Translational regulation of mRNAs and lncRNAs involved in chromatin remodeling and post-transcriptional gene silencing during root nodule symbiosis

REYNOSO, MAURICIO; HOBECKER, KAREN; ZANETTI, MARÍA EUGENIA; TRAUBENIK, SOLEDAD; BLANCO, FLAVIO

Rosario

Simposio; Simposio de Genómica Funcional de Plantas; 2017

Regulation of gene expression occurs at multiple levels within eukaryotic cells, including chromatin-based, transcriptional and post-transcriptional events. We have previously shown that genes with key roles in the root nodule symbiosis established between Medicago truncatula and Sinhorihizobium meliloti are regulated at translational level. Here, we combined Translating Ribosome Affinity Purification (TRAP) with RNA-seq to characterize dynamic changes in the population of mRNAs associated to the translational machinery (the translatome) at early stages of the symbiotic interaction. We identified hundred of transcripts that were either up- or down-regulated at the translational level, including genes that are essential for nodulation. Some of these mRNAs encode proteins involved in chromatin remodeling and post-transcriptional gene silencing (a lysine specific demethylase, an RNA-directed DNA methylation protein and a Superkiller), which also showed a cell-specific expression pattern in roots reprogrammed for nodulation. In addition, a number of putative long non-coding RNAs (lncRNAs) were identified among transcripts that changed their association to the translational machinery during symbiosis. Remarkably, the distribution of reads along the Trans Acting Short interfering RNA3 (TAS3) present in the translatome was greatly altered at early stages of the symbiotic interaction. TAS3 results in the production of trans-acting siRNAs (tasiRNAs) when targeted at two sites by miR390. As its counterparts in Arabidopsis, the Medicago TAS3 transcript contains an open reading frame upstream of the non-cleavable miR390 target site, which could modulate the production of tasiRNAs. These selective changes in the translatome might contribute to the reprogramming of root cells for symbiosis.