Fig. 4. RNA-Rx enables refining gene regulatory pathways during cotyledon de-etiolation.

A Percentage of genes up- or downregulated after 24 h of light (q-value < 0.01 for a |Log2 FC | > 0.5) at target genes of major transcription factors involved in light signaling. All analyzed TF target genes were previously identified, as detailed in Supplementary Data 4. Source data are provided as a Source Data file. B Expression Log2 FC of genes bound by GLK1/2, HY5, FHY1, and PIF3 transcription factors that are also differentially expressed upon 24 h of light exposure using Standard or Spike-in RNA-Rx analyses, respectively. Genes are ranked by their Log2 FC at 24 h. C DREM analysis of coregulated gene paths using expression Log₂ FC from Standard RNA-seq and Spike-in RNA-Rx. Seven paths were found in both cases, called A to G (Standard) or A’ to G’ (Spike-in), that largely overlap. The inlays display the percentage of DEGs in paths A to G at the 24 h time point and the percentage of genes shared between paths A to G and A’ to G’. D Metaplot profiles of RNA Pol II S2P and H2Bub enrichment in dark and light-grown cotyledons at the genes corresponding to the DREM paths A’ to G’. E Distribution of mRNA half-lives in the DREM paths A’ to G’ according to Sorenson et al. (2018), Chantarachot et al. (2020), and Szabo et al. (2020)^44–46. The distributions over all TAIR10 genes are shown as reference in gray and compared to each DREM path with a Welch’s t test (* < 0.1, ** < 0.01 and ***< 0.001). Source data are provided as a Source Data file. F Over-represented gene ontology (GO) categories within the DREM path A’ to G’. Numbers correspond to the genes falling in each GO category. G Variations of expression Log₂ FC upon Standard RNA-seq or Spike-in RNA-Rx analysis of genes encoding proteins of the photosynthetic chain, ribosomes, and replication machinery. Source data are provided as a Source Data file.