Table_5_Regulation of alternative splicing by retrograde and light signals converges to control chloroplast proteins.xlsx

Retrograde signals sent by chloroplasts control transcription in the nucleus. These signals antagonistically converge with light signals to coordinate the expression of genes involved in chloroplast functioning and seedling development. Although significant advances have been made in understanding the molecular interplay between light and retrograde signals at the transcriptional level, little is known about their interconnection at the post-transcriptional level. By using different publicly available datasets, this study addresses the influence of retrograde signaling on alternative splicing and defines the molecular and biological functions of this regulation. These analyses revealed that alternative splicing mimics transcriptional responses triggered by retrograde signals at different levels. First, both molecular processes similarly depend on the chloroplast-localized pentatricopeptide-repeat protein GUN1 to modulate the nuclear transcriptome. Secondly, as described for transcriptional regulation, alternative splicing coupled with the nonsense-mediated decay pathway effectively downregulates expression of chloroplast proteins in response to retrograde signals. Finally, light signals were found to antagonistically control retrograde signaling-regulated splicing isoforms, which consequently generates opposite splicing outcomes that likely contribute to the opposite roles these signals play in controlling chloroplast functioning and seedling development.

叶绿体（chloroplast）释放的逆行信号（retrograde signals）可调控细胞核（nucleus）内的转录过程。此类信号可与光信号发生拮抗汇聚，协同调控参与叶绿体功能与幼苗发育的基因表达。尽管目前在转录水平（transcriptional level）上解析光信号与逆行信号间的分子互作已取得显著进展，但二者在转录后水平（post-transcriptional level）的关联机制仍鲜为人知。本研究借助多套公开可用数据集（publicly available datasets），解析了逆行信号对可变剪接（alternative splicing）的调控作用，并明确了该调控的分子与生物学功能。分析结果显示，可变剪接在多个层面上模拟了逆行信号诱导的转录应答：其一，两类分子过程均依赖定位于叶绿体的五肽重复蛋白（pentatricopeptide-repeat protein）GUN1，以调控细胞核转录组（nuclear transcriptome）；其二，正如转录调控中的情况，可变剪接与无义介导的降解通路（nonsense-mediated decay pathway）协同作用，可响应逆行信号有效下调叶绿体蛋白的编码基因表达；最后，研究发现光信号可拮抗调控逆行信号介导的剪接异构体（splicing isoforms），由此产生相反的剪接产物，这或有助于解释两类信号在调控叶绿体功能与幼苗发育中发挥的相反作用。