Gene expression profiling (RNA-seq) in wild-type and bdrs triple mutant Arabidopsis seedlings in response to light or to a heat shock

We analyzed by RNA-seq the modulation of the transcriptome in response to light or a heat shock in wild-type and bdrs triple mutant Arabidopsis thaliana seedlings (bdrs: cross of bdr1/AT5G25520 mutant SALK_142108C, bdr2/AT5G11430 mutant CS852350 and bdr3/AT2G25640 mutant SALK_059905). We showed that the overall changes in the transcriptome were very similar in the two genotypes. However, when studying specifically gene pairs organized in tandem and with short intergenic distances, we showed that the rapid and strong regulations of upstream genes was associated with bdrs-dependent changes on the downstream gene expression that are consistent with bdrs-dependent transcriptional interferences. Overall design: mRNA profiles in seedlings from wild-type (Col0), or bdr triple mutant were generated by deep sequencing, in triplicates, on Illumina NextSeq500. In the photomorphogenesis experiment, seedlings were grown for 5 days in the dark and exposed or not (DARK) to 2h (LIGHT2h) or 4h (LIGHT4h) of white light. In the heat shock experiment, seedlings were grown for 12 days in the cold (12°C) and exposed (HEAT) or not (COLD) to a heat shock of 4h at 27°C.