Identification of Key Tissue-Specific, Biological Processes by Integrating Enhancer Information in Maize Gene...

Area of Science:

• Plant molecular biology
• Genomics and epigenomics
• Developmental biology

Background:

• Enhancers regulate gene expression critical for development and differentiation.
• Identifying enhancer-target gene interactions is challenging in large plant genomes.
• The role of enhancers in plant regulatory networks is not well understood.

Purpose of the Study:

• To investigate enhancer-driven regulatory networks in two distinct maize tissues: seedling leaves (V2-IST) and flowering husks.
• To model regulatory relationships between transcription factors (TFs) and target genes.
• To identify tissue-specific regulatory modules and understand their evolutionary origins.

Main Methods:

• Systems biology approach integrating genomic, epigenomic, and transcriptomic data.
• Analysis of TF families and their target genes in specific maize tissues.
• Comparative analysis of enhancer sequences, including transposable elements.

Main Results:

• Maize V2-IST leaves show regulation of hormone response and macromolecule biogenesis by BBR/BPC and AP2/ERF TFs.
• Maize husks exhibit regulation of cell wall modification and abiotic stress response by C2C2/DOF and AP2/EREB TFs.
• Transposable elements, specifically TIR transposons (Mutator) and MITEs (Pif/Harbinger), have shaped these regulatory networks, with MITEs contributing to husk-specific TF binding sites.

Conclusions:

• Enhancers play crucial, tissue-specific roles in maize development and stress adaptation.
• Distinct TF families and transposable elements are key drivers of tissue-specific gene regulation.
• This study provides insights into the evolution of plant regulatory networks through enhancer innovation.