Extended Data Fig. 5: Examples of SWR regions with maintenance of gene repression or activation.
From: DNA methylation shapes the Polycomb landscape during the exit from naive pluripotency
a. Schema showing a hypothetical H3K27me3-to-5mC SWitch Region (SWR) that overlaps a genic promoter. In this case, dense methylation of the promoter region results in the maintained repression of expression. b. UCSC Genome Browser screenshot of an example SWR overlapping the Piwil1 germline gene promoter. The Refseq gene annotation, CpG density, individual CpGs, CpG islands and scale bar are included. Promoter region is highlighted in yellow. Note the anticorrelated enrichment of 5mC and H3K27me3 in WT cells, and the aberrant maintenance of H3K27me3 in TKO EpiLCs. Coordinates: chr5:128,733,977-128,756,805. c. Heatmap of Piwil1 expression levels (RPKM) in vitro and in vivo differentiation. ESCs: D0; EpiLCs: D2, D4, D7; E3.5-, E4.5-: embryonic days 3.5 and 4.5 inner cell mass cells; E5.5-, E6.5: embryonic days 5.5 and 6.5 epiblasts. d. UCSC Genome Browser screenshots of SWRs that overlap genes activated in WT EpiLCs (see schema, Fig. 3b). Coordinates: Pdyn chr2:129,673,296-129,713,102, Krt80 chr15:101,345,735-101,394,892, Pga5 chr19:10,666,677-10,680,350.
