Skip to main content
Fig. 6 | BMC Plant Biology

Fig. 6

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

Fig. 6

Pol IV silenced loci are enriched in class I transposable elements and are preferentially co-localized. Relative percentage of up- and down-regulated TE superfamilies, compared to their abundance in the gene annotation (a), indicate that the RLC-Copia and RLG-Gypsy class I retroelement super-families are notably enriched among the rpd1/rmr6 up-regulated genes, while DTC-CACTA and other class II DNA transposon super-families ore over-represented among down-regulated genes. The distribution plot (b) of the differentially expressed genes along chromosome 1 indicates the preferential co-localization of rpd1/rmr6 de-repressed genes. The chromosome was divided in 100 Kbp not-overlapping windows and for each window the percentage of genes (with respect to the total chromosome genes; blue bars) and over-expressed genes (with respect to the window gene content) are reported. Yellow and red bars depict the window percentage of up-regulated genes shared in at least three or two independent comparisons, respectively. Permutation test using the regioneR R package (c) showed that rpd1/rmr6 strongly up-regulated genes (bin 3) were closer to TEs than moderately or slightly up-regulated ones (bins 2 and 1): 1500 bp, 1547 bp and 1605 bp are the corresponding average distances from the closest TEs for each bin (the average distance for the whole gene set is 2017 bp; grey distribution). Similarly, slightly and moderately down-regulated genes (bins −1 and −2) were located progressively farther from TEs (2461 bp and 2514 bp, respectively), while genes of bin −3 (those showing the strongest down-regulation) did not shown any positional deviation from the whole gene set (2008 bp average distance). Differentially expressed genes for permutation analysis (log2FC > |1|, FDR < 0.05) were obtained with Cuffdiff starting from all the sequenced samples .This graph was produced by combining the single graphs obtained from the independent analysis of up- and down-regulated bins

Back to article page