Analysis of the transcriptional activity of transposable elements in maize (Zea mays)

Transposable elements are ubiquitous members of all higher eukaryotic genomes and make up the majority of genetic material present in the maize genome. These mobile DNAs are critical elements in the creation of variation that can drive the evolution of genomes. The goal of the research described in this dissertation was to characterize transposon transcription in maize tissue culture. A novel hAT transposon Tissue Culture UP regulated (TCUP) was identified that has increased transcription in old suspension culture. The potential of epigenetic repression of this element was tested by treating newly initiated maize cultures with the DNA methyltransferase inhibitor 5-aza-2-deoxcytidine, and the histone deacetylase inhibitor, trichostatin A. TCUP transcription increased in response to 5-aza-2-deoxycytidine, but not the trichostatin A treatment. Transposon display detected movement of TCUP in long-term tissue culture cell lines. This research implicates TCUP as a transposon that is highly sensitive to the stress of the tissue culture environment, and is consistent with the hypothesis that altered chromatin structure in tissue culture can lead to the activation of transposable elements.; A custom microarray was developed to test transcription of 247 repeated sequences in cell culture relative to non-cultured control tissues by single probe analysis and by tiling 70-mers at 35bp intervals. This array was interrogated with RNA from long-term Black Mexican Sweet cultures, and non-cultured control tissue. Poly-T versus random-primed labeling was used to assess transcript differences in the poly-adenylated versus non poly-adenylated fraction. 45% of the Class I transposons, 49% of the Class II transposons, and 36.8% of non-coding repeats had significant sense expression in at least one tissue. Antisense transcription was detected at similar frequencies to sense transcription with 44% of the Class I transposons, 32% of the Class II transposons, and 50% of non-coding repeats expressed. Transcription of repeats was generally similar in intensity and frequency across tissues, but tissue-specific differences were observed for specific sequences. Some repeats had high expression in non-polyadenylated RNA. This research demonstrates that repetitive sequences are an active and important part of the plant transcriptome.