Additional file 8: of Maize RNA PolIV affects the expression of genes with nearby TE insertions and has a genome-wide repressive impact on transcription

TEs inserted into gene boundaries affect expression of neighboring genes in rpd1/rmr6 mutant. Histograms of expression distribution (left) and cumulative frequency (right) for genes with >0 FPKM are reported for genes with TEs inserted within 1 kb upstream of the transcription start site (−1 kb TSS; A), within 1 kb downstream of the transcription termination site (+1 kb TTS; B), in the gene body (C) or without TE insertions (D). For the three groups of genes with nearby TE insertions the distributions of gene expression (including only genes with FPKM > 0) are statistically different between the two genotypes (P < 0.01 by Kolmogorov-Smirnov test), with higher expression in rpd1/rmr6 mutants compared to B73 for expression values ranging from 0.5 to 10 FPKM (expression bins −1 to 3). On the contrary, genes without TE insertions (inside or nearby) show similar distribution of gene expression between genotypes. Graph (E) represents instead the average gene expression levels as a function of the distance to the nearest TE for both genotypes. Distance was binned into 500 bp windows and a distance of 0 indicates genes that contain a TE in their gene bodies. Standard errors are shown. (TIFF 1251 kb)