ChIP-seq revealed the role of tomato SNAC4 in response to biological and abiotic stresses and mediating auxin signaling response

Identification of target genes of transcription factors in the whole genome is important for a comprehensive understanding of transcription factor regulatory networks. Our interest is to refine the spectrum of loci regulated by the tomato ( Solanum lycopersicum L. ) NAC transcription factor SNAC4 (NM_001279348.2) and to fully understand the important role of SNAC4 in regulating various life activities in tomato. We identified a large number of SNAC4 target genes enriched in pathogen resistance, stress response, phytohormone signaling, and development-related pathways by ChIP-seq. SNAC4 interacts at the protein level with IAA3 and IAA27 in the auxin signaling pathway . SNAC4 can directly act on the promoter regions of B. cinerea defense ( JA2L and SRN1 ), auxin ( ARF1 , ARF5 , ARF7 , IAA3 , IAA9 , IAA13 and IAA27 ), ABA ( PP2C 37 , ABI2 , NCED6 and SnRK2.2 ), ethylene ( CTR3 , ACO6 and EBF1 ), softening ( XYL1 and TBG ), and pigment ( Psy1 , SGR1 , and CrtR-b2 ) related genes. The expression levels of auxin pathway genes were affected by SNAC4 overexpression and the SNAC4 expression levels were affected by ethylene and auxin treatments. Our results indicate that target genes downstream of SNAC4 are involved in biotic and abiotic stress responses, auxin signaling, phytohormone crosstalk, and plant growth and maturation in tomato. SNAC4 regulates their expression by interacting with target genes. • SNAC4 plays roles in abiotic stress response in tomato. • SNAC4 binds to biological stress-related genes and regulates their expression. • SNAC4 binds to auxin-related genes and regulates their expression. • SNAC4 is involved in phytohormone crosstalk. • SNAC4 regulates tomato plant growth and fruit ripening.