Zea mays

Maize RNA Polymerase D1 (RPD1), the largest subunit of RNA polymerase IV (Pol IV), is required for normal plant development, repression of transposable elements (TEs), and for the regulation of specific alleles associated with TEs. Here, we define the nascent transcriptomes of rpd1 mutant and wild-type (WT) seedlings using global run-on sequencing (GRO-seq) to identify the broader targets of RPD1-based transcriptional regulation. Surprisingly, although TE-like sequences comprise >85% of the maize genome, most TEs are not transcribed at the seedling stage, even in rpd1 mutants. Profile comparisons identify the global set of genes and TEs whose transcription is altered in the absence of RPD1, in some cases in antisense orientation. These results indicate that maize Pol IV specifies Pol II-based transcriptional regulation for certain regions of the maize genome. Overall design: Nuclei isolated from 10 wild-type and 10 rpd1 mutant seedlings were pooled and used to make two global run-on sequencing libraries.