Comprehensive Transcriptome Analysis of Arabidopsis thaliana DNA Polymerase Epsilon Catalytic Subunit A and B Mutants

Abstract

In Arabidopsis, the catalytic subunit of DNA polymerase ε (POLE) is encoded by two genes: DNA polymerase epsilon catalytic subunit A (AtPOL2A) and B (AtPOL2B). Although studies have shown AtPOL2A to be involved in various biological processes, the role of AtPOL2B remains to be determined.In the present study, leaf cDNA libraries of one AtPOL2A mutant (atpol2a-1) and three AtPOL2B mutants (atpol2b-1, -2 and -3) were sequenced using the Illumina platform. Analysis of gene expression profiles identified a total of 198, 76, 141 and 67 differentially expressed genes (DEGs) in atpol2a-1, atpol2b-1, atpol2b-2 and atpol2b-3, respectively. It was noted that the majority of pericentromeric transposable elements were transcriptionally active in atpol2a-1 as compared to atpol2b mutants and wild-type plants. Computational analysis of the proteins encoded by the DEGs identified CER1, Replication Protein A 1E (RPA1E) and AT5G60250 as potential interactors of AtPOL2A, and Pathogenesis-related gene 1 (PR1) and AT5G48490 as potential interactors of AtPOL2B. Interestingly, all these proteins showed a significant interaction with the POLE catalytic subunit of Saccharomyces cerevisiae. Furthermore, the in silico promoter analysis showed that the AtPOL2A promoter sequence is overrepresented with cis-acting regulatory elements associated with cell cycle regulation, meristematic/reproductive tissue-specific pattern of expression and MYB protein recognition, whereas the AtPOL2B promoter sequence was mainly enriched with stress-responsive elements; defense--2 -responsive elements were only detected in the AtPOL2B promoter. Our data support the idea that AtPOL2B may coexpress with stress-responsive genes. The findings of the present study begin to unravel the potential molecular interactors of AtPOL2 genes at the molecular level and suggest new avenues for future studies.