GSE192568
Genome-wide binding patterns of the Plastid-encoded polymerase in Arabidopsis
Plastids are endosymbiotic organelles containing their own genomes, which are transcribed by two types of RNA polymerases. One of those enzymes is a bacterial-type, multi-subunit polymerase encoded by the plastid genome. The plastid-encoded polymerase (PEP) is required for efficient expression of genes encoding proteins involved in photosynthesis. Despite the importance of PEP, its DNA binding locations have not been studied on the genome-wide scale at high resolution. We established a highly specific approach to detect the genome-wide pattern of PEP binding to chloroplasts DNA using ptChIP-seq. We found that in mature Arabidopsis thaliana chloroplasts, PEP has a complex pattern of binding to DNA with preferential association at genes encoding rRNA, tRNA and a subset of photosynthetic proteins. Sigma factors SIG2 and SIG6 strongly impact PEP binding to a subset of tRNA genes and have more moderate effects on PEP binding throughout the rest of the genome. PEP binding is commonly enriched on gene promoters, around transcription start sites. Finally, the levels of PEP binding to DNA are correlated with the levels of RNA accumulation, which allowed estimating the quantitative contribution of transcription to RNA accumulation. Overall design: The data consists of 2 or 3 replicates of ptChIP from pTAC12-HA or RpoB protein in Arabidopsis thaliana Col-0 wild type, sig2-2 or sig6-1 genotypes from 4 or 14 days-old plants. Different formaldehyde cross-linking treatment lengths were tested. Input or no antibody controls were included. Additionally 14 days-old plants TSS RNA-seq data in Col-0 plants were generated and 3 replicates are included