Cryptochromes induce genome-wide changes in alternative transcription start site selection in arabidopsis

Cryptochromes (CRYs) are blue-light photoreceptors that regulate diverse physiological responses in plants. CRYs intervene the transcript level of numerous genes by modulating specific transcription factors, including ELONGATED HYPOCOTYL 5 (HY5) and HY5 HOMOLOGUE (HYH). In this study, we conducted a genome-wide analysis to profile blue light-induced changes in alternative transcription start site (TSS) selection in Arabidopsis. We identified 3587 genes exhibiting CRY-dependent and blue light-responsive changes in alternative TSS usage, among which 2197 were predicted to produce multiple protein isoforms with different N-terminal ends through this mechanism. These findings suggest that CRYs contribute to proteome complexity through the control of alternative TSS selection. Furthermore, mutants lacking both HY5 and HYH displayed abnormal blue light-induced changes in alternative TSS selection for a subset of CRY target genes, implicating these transcription factors as downstream components in this regulatory pathway. Our results uncover a previously unrecognized function of CRYs in controlling qualitative aspects of transcriptome via blue light-dependent alternative TSS selection.