Interplay between coding and non-coding regulation drives the Arabidopsis seed-to-seedling transition

Area of Science:

• Plant molecular biology
• Transcriptional regulation
• Seed germination

Background:

• Seed germination requires translation of stored mRNAs.
• The precise timing of RNA Polymerase II (RNAPII) re-engagement in RNA synthesis during the seed-to-seedling transition is not fully understood.
• Non-coding RNAs play crucial roles in gene regulation.

Purpose of the Study:

• To investigate the dynamics of active transcription initiation during seed germination.
• To characterize the role of non-coding RNAs and chromatin accessibility in regulating gene expression during germination.
• To explore the mechanisms of abscisic acid (ABA) sensitivity during this developmental stage.

Main Methods:

• Combined computational small RNA sequencing (csRNA-seq), Assay for Transposase-Accessible Chromatin using sequencing (ATAC-seq), and single-molecule Fluorescence In Situ Hybridization (smFISH).
• Utilized Arabidopsis thaliana as the model organism.
• Employed genetic validation for key findings.

Main Results:

• Active transcription initiation is detectable throughout the entire germination process in Arabidopsis.
• Widespread non-coding RNA regulation, including antisense transcription and bidirectional promoters, was observed.
• Germination sensitivity to exogenous abscisic acid (ABA) is linked to proximal promoter accessibility at ABA-responsive genes.
• Divergent transcription and transcribed enhancer elements producing enhancer RNAs (eRNAs) were genetically validated.

Conclusions:

• This study defines the extent and function of both coding and non-coding transcription during key germination stages.
• Findings expand the understanding of transcriptional mechanisms governing plant developmental transitions.
• Active transcription and non-coding regulatory elements are integral to successful seed germination.