Noncoding RNA-mediated DNA methylation directs nucleosome positioning

We explored the mechanism by which RdDM affects nucleosome positioning in Arabidopsis thaliana. We showed that POLV has a direct effect on nucleosomes through the SWI/SNF complex. We found that the AGO4-siRNA complex is involved in nucleosome positioning via IDN2. Moreover, the SWI/SNF complex is not required for DNA methylation in positioned nucleosomes. Instead, we found that DNA methylation is needed for nucleosome positioning in differentially methylated regions. Taken together, we propose a model where the RdDM pathway directs nucleosome positioning through DNA methylation to establish transcriptional gene silencing. Overall design: 14 samples of MNase-H3-ChIP-Seq with 6 different genotypes and 2 replicates of each (Col-0, nrpe1, swi3b, drm2, cmt3, met1-3) 6 samples of WGBS with 3 different genotypes and 2 replicates of each (Col-0, nrpe1, swi3b) Please note that as processed data was generated from multiple samples (as indicated in the corresponding sample description field) and is linked to the Series records.