Mu killer-mediated and spontaneous silencing of Zea mays Mutator family transposable elements define distinctive paths of epigenetic inactivation

Mu killer contains a partial inverted duplication of the mudrA transposase gene and two copies of the terminal inverted repeat A region of MuDR. Mu killer can effectively silence single copy MuDR/Mu lines but failed to silence about 25% of the time in multiple copy lines. Mu killer was partially sequenced and shown to be collinear with mudrA. Mu killer individuals that silenced MuDR contained two short antisense transcripts, while individuals that failed to silence MuDR contained multiple sense transcripts but no antisense transcripts. Transcriptomes from Mu killer-silenced individuals were compared to epigenetically silenced lines; the 2 silencing mechanisms were shown to affect different pathways. 4 replicates of the Mu-active and Mu-inactive lines at 2 anther stages (1.0mm, 2.00mm) with a balanced dye-swap design. Normalized intensities for each channel are provided.