Autumn-winter progression triggers distinct transcriptional programmes in Arabidopsis thaliana (RNA-seq)

However, the global regulatory landscape underlying cold acclimation and adaption of plants to noisy and fluctuating natural cold conditions remain poorly investigated. Here, we perform a deep-coverage RNA-seq to investigate the transcriptome dynamics of Arabidopsis thaliana plants grown over weeks of a fluctuating temperature regime, mimicking natural cold conditions of autumn and early winter, or grown using an average daily temperature profile without any temperature fluctuations.

We show that progressive cold induces three main patterns of transcriptional response: dynamic-, cooling- and chilling-responsive gene activation. Progressive cold induces a complex network of regulators that could be responsible for the regulation of distinct transcriptional programs. Surprisingly, we find only small differences in cold-responsive gene expression between average and fluctuating conditions.