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Genomic Identification of Direct Target Genes of LEAFY

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Genomic Identification of Direct Target Genes of LEAFY Genomic identification of direct target genes of LEAFY Dilusha A. William*, Yanhui Su*, Michael R. Smith*, Meina Lu*, Don A. Baldwin†, and Doris Wagner*‡ *Department of Biology and †Penn Microarray Facility, University of Pennsylvania, 415 South University Avenue, Philadelphia, PA 19104 Communicated by Anthony R. Cashmore, University of Pennsylvania, Philadelphia, PA, November 25, 2003 (received for review September 5, 2003) The switch from vegetative to reproductive development in plants AP1 acts as a floral homeotic gene in addition to its role as a necessitates a switch in the developmental program of the descen- meristem identity regulator (17, 18). The latter function does not dents of the stem cells in the shoot apical meristem. Genetic and depend on LFY, however, because lfy null mutants show strong AP1 molecular investigations have demonstrated that the plant-specific expression in flowers from stage three onward (11, 13, 16, 19). The transcription factor and meristem identity regulator LEAFY (LFY) LFY-independent induction of AP1 expression makes it difficult to controls this developmental transition by inducing expression of a detect LFY-dependent induction of AP1 at the floral transition by second transcription factor, APETALA1, and by regulating the expres- using quantitative methods in entire inflorescences (13). To identify sion of additional, as yet unknown, genes. Here we show that the the additional unknown LFY targets that act at the transition to additional LFY targets include the APETALA1-related factor, CAULI- reproductive development together with AP1, it is, therefore, FLOWER, as well as three transcription factors and two putative signal important to first identify a developmental stage at which quanti- transduction pathway components. These genes are up-regulated by tative induction of AP1 can be observed in response to LFY. LFY even when protein synthesis is inhibited and, hence, appear to be Here we report that quantitative up-regulation of AP1 can be direct targets of LFY. Supporting this conclusion, cis-regulatory re- readily observed in 9-day-old seedlings. Using posttranslational gions upstream of these genes are bound by LFY in vivo. The newly activation of LFY-GR, we demonstrate that the closest AP1 ho- identified LFY targets likely initiate the transcriptional changes that molog, CAULIFLOWER (CAL), is a direct LFY target at this are required for the switch from vegetative to reproductive devel- stage in development and that cis-regulatory elements in the opment in Arabidopsis. putative CAL promoter are bound by LFY. We used microarray analysis to identify direct targets of LFY and chromatin immuno- he plant-specific LEAFY (LFY) protein is necessary and precipitation (ChIP) to demonstrate in vivo LFY binding to the Tsufficient for the vital switch from vegetative to reproductive putative promoter regions of these genes. The predicted function of development in dicotyledonous plant species (1–9). LFY controls the proteins encoded by these genes is consistent with their role in the production of the flowers, which are formed in lieu of secondary the meristem identity switch. inflorescences from the flanks of the shoot apical meristem. Be- Methods cause LFY is required for all of the major features that differentiate flowers from inflorescence branches, it is referred to as a meristem Plant Growth and Steroid Treatments. Seedlings were germinated on identity gene. half-strength Murashige and Skoog medium after 7 days of cold After initiating the meristem identity switch, LFY has a second treatment at 4°C. Growth was at 21°C in continuous light at a ␮ ͞ 2⅐ role in the activation of the floral homeotic genes that specify the fluence rate of 50 mol m sec. Steroid treatments were performed identity of organs in the flower (10). The two roles of LFY are essentially as described (see ref. 13 and Supporting Text, which is separable genetically and molecularly (11, 12). LFY exerts its published as supporting information on the PNAS web site). developmental effects by means of transcriptional regulation; LFY has been shown to be a transcription factor in vivo (13, 14). RT-PCR. Frozen seedling tissue was ground five times for 10 sec with Despite the critical importance of this regulator, only three direct 1.0-mm glass beads (Biospec Products, Bartlesville, OK) by using a PLANT BIOLOGY targets of LFY have been identified (13–15). Two of the targets, Mini-BeadBeater (Biospec Products), followed by extraction with AGAMOUS and APETALA3, are floral homeotic genes that act TRI (total RNA-isolating) reagent (Molecular Research Center) directly downstream of LFY in flower morphogenesis. Only one according to the manufacturer’s instructions. The resulting RNA was further purified by using RNeasy columns (Qiagen, Valencia, known direct LFY target gene product, APETALA1 (AP1), acts in ␮ the meristem identity pathway (13). CA). For reverse transcription, 2 g of the purified RNA was used with the Thermoscript kit (Invitrogen) according to the manufac- The ap1-1 mutation partly suppresses the LFY gain-of-function ␮ phenotype (9, 16), indicating that AP1 acts downstream of LFY in turer’s instructions. We used 0.8 l of the reverse transcription reaction in a 25-␮l PCR with Platinum TAQ (Invitrogen), except the floral transition, which culminates in flower formation. Post- ␮ translational activation of a biologically active fusion protein be- for CAL and AT5g60630, for which we used 2 l of the reverse tween LFY and the rat glucocorticoid receptor (GR) hormone- transcription reaction. PCR conditions are detailed in Supporting binding domain demonstrates that LFY directly activates AP1 in the Text. anlagen of the flower primordia in a protein synthesis-independent Microarrays. RNA was extracted and purified as described above. fashion (13). In addition, LFY binds to cis-regulatory elements that ␮ control AP1 expression (11). Thus, LFY regulates the transition to Total RNA input was 5 g. Probe synthesis was performed as flower development, at least in part, by inducing AP1 expression in described in the GENECHIP Expression Analysis Technical Manual regions of the shoot apical meristem that give rise to flower (www.affymetrix.com; Affymetrix, Santa Clara, CA). After first- primordia. LFY null mutations cause striking defects in the transition to Abbreviations: AP1, APETALA1; CAL, CAULIFLOWER; ChIP, chromatin immunoprecipita- reproductive development; lfy-6 plants, for example, produce a tion; FUL, FRUITFUL; GR, glucocorticoid receptor; Ler, Landsberg erecta; LFY, LEAFY. large number of secondary inflorescences until very late in devel- Data deposition: The ATH1 microarray hybridization dataset has been deposited in the opment when defective flowers are formed (1–3). In contrast, the Gene Expression Omnibus (GEO) database, www.ncbi.nlm.nih.gov͞geo (series accession strongest available AP1 mutation has a much weaker effect on no. GSE 911). inflorescence morphology, implying that other LFY target genes ‡To whom correspondence should be addressed. E-mail: [email protected]. must exist in the meristem identity pathway. © 2004 by The National Academy of Sciences of the USA www.pnas.org͞cgi͞doi͞10.1073͞pnas.0307842100 PNAS ͉ February 10, 2004 ͉ vol. 101 ͉ no. 6 ͉ 1775–1780 Downloaded by guest on September 29, 2021 and second-strand cDNA synthesis, all reactions were tested by PCR for induction and equal template presence by using AP1- and EIF4-specific primers. After fragmentation, 15 ␮g of cRNA was used for hybridization. Microarray hybridization, data acquisition, and first-pass analysis were performed as described (www. med.upenn.edu͞microarr) by the Penn Microarray Facility (Uni- versity of Pennsylvania, Philadelphia). Fold up-regulation required for each condition was chosen arbitrarily. Variance per gene was generally less than the randomly chosen cutoffs, allowing for their use as a criterion for prioritizing candidate genes for independent confirmation. Moreover, all pu- tative candidate genes exhibit very low variance within treatment comparisons for all six treatments͞genotypes; 96% of identified LFY target genes fall within the arbitrary boundaries chosen for all six comparisons. ChIP. Seedlings (9-day-old) grown on half-strength Murashige and Skoog plates were treated with dexamethasone or mock solution, as described above, washed in PBS, and crosslinked with 1% formal- dehyde for 10 min by using vacuum infiltration. The crosslinking reaction was stopped by addition of 0.1 M glycine. Nuclear extracts were prepared according to ref. 21, lysed as described by the Farnham laboratory (http:͞͞mcardle.oncology.wisc.edu͞farnham͞ ͞ protocols chips.html), and diluted 10-fold in lysis dilution buffer Fig. 1. (A) RT-PCR analyses of two direct targets of the LFY transcription factor (Farnham protocol). Extracts were sonicated in the presence of indicate that AP1 is expressed independently of LFY in whole inflorescences glass beads (Biospec Products) to achieve a DNA size range (Left). By contrast, API expression depends on LFY and is directly induced by LFY between 50 and 1,600 bp with an average of 600 bp for ChIP in 9-day-old seedlings (Right). Treatments were as follows: dexamethasone (D), experiment 1 (ChIP1) and a size distribution from 100 to 3,000 bp dexamethasone plus the protein synthesis inhibitor cycloheximide (DC), cyclo- with an average of 900 bp in a ChIP experiment 2 (ChIP2). We heximide alone (C), and mock (M). The ubiquitously expressed EIF4 gene was removed 1͞25 of the sample as input. Affinity-purified LFY amplified to test for equal template presence. Two 4-hr treatments were per- antiserum (13) was bound to 40 ␮l of protein A magnetic beads formed sequentially. (B) Rapid, protein synthesis-independent up-regulation of (Dynal Biotech, Lake Success, NY) that had been pretreated with AP1 and its closest homolog, CAL. Treatments were performed as in A, except durations (indicated above each lane) were shorter. Wild-type Landsberg erecta 0.5% BSA in PBS. For ChIP2, twice as much antiserum prebound (Ler) was treated with steroid as a negative control. Genotypes are indicated at to beads was used as for ChIP1. After antibody binding (90 min at ͞ the top.
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