Genome-wide binding analysis of the tomato transcription factor SlDof1 reveals its regulatory impacts on fruit ripening

Yuying Wang,Shiping Tian,Lingxi Kong,Guozheng Qin,Weihao Wang,Peiwen Wang

doi:10.1186/s43897-021-00011-y

Abstract

The DNA binding with one finger (Dof) proteins are plant-specific transcription factors involved in a variety of biological processes. However, little is known about their functions in fruit ripening, a flowering-plant-specific process that is required for seed maturation and dispersal. Here, we found that the tomato Dof transcription factor SlDof1, is necessary for normal fruit ripening. Knockdown of SlDof1 expression by RNA interference delayed ripening-related processes, including lycopene synthesis and ethylene production. Transcriptome profiling indicated that SlDof1 influences the expression of hundreds of genes, and a chromatin immunoprecipitation sequencing revealed a large number of SlDof1 binding sites. A total of 312 genes were identified as direct targets of SlDof1, among which 162 were negatively regulated by SlDof1 and 150 were positively regulated. The SlDof1 target genes were involved in a variety of metabolic pathways, and follow-up analyses verified that SlDof1 directly regulates some well-known ripening-related genes including ACS2 and PG2A as well as transcriptional repressor genes such as SlIAA27. Our findings provide insights into the transcriptional regulatory networks underlying fruit ripening and highlight a gene potentially useful for genetic engineering to control ripening.

Highlights

Fruits play a major role in seed dispersal and reproductive development in the life cycle of higher plants
To identify DNA binding with one finger (Dof) genes associated with fruit ripening, we examined the expression patterns of all 34 Dof genes at different ripening stages using quantitative RTPCR analysis
The results indicated that only plants silenced for SlDof1 exhibited an obvious phenotype, fruit color patchiness, suggesting that SlDof1 participates in the regulation of fruit ripening (Fig. 1B)

Summary

Introduction

Fruits play a major role in seed dispersal and reproductive development in the life cycle of higher plants. Understanding the molecular mechanisms underlying the regulation of fruit ripening can facilitate the development of new strategies for the improvement of fruit quality and extension of shelf life. Research on fruit ripening has been more focused on transcriptional control, which might lie upstream of ethylene signaling and, in some cases, could impact ripening independently of ethylene. Understanding the functional role of transcription factors in fruit ripening will facilitate genetic engineering for the control of ripening and the development of new strategies for the improvement of fruit quality and extension of shelf life

Methods

Results

Conclusion