Chapter 3 80 and PHB/PHV-LIKE1 and SlCNAL1 in tomato root xylem for instance, have a wellconserved function in cell type differentiation, such as in endodermis and xylem (Wada et al., 1997; Bernhardt et al., 2003; Feller et al., 2011; Zhao et al., 2012; Kim et al., 2014; Wang et al., 2015; Sakaoka et al., 2018; Nagao and Tominaga, 2020; Kajala et al., 2021). Our specific objective was to investigate whether our FR-responsive DEGs share common regulatory motifs. To address this, we conducted motif enrichment analysis using the 500bp promoters of all FR-responsive upregulated DEGs and identified the presence of 5 enriched motifs with MEME suite (Motif based sequence analysis tool) (https:// meme-suite.org/meme/index.html)(Figure 3.17). Then the enrichment was submitted again to TOMTOM to find Arabidopsis TFs according to the database (O’Malley et al., 2016). First motif was found in MYB17, 41, 49, 107, WRKY22, 27, 29 and motif 2 was found in TCPs (At1g72010, At1g72010, At5g08330, At5g08330, At1g69690, the third motif are found in TCPs, MYBs and BPCs (BASIC PENTACYSTEINES) in Figure 3.17. Homologs of five TFs belonging to our DEGs have been also identified in FR response in Arabidopsis from a yeast 1-hybrid screen (Solyc10g079070 (AT3G57800), Solyc06g083170 (AT3G07340), Solyc01g109700 (AT4G34530), Solyc04g005660 (AT3G28857), Solyc07g056360 (AT2G42870)) (Buti, 2008). In our list of 25 differentially expressed TFs in response to FR (Table S3.2), there are members of the TCP, MYB, and bHLH TF families that could be the candidates to bind the identified motifs (Figure 3.17). This can provide clues on FR regulatory elements and provide insight into the transcriptional dynamics orchestrated by FR light in plants. 3.2.12 Candidate TFs were selected for follow-up study We further screened the DEG TF list based on the functions reported in literature, and selected three upregulated TFs for further analysis. These TFs are encoded by Solyc08g080150, Solyc01g090760, Solyc07g053450, which are all highly upregulated in FR (Figure 3.18). Full details can be found in Table S3.2, below are the descriptions of the selected TFs for further study: Solyc01g090760, a GATA transcription factor from the zinc finger DNA binding protein family. This TF plays a crucial role in regulating transcription processes essential for development and cell differentiation (Gao et al., 2015). Additionally, BLAST results indicate that its homologs in Arabidopsis may be involved in elongation processes (Lu et al., 2021; Hou et al., 2022).
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