LEFKOTHEA modulates gene expression at the transcriptional and post-transcriptional levels during early light response

Light is the source of energy for photosynthetic organisms such as plants. Due to the great significance of light in the regulation of development, plants possess a sophisticated signaling network that controls light response including a massive gene expression reprogramming as well as post-transcriptional mechanisms such as alternative splicing. LEFKOTHEA is a nucleus-encoded splicing factor found in both the nucleus and chloroplast and its nuclear compartmentalization ensures the early embryonic development in Arabidopsis. LEFKOTHEA gene mutations (lefko1, an EMS mutant allele exhibiting aberrant nuclear partitioning and an albino cotyledon phenotype, and lefko2, a severe allele that results in embryo developmental arrest) have defects in splicing of nuclear and chloroplast genes. Time-series transcriptomic analysis upon light encounter revealed an aberrant response to light in lefko1, characterized by down-regulation of genes involved in photosynthetic apparatus and signal transduction pathways. Further, LEFKOTHEA significantly affects the number and the mode of alternative splicing events during light response. A majority of such events occur on spliceosomal components, light-related transcription factors and genes involved in signal transduction. Altogether, the results indicate that LEFKOTHEA is an active component of early light response signaling, regulating gene expression both transcriptionally and post-transcriptionally. Overall design: RNAseq profiling of dark-grown Arabidopsis wild-type and lefko1 mutant seedlings upon light encounter in a time-series experiment