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The RNA polymerase II drives the biogenesis of coding and non-coding RNAs for gene expression. Here, we describe new roles for its second-largest subunit, NRPB2, on root organogenesis and regeneration. Down-regulation of NRPB2 activates a determinate developmental program, which correlated with a reduction in mitotic activity, cell elongation, and size of the root apical meristem. Noteworthy, nrpb2-3 mutants manifest cell death in pro-vascular cells within primary root tips of plants grown in darkness or exposed to light, which triggers the expression of the regeneration gene marker ERF115 in neighbor cells close to damage. Auxin and stem cell niche (SCN) gene expression as well as structural analysis revealed that NRPB2 maintains SCN activity through distribution of PIN transporters in root tissues. Wild-type seedlings regenerated the root tip after excision of the QC and SCN, but nrpb2-3 mutants did not rebuild the missing tissues, and this process could be genotypified using pERF115:GFP, DR5:GFP, and pWOX5:GFP reporter constructs. The levels of reactive oxygen species increased in the mutants four days after germination and strongly decreased at later times, whereas nitric oxide accumulated as the root tip differentiates. These results show the importance of the transcriptional machinery for root organogenesis, cell viability, and regenerative capacity for reconstruction of tissues and organs upon injury.