Analysis of the heso1 and urt1-dependent ski2 transcriptome profile in Arabidopsis

Non templated uridine addition at the 3' ends of RNAs (RNA uridylation) is a widespread post transcriptional modification of eukaryotic RNAs. Uridylation regulates diverse RNA metabolism processes including maturation, localization and stabilization. To date, the primary function of RNA uridylation is to promote RNA turn over. Here we demonstrate that HESO1, URT1 and SKI2 redundantly regulate Arabidopsis leaf chlorophyll content. This phenotype was mainly caused by disturbance of mRNA degradation of the Transketolase 1 (TKL1) and was substantially suppressed by the rdr6. mRNA seq approach was used to investigate the physiological relevance veiled by the developmental phenotypes in Ler, ski2_6 (s), heso1_2 urt1_3 (hu), heso1_2 urt1_3 ski2_6 (hus) and heso1_2 urt1_3 ski2_6 rdr6_8 (husr). Compared with Ler, 4110 genes exhibited differential expression in heso1_2 urt1_3 ski2_6, much more than those in the heso1_2 urt1_3 (841 genes) or ski2_6 (2851 genes) mutats (2_fold cutoff, p < 0.01, FDR < 0.05), suggesting a largely disturbed transcriptome in the absence of both HESO1 URT1 and SKI2. The gene lists from hus vs Ler and husr vs Ler was largely overlapped which each other, indicating that even rdr6 suppressed the phenotype of hus can not recover most of the gene expression changes in hus. There were 270 increased and 292 decreased genes in specific changed in hus compared with Ler, among them TKL1 was identified. Combine with our small RNA sequencing data with the same materials, the phenotype of hus was mainly caused by disturbance of mRNA degradation and spurious siRNA biogenesis from TKL1 locus. Taken together, our study highlights the significance of mRNA uridylation for plant development.