A cis-regulatory atlas in maize at single-cell resolution

Area of Science:

• Plant genomics
• Molecular biology
• Developmental biology

Background:

• cis-regulatory elements (CREs) control gene expression crucial for specialized cell functions.
• Understanding CREs and transcription factors (TFs) is key to deciphering gene regulation and cellular diversity.

Purpose of the Study:

• To map CREs and TFs across six maize organs using single-cell genomics.
• To identify regulatory factors defining cell identity, chromatin organization, and gene expression.
• To investigate the evolutionary dynamics of CREs and TFs between maize and Arabidopsis thaliana.

Main Methods:

• Single-cell genomics profiling of six maize organs.
• Analysis of transcription factor (TF) combinatorics and non-cell-autonomous activity.
• Identification of TFs involved in higher-order chromatin interactions.
• Comparative genomics analysis with Arabidopsis thaliana.

Main Results:

• Cell-type-specific CREs are enriched for enhancer activity and located in unmethylated LTR retrotransposons.
• CREs are hotspots for phenotype-associated genetic variants and targets of selection in maize breeding.
• Identified conserved and divergent TF and CRE dynamics between maize and Arabidopsis, revealing gene regulatory network evolution.
• Developed Socrates, a single-cell analysis software for cis-regulatory variation.

Conclusions:

• This CRE atlas provides a foundational resource for understanding maize gene regulation and development.
• CREs play significant roles in plant adaptation and breeding, harboring important genetic variants.
• Comparative analyses highlight the evolutionary plasticity of gene regulatory networks in plants.
• The Socrates software offers a versatile tool for cis-regulatory studies across species.