Correct spatial and temporal gene expression depends on transcription factors (TFs) recognizing specific cis-regulatory elements, and RNA polymerase II engaging mRNA synthesis from transcription start sites (TSSs). Both of these events are potentially susceptible to the base pair substitutions and small insertion/deletions that characterize the gene regulatory regions when comparing any two maize inbred lines. Indeed, it is well established that the phenotypic variation that characterizes maize is provided by the genome fraction that comprises coding and proximal regulatory regions. However, the impact of specific regulatory changes on gene expression and TSS preference remain poorly understood. Here, I will discuss the impact of heterogeneity in gene regulatory regions on the alternate selection of TSSs as established by cap analysis of gene expression (CAGE). I will also present results that illustrate the impact of promoter variation on gene expression by combining DNA affinity purification (DAP-Seq) with RNA-Seq and transient expression. The use of parental lines and F1 hybrids presents unique opportunities to establish cis and trans effects on TSS selection and gene expression.
Funding for this project is provided by NSF IOS-1733633
Coauthors: Yi-Hsuan Chu – Michigan State University; Fabio Gomez cano – Michigan State University; Allison Barbaglia – Michigan State University; Aimer Gutierrez-Diaz – Michigan State University; nan Jiang – Michigan State University; Andrea Doseff – Michigan State University