Extended Data Fig. 4: Transcription factors-driven Pol IV transcription complex localizes to siren loci for siRNA production and DNA methylation. | Nature Cell Biology

Extended Data Fig. 4: Transcription factors-driven Pol IV transcription complex localizes to siren loci for siRNA production and DNA methylation.

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

Extended Data Fig. 4: Transcription factors-driven Pol IV transcription complex localizes to siren loci for siRNA production and DNA methylation.

a, TOMTOM analysis showing the similarities of siren loci and CLSY3 CLSY4 motif 1. E value is the expected number of false positives in the matches up to this point. b, Metaplot and heatmap showing enrichment of VDD, VAL, REM13, REM19, REM22 and REM8 ChIP-seq signal over siren loci (n = 133). c, Heatmap showing enrichment of GDE1, CLSY3 and CLSY4 ChIP-seq signal over siren loci (n = 133). The region is −2Kb to 2Kb from the center. d, Heatmap showing the 24nt-siRNA levels at siren loci (n = 133) in the indicated genotypes. e, Screenshots of VDD, VAL, REM13, GDE1, CLSY3, CLSY3 gde1-1, CLSY4, CLSY4 gde1-1, Pol IV and Pol IV gde1-1 ChIP-seq signals with control ChIP-seq signals subtracted and 24nt-siRNA by sRNA-seq and CHG/CHH DNA methylation level by WGBS over a representative siren site in the indicated genotypes. Square brackets indicate the range on a bar graph. f, Metaplot and heatmap showing enrichment of CLSY3/4 ChIP-seq signal over CLSY3/4-bound siren loci (n = 133) and CLSY3/4 non-siren regions in WT and gde1-1 backgrounds. The region is −2Kb to 2Kb from the center. g, Metaplot and heatmap showing enrichment of Pol IV ChIP-seq signal over Pol IV-bound siren loci (n = 133) and Pol IV non-siren regions in WT and gde1-1 backgrounds. The region is −2Kb to 2Kb from the center. h, Heatmap showing the CHH and CHG methylation levels at siren loci (n = 133) in the indicated genotypes.

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