Role of a ZF-HD transcription factor in miR157-mediated feed-forward regulatory module that determines plant architecture in arabidopsis

Authors: LEE, YOUNG KOUNG - Korea Atomic Energy Research Institute (KAERI); KUMARI, SUNITA - Cold Spring Harbor Laboratory; OLSON, ANDREW - Cold Spring Harbor Laboratory; HAUSER, FELIX - University Of California, San Diego; Ware, Doreen

Submitted to: International Journal of Molecular Sciences
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/28/2022
Publication Date: 8/4/2022
Citation: Lee, Y., Kumari, S., Olson, A., Hauser, F., Ware, D. 2022. Role of a ZF-HD transcription factor in miR157-mediated feed-forward regulatory module that determines plant architecture in arabidopsis. International Journal of Molecular Sciences. https://doi.org/10.3390/ijms23158665.
DOI: https://doi.org/10.3390/ijms23158665

Interpretive Summary: It is very important to understand the molecular basis of agricultural important traits related to increasing yield, grain quality, disease resistance and stress tolerance to improve the performance in crop plants. To understand the molecular mechanisms, the role of Zinc finger homeodomain (ZF-HD) transcription factor was used to study its role in growth and development in Arabidopsis by using system biology approaches and functional genomics tools like RNA-seq, Chip-see and loss of function mutants studies. Based on these studies, it was found that this transcription factor is involved in the regulatory network of shoot development and inflorescence architecture.

Technical Abstract: In plants, vegetative and reproductive development are associated with agronomically important traits that contribute to grain yield and biomass. Zinc finger homeodomain (ZF-HD) transcription factors (TFs) constitute a relatively small gene family that has been studied in several model plants, including Arabidopsis thaliana L. and Oryza sativa L. The ZF-HD family members play important roles in plant growth and development, but their contribution to the regulation of plant architecture remains largely unknown due to their functional redundancy. To understand the gene regulatory network controlled by ZF-HD TFs, we analyzed multiple loss-of-function mutants of ZF-HD TFs in Arabidopsis that exhibited morphological abnormalities in branching and flowering architecture. We found that ZF-HD TFs, especially HB34, negatively regulate the expression of miR157 and positively regulate SQUAMOSA PROMOTER BINDING–LIKE 10 (SPL10), a target of miR157. Genome-wide chromatin immunoprecipitation sequencing (ChIP-Seq) analysis revealed that miR157D and SPL10 are direct targets of HB34, creating a feed-forward loop that constitutes a robust miRNA regulatory module. Network motif analysis contains overrepresented coherent type IV feedforward motifs in the amiR zf-HD and hbq mutant background. This finding indicates that miRNA-mediated ZF-HD feedforward modules modify branching and inflorescence architecture in Arabidopsis. Taken together, these findings reveal a guiding role of ZF-HD TFs in the regulatory network module and demonstrate its role in plant architecture in Arabidopsis.