Functional investigation of five R2R3-MYB transcription factors associated with wood development in Eucalyptus using DAP-seq-ML

• Published in: Plant molecular biology 2023-10, Vol.113 (1-3), p.33-57
• Main Authors: Takawira, Lazarus T., Hadj Bachir, Ines, Ployet, Raphael, Tulloch, Jade, San Clemente, Helene, Christie, Nanette, Ladouce, Nathalie, Dupas, Annabelle, Rai, Avanish, Grima-Pettenati, Jacqueline, Myburg, Alexander A., Mizrachi, Eshchar, Mounet, Fabien, Hussey, Steven G.
• Format: Article
• Language: English
• Subjects: Arabidopsis; Arabidopsis thaliana; Biochemistry; Biomedical and Life Sciences; Cell differentiation; Cell walls; Chromatin; Conserved sequence; DNA binding proteins; Eucalyptus; Genes; Genetic engineering; Genomes; Genomics; Hairy root; Hardwoods; Investigations; Learning algorithms; Life Sciences; Machine learning; Nucleotide sequence; Plant Pathology; Plant Sciences; Transcription factors; Vegetal Biology; Wood; Xylem
• ISSN: 0167-4412; 1573-5028
• DOI: 10.1007/s11103-023-01376-y

A multi-tiered transcriptional network regulates xylem differentiation and secondary cell wall (SCW) formation in plants, with evidence of both conserved and lineage-specific SCW network architecture. We aimed to elucidate the roles of selected R2R3-MYB transcription factors (TFs) linked to Eucalyptus wood formation by identifying genome-wide TF binding sites and direct target genes through an improved DAP-seq protocol combined with machine learning for target gene assignment (DAP-seq-ML). We applied this to five TFs including a well-studied SCW master regulator (EgrMYB2; homolog of AtMYB83), a repressor of lignification (EgrMYB1; homolog of AtMYB4), a TF affecting SCW thickness and vessel density (EgrMYB137; homolog of PtrMYB074) and two TFs with unclear roles in SCW regulation (EgrMYB135 and EgrMYB122). Each DAP-seq TF peak set (average 12,613 peaks) was enriched for canonical R2R3-MYB binding motifs. To improve the reliability of target gene assignment to peaks, a random forest classifier was developed from Arabidopsis DAP-seq, RNA-seq, chromatin, and conserved noncoding sequence data which demonstrated significantly higher precision and recall to the baseline method of assigning genes to proximal peaks. EgrMYB1, EgrMYB2 and EgrMYB137 predicted targets showed clear enrichment for SCW-related biological processes. As validation, EgrMYB137 overexpression in transgenic Eucalyptus hairy roots increased xylem lignification, while its dominant repression in transgenic Arabidopsis and Populus reduced xylem lignification, stunted growth, and caused downregulation of SCW genes. EgrMYB137 targets overlapped significantly with those of EgrMYB2, suggesting partial functional redundancy. Our results show that DAP-seq-ML identified biologically relevant R2R3-MYB targets supported by the finding that EgrMYB137 promotes SCW lignification in planta . Key message We combined DAP-seq with machine learning to identify biologically relevant gene targets for five Eucalyptus R2R3-MYB transcription factors linked to wood formation, additionally demonstrating that EgrMYB137 promotes lignification in planta.