The regulatory potential of transposable elements in maize.

Area of Science:

• Genomics
• Epigenetics
• Plant Biology

Background:

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

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:

• Utilized long-read chromatin fibre sequencing (Fiber-seq) for high-resolution genome-wide analysis.
• Analyzed patterns of chromatin accessibility and CpG methylation associated with TEs of varying evolutionary ages.

Main Results:

• Identified distinct ACR patterns at young TEs that change with age.
• Discovered a novel plant-specific epigenetic feature: simultaneous hyper-CpG methylation and chromatin accessibility at TE enhancers.
• Demonstrated co-option of TE ACRs as gene promoters and their role in gene amplification.
• Uncovered an epigenetic signature (hypo-5mCpG methylation and diffuse chromatin accessibility) guiding TEs to specific genomic loci.

Conclusions:

• Fiber-seq provides a comprehensive view of TE regulatory potential and epigenetic states in plants.
• TEs possess unique epigenetic features that enable them to function as regulatory elements, influencing gene expression and genome organization.
• Epigenetic signatures play a crucial role in directing TEs to specific genomic locations, impacting genome evolution.