Transcriptional Dynamics and Chromatin Accessibility in the Regulation of Shade-Responsive Genes in Arabidopsis [RNA-Seq]
Accessible chromatin regions host DNA regulatory motives and are highly accessible to the transcription factors and transcriptional machinery. In Arabidopsis, responses to light are heavily regulated at the transcriptional level.  Shade, for example, can limit photosynthesis and is rapidly perceived by phytochromes as a reduction of red to far-red light ratio. Under shade, phytochromes inactivate and allow PHYTOCHROME INTERACTING FACTORs (PIFs) to promote a wide scale genome reprogramming. A strong and fast initial regulation of shade responsive genes is followed by an attenuation of this response under prolonged shade. We wanted to determine if transcriptional response pattern to shade depends on chromatin accessibility. For this we used ATAC-seq to profile the chromatin of seedlings exposed to short (1h) and long (25h) simulated shade. Transcription pattern of most acute shade responsive genes correlates with the rapid increase in PIF levels/activity at 1h, and its decrease at 25h of shade exposure. For a set of acute responding genes, PIFs also modulate chromatin accessibility at their binding sites in response to shade. Our results suggest that permanent state of open chromatin conformation allows PIFs to easily access and recognize their binding motifs, rapidly initiating a burst in gene expression triggered by shade. This transcriptional response primarily depends on a transient increase in stability of PIFs and gene occupancy and is followed by a moderate change of chromatin accessibility. Overall design: RNA-seq profiling of 7 day-old seedlings grown in high red:far-red light ratio (HRFR) or exposed to 1h or 25h of low red:far-red light ratio (LRFR). Three replicates of Col-0 and pif457 for each condition were collected at ZT3.