Fig. 4

TE insertions spanning gene TSS affect expression of neighboring genes in rpd1/rmr6 mutant, independently of siRNAs loci. Histograms of expression distribution (left) and cumulative frequency (right) for genes with >0 FPKM, reveal the high variance in expression distributions between rpd1/rmr6 and B73 for genes with TE insertions spanning the TSS (−500/+500 bp TSS; a; P < 0.01 by K-S test). These genes present the maximum distance between the two genotypes’ cumulated frequency (3.8%) compared to genes with TEs inserted within 1 Kb upstream of the transcription start site (−1Kb TSS), 1 Kb downstream of the transcription termination site (+1Kb TTS) or in the gene body (see Additional file 8). Genes with nearby TEs insertion (−500/+500 bp TSS) were further subdivided in: without associated siRNA loci (b), with siRNA loci associated in their upstream region (−1Kb TSS; c) and with siRNA loci previously identified as down-regulated in rpd1/rmr6 mutant (d). The distributions of gene expression are strongly statistically different between the two genotypes (D-obs = 5.4%; P < 0.01 by K-S test) for genes without siRNA-associated loci (b) and, to a lesser extent (D-obs = 3%) for genes with associated siRNA loci (c). The genes with an siRNA-associated locus down-regulated in the rpd1/rmr6 mutant show instead non dissimilar profiles between the two genotypes (P = 0.04 by K-S test)