Fig. 2: GDE1 localizes at a subset of CLSY3 CLSY4-dependent siRNA loci for siRNA production and the loss of GDE1 redistributes the CLSY3/4–Pol IV complex to other loci. | Nature Cell Biology

Fig. 2: GDE1 localizes at a subset of CLSY3 CLSY4-dependent siRNA loci for siRNA production and the loss of GDE1 redistributes the CLSY3/4–Pol IV complex to other loci.

From: REM transcription factors and GDE1 shape the DNA methylation landscape through the recruitment of RNA polymerase IV transcription complexes

Fig. 2: GDE1 localizes at a subset of CLSY3 CLSY4-dependent siRNA loci for siRNA production and the loss of GDE1 redistributes the CLSY3/4–Pol IV complex to other loci.

a, A pie chart showing the percentage of three groups of CLSY3 CLSY4-dependent siRNA sites. b,c, Violin plots and heatmaps showing 24-nt siRNA levels in group 1 (b) (n = 429) and group 2 (c) (n = 262) of CLSY3 CLSY4-dependent sites. Pairwise t-tests showed P = 4.4805 × 10−123 (Col-0 versus gde1-1) and P = 1.4105 × 10−114 (Col-0 versus clsy3 clsy4) for group 1, and P = 2.71776 × 10−52 (Col-0 versus gde1-1) and P = 2.81529 × 10−48 (Col-0 versus clsy3 clsy4) for group 2. The line in the centre of each violin plot represents the median. The thick grey bar in the centre represents the interquartile range. The whiskers represent the rest of the distribution. d, Metaplots showing enrichment of CLSY3/4 and Pol IV ChIP-seq signal over three groups of CLSY3 CLSY4-dependent sites in WT and gde1-1 backgrounds. The region is −2 kb to 2 kb from the centre. Same regions in gde1-1 were used for all metaplots. e, A metaplot showing enrichment of GDE1 ChIP-seq signal over three groups of CLSY3 CLSY4-dependent sites. f, A circular genome view showing the enrichment of groups 1 and 2 of CLSY3 CLSY4-dependent siRNA across all five chromosomes, with the pericentromeric heterochromatin marked in red along the inner circle.

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