Fig. 1 | Nature Communications

Fig. 1

From: CryoEM structures of Arabidopsis DDR complexes involved in RNA-directed DNA methylation

Fig. 1

DMS3, RDM1, and DRD1 form complexes in vivo and in vitro. a List of proteins co-purified with RDM1 identified by mass spectrometry (MS). Only proteins present in all three independent IP experiments using RDM1-3xFLAG lines but absent in two independent IP experiments using untransformed WS control are shown. Normalized spectral abundance factor value (NSAF × 105)59 is indicated for each protein. Estimated stoichiometry is shown as the percentage of RDM1 using NSAF values. All proteins except for the RDM1, DMS3 and DRD1 are common contaminants present in different IP-MS experiments performed in our laboratory. N/A is denoted when protein name not available. b Metaplot showing DRD1, DMS3 and RDM1 ChIP-seq signals over Pol V peaks. c Representative screenshot of a genomic region showing CG, CHG and CHH methylation levels from WGBS in wild-type control31, as well as ChIP-seq signals of RDM1, DMS3, DRD1 and Pol V,  expressed as log2 ratio over controls. d Gel filtration analyses of His tag affinity-purified DR complex (top) or Strep II tag affinity-purified DDR′ complex (bottom) showing that both complexes are stable and isolatable from E. coli. Protein molecular weight marker is indicated above each profile. Peaks eluted around 670 kDa represent void/large aggregate and will not be further characterized. e Y3H experiment showing interactions of the DMS3-RDM1 complex with different DRD1 fragments. Upper panel: explanatory cartoon of Y3H technique. BD: GAL4 binding domain fusion, AD: GAL4 activation domain fusion. pYES: expression plasmid under a constitutive ADH1 promoter. Growth of two independent colonies in minimal medium (SD) supplemented with increasing concentrations of 3-amino-1,2,4-triazole (3-AT) is shown. Cartoon depicting the length of the different DRD1 fragments tested is shown on the right. Numbers above each fragment indicate the position of the first and last amino acid with respect to full-length DRD1. N-terminal domain (NTD) and SWI2/SNF2 domain are indicated

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