RESEARCH-PGR: Transcriptional Control of the Maize Genome

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This project defines the passages of information encoded in the maize genome thus enabling the selection, deciphering, and editing, essential to current and future corn improvement strategies. A novel technique is used to delimit the beginning and ends of genome sequences that cellular machines read and transcribe into transient instructions. Three types of these machines transcribe fundamentally different passages in all organisms, but plants have two additional types that transcribe enigmatic regions referred to as "dark matter". In some manner, these "dark matter" instructions impact traits of economic interest by helping guide the coordinate reading of the genetic blueprint necessary for proper growth and optimal health. Although these "dark matter" regions represent the single largest source of genetic variation in worldwide plant varieties, their functions remains poorly understood. This project aims to decipher some of these functions by evaluating the effects of interfering with the transcription machinery dedicated to these "dark matter" regions in diverse maize varieties. The publicly available information, analytical tools, and materials generated by this project will significantly elevate the utility of existing resources and provide an essential reference for novel discoveries in plant biology and genetics. The activities will integrate the training of young scientists at both undergraduate and graduate levels and, in collaboration with the American Chemical Society, provide research experiences for high school students of economic disadvantage. Additionally, educational materials for teaching both basic and advanced genetic concepts will be generated and made available through an existing outreach program of the Arabidopsis Biological Resource Center.Gene expression is controlled at transcriptional and post-transcriptional levels; yet the contribution of each to RNA abundance is often unknown. In plants, heritable changes to these controls can be impacted by action(s) of Pol II-related RNA polymerase (RNAP) complexes. At least five of these RNAPs are found in grasses but their functional significance(s) remains unclear. This project defines the nascent transcriptional landscape of maize, identifies potential cases of co- or post-transcriptional control, and uses mutant analyses to understand how these Pol II-related RNAP complexes affect gene expression. Specifically, this project will 1) optimize protocols for global run-on sequencing and generate reference nascent transcriptome datasets to enable novel genome annotations; 2) use specific mutants and comparative RNA profiling to differentiate gene regulation due to RNA-directed DNA methylation versus RNAP IV competitions and to allow individual RNA stabilities to be inferred; 3) identify features where regulation is heritably altered in the absence of RNAP IV to catalog epialleles whose transcriptional behaviors resemble those susceptible to paramutation; and 4) use mutant analyses to evaluate the hypothesis that RNAP IV translates environmental perception into changes in heritable transcriptional control. Project outcomes will provide important community resources to understand the nuclear systems that generate and maintain epigenome diversity in a crop species. All data generated from this project will be made immediately available, integrated into existing database frameworks, and promoted through training and outreach opportunities to empower a greater understanding of eukaryotic genetics and the genome biology of crop species.