RNA-Seq analysis discloses early senescence and nucleolar dysfunction triggered by Tdp1alpha depletion in Medicago truncatula

An intron-spliced hairpin RNA approach was used for the targeted silencing of the MtTdp1 gene encoding the isoform of tyrosyl-DNA phosphodiesterase 1 in Medicago truncatula Gaertn. Tyrosyl-DNA phosphodiesterase 1, involved in the repair of DNA topoisomerase I-mediated DNA damage, has been poorly investigated in plants. RNA-Seq analysis, carried out in the MtTdp1-depleted plants revealed different levels of transcriptional modulation (up- and down-regulation, alternative splicing, activation of alternative promoter) in genes involved in DNA damage sensing, DNA repair and chromatin remodeling. We suggest that the MtTdp1alpha gene has new, previously undetected roles in maintaining genome integrity. Up-regulation of senescence-associated genes and telomere shortening were observed. Moreover, impaired ribosome biogenesis indicated that the MtTdp1alpha gene is required for the nucleolar function. In agreement with the RNA-Seq data, Transmission Electron Microscopy detected an altered nucleolar architecture in the MtTdp1alpha-depleted cells. Based on the reported data, a working hypothesis related to the occurrence of a nucleolar checkpoint in plant cells is proposed.