Arabidopsis Epitranscriptome: Clock Gene Knockouts

Introduction to the Plant Circadian Clock

Plants do not just respond to light and temperature in the moment. They also anticipate daily change. The circadian clock is an internal timing system that helps a plant align biology with the day–night cycle, so processes like metabolism, growth, and stress responses occur at appropriate times of day.

In Arabidopsis, this timing system is built from a set of clock genes that regulate one another in feedback loops. Together, they generate rhythmic activity that repeats about every 24 hours, even under constant conditions. One common way to visualize these rhythms is to fuse a clock-controlled promoter to a luciferase (LUC) reporter. As clock-regulated transcription rises and falls, luminescence oscillates in a regular wave over time (Panel A).

Importantly, the circadian system is not controlled only at the level of DNA and transcription. The cell also tunes clock behavior after an mRNA is made, through processes such as RNA processing and chemical modifications. One of the best-studied RNA marks is m6A RNA methylation, which is deposited by a dedicated writer complex and is enriched on transcripts from clock-regulated and clock-associated genes. In plants, m6A can help connect environmental light signals to clock regulation, for example through light-sensing cryptochromes that recruit m6A machinery to influence clock transcripts.

When individual clock genes are disrupted, the oscillator can keep time differently. Some mutations make the rhythm run faster (short period), some make it run slower (long period), and some weaken rhythmicity altogether (arrhythmic) (Panel B). These oscillator changes matter because the clock helps coordinate downstream "output" traits, including seedling growth (often measured as hypocotyl length) and seasonal development such as photoperiodic flowering (Panel C). Changes to RNA methylation and RNA processing can also shift clock timing, and reduced m6A activity has been associated with longer circadian periods in Arabidopsis.

This demo dataset provides late-day snapshots (CT20 and CT24) from wild type and selected clock-gene knockouts. It is designed to illustrate how perturbing the clock can be reflected in molecular readouts, including RNA-state and epitranscriptomic signatures, at defined times of day.