The regulatory potential of transposable elements in maize

Area of Science:

• Plant genomics
• Epigenetics
• Molecular biology

Background:

• Plant genomes are rich in transposable elements (TEs), which can affect gene regulation.
• Short-read sequencing limits the study of individual TEs and their regulatory roles.

Purpose of the Study:

• To comprehensively map accessible chromatin regions (ACRs) and CpG methylation across the maize genome using long-read sequencing.
• To investigate the regulatory potential and epigenetic characteristics of transposable elements (TEs).

Main Methods:

• Long-read chromatin fiber sequencing (Fiber-seq) was employed.
• Analysis of accessible chromatin regions (ACRs) and CpG methylation patterns in the maize genome.

Main Results:

• Fiber-seq identified ACRs and CpG methylation across the maize genome.
• Young TEs exhibit distinct ACR patterns that change with age.
• A novel plant-specific epigenetic feature of simultaneous hyper-CpG methylation and chromatin accessibility was found at TE-enhancers.
• TE ACRs are repurposed as gene promoters, and TEs can drive gene amplification.
• A distinct epigenetic signature (hypo-5mCpG methylation and diffuse chromatin accessibility) guides TEs to specific genomic locations.

Conclusions:

• Long-read Fiber-seq provides a comprehensive view of TEs and their regulatory roles in plants.
• Transposable elements possess significant regulatory potential, influencing gene expression, amplification, and genome organization through unique epigenetic mechanisms.