expressed |
| GIBBERELLIN-REQUIRING1 (GA1) | At4g02780 | 5.41 | Not expressed |
| GRAND CENTRAL (GCT) | At1g55325 | −1.21 | 1.44 |
| HANABA TARANU (HAN) | At3g50870 | −9.94 | −0.35 |
| INDOLE ACETIC ACID-INDUCED PROTEIN13 (IAA13) | At2g33310 | −1.15 | 0.94 |
| INDOLE ACETIC ACID-INDUCED PROTEIN2 (IAA2) | At3g23030 | −1.15 | Not expressed |
| LONESOME HIGHWAY (LHW) | At2g27230 | −2.07 | 0.46 |
| MONOPTEROS/AUXIN RESPONSE FACTOR5 (MP/ARF5) | At1g19850 | −11.27 | −0.14 |
| PHABULOSA (PHB) | At2g34710 | −1.51 | 2.87 |
| PIN-FORMED1 (PIN1) | At1g73590 | −5.22 | 0.86 |
| PINHEAD (PNH)/ZWILLE (ZLL) | At5g43810 | −2.28 | 0.15 |
| REVOLUTA (REV) | At5g60690 | 1.41 | 1.26 |
| SCARECROW (SCR) | At3g54220 | 1.15 | −1.66 |
| SERRATE (SE) | At2g27100 | −1.77 | 0.25 |
| SHORT ROOT (SHR) | At4g37650 | 1.11 | 0.93 |
| TARGET OF MONOPTEROS5 (TMO5) | At3g25710 | −1.73 | 0.85 |
| TMO5-LIKE1 (T5L1) | At1g68810 | 1.06 | −3.12 |
| TARGET OF MONOPTEROS6 (TMO6) | At5g60200 | −12.42 | nd dcl1-5 |
| VASCULAR HIGHWAY1/BRASSINOSTEROID INSENSITIVE1-LIKE2 (VH1/BRL2) | At2g01950 | −2.09 | Not expressed |
| Transcripts enriched in the peripheral/abaxial domain | |||
| FILAMENTOUS FLOWER (FIL) | At2g45190 | −6.65 | Not expressed |
| KANADI1 (KAN1) | At5g16560 | −2.05 | Not expressed |
| KANADI3 (KAN3) | At4g17695 | 1.62 | Not expressed |
| KNOTTED-LIKE HOMEOBOX PROTEIN1 (KNAT1) | At4g08150 | −7.22 | Not expressed |
| KANADI2 (KAN2) | At1g32240 | −3.78 | Not expressed |
| Transcripts expressed broadly, developmentally important genes | |||
| ARABIDOPSIS THALIANA DEFECTIVE KERNEL1 (AtDEK1) | At1g55350 | −1.45 | −0.12 |
| CENTER CITY (CCT) | At4g00450 | −1.25 | −0.68 |
| FACKEL (FK) | At3g52940 | 1.68 | 0.41 |
| GNOM/EMBRYO DEFECTIVE30 (GN/EMB30) | At1g13980 | −1.04 | 2.38 |
| GRAND CENTRAL (GCT) | At1g55325 | −1.21 | 1.44 |
| GURKE/PASTICCINO3 (GK/PAS3) | At1g36160 | −1.01 | 1.22 |
| HOBBIT (HBT) | At2g20000 | −1.94 | 1.04 |
| HYDRA1 (HYD1) | At1g20050 | −1.05 | 0.25 |
| LEAF CURLING RESPONSIVENESS (LCR) | At1g27340 | 1.2 | 2.03 |
| NONPHOTOTROPIC HYPOCOTYL4/AUXIN RESPONSE FACTOR7 (NPH4/ARF7) | At5g20730 | −2.47 | 1.49 |
| OBERON1 (OBE1) | At3g07780 | −1.04 | 0.50 |
| OBERON2 (OBE2) | At5g48160 | Not on array | 0.66 |
| POPCORN (PCN) | At4g07410 | −1.11 | 0.79 |
| RECEPTOR-LIKE PROTEIN KINASE1 (RPK1) | At1g69270 | −2.45 | −1.33 |
| RETINOBLASTOMA-RELATED (RBR) | At3g12280 | −1.81 | 0.85 |
| ROOT-SHOOT-HYPOCOTYL DEFECTIVE (RSH) | At1g21310 | 1.67 | 2.15 |
| TITANIA1 (TTA1) | At1g14740 | 1.55 | 0.48 |
| SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE10 (SPL10) | At1g27370 | −1.16 | 7.06 |
| SQUAMOSA-PROMOTER BINDING PROTEIN-LIKE11 (SPL11) | At1g27360 | −1.07 | 2.76 |
| TITANIA2 (TTA2) | At3g63500 | 1.07 | nd wild type |
| TOADSTOOL2 (TOAD2) | At3g02130 | −2.00 | 1.10 |
| TOPLESS (TPL) | At1g15750 | −1.52 | 0.56 |
| TOPLESS-RELATED1 (TPR1) | At1g80490 | Not on array | 0.68 |
| TOPLESS-RELATED2 (TPR2) | At3g16830 | 1.08 | 0.57 |
| TOPLESS-RELATED3 (TPR3) | At5g27030 | Not on array | 2.85 |
| TOPLESS-RELATED4 (TPR4) | At3g15880 | 1.07 | 0.78 |
| TRANSPARENT TESTA GLABRA1 (TTG1) | At5g24520 | −1.10 | 1.09 |