MOESM1 of ZFP57 regulation of transposable elements and gene expression within and beyond imprinted domains

Additional file 1: Figure S1. Analysis of blastocyst-derived ZFP57 null ES cells. a Western Blot analysis confirming absence of detectable ZFP57 protein. b, Bisulfite pyrosequencing of ICRs in WT, ZFP57 KO and ZFP57 MZ-KO ES cells. Figure S2. IGB viewer snapshot showing representative ZFP57 peak at IAPLTR2a2_Mm retroelements, which harbors the most number of ZFP57 peaks. Paired-end sequencing, together with sequence divergence of the retroelements allowing us to map ChIP-seq reads to individual transposable elements in the genome. The color scale indicates the mapping quality score (MAPQ) for each read pair. MAPQ =  $$ - 10log_{10} P $$ - 10 l o g 10 P where P is the probability that true alignment belongs elsewhere. b, Transposable elements indicated by alignments of “multi-mapping reads. ZFP57 targets of these elements show KAP1 binding and H3K9me3 enrichment in both WT and KO cells, and no reactivation has been observed (data not shown). Figure S3. Genome browser screenshots for Snrpn, H19 and KvDMR1 imprinted loci. Figure S4. Genome browser screenshots for Grb10, Fkbp6 and Peg10 imprinted loci. Figure S5. Heat maps showing signal enrichment of H3K9me3 at ZFP57 binding sites in ZFP57 KO and MZ-KO ES cells. Figure S6. Transposable elements bound by ZFP57 are not reactivated in ZFP57 KO ES cells. a, Expression status of ZFP57 bound transposable elements in WT and ZFP57 mutants. b, Scatterplot showing no transcriptional changes of TEs (FPKM ≥ 0.1 in WT or KO) in ZFP57 KO cells versus WT. Figure S7. Analysis of expression of transposable elements jointly bound by ZFP57, ZFP932 and/or Gm15446 in different mutant ES cells. Top left – ZFP57 KO, Top right – ZFP932/Gm15446 DKO, Bottom left – KAP1 KO. The IAP retroelement in vicinity of Bglap3 locus is not shown in the ZFP932/Gm15446 DKO as its expression far exceeds other jointly bound TEs [6]. Figure S8. Genome browser screenshot showing loss of ZFP57 binding at MER20 DNA transposon resulting in loss of KAP1 and H3K9me3 and upregulation of an unannotated transcript. Figure S9. Genome browser screenshot showing loss of KAP1 and H3K9me3 in solo LTRs located within and adjacent to Mapk4 gene, and an increase in Mapk4 levels in ZFP57 KO ES cells. Figure S10. Heat maps of DNA methylation-dependent H3K9me3 enriched regions in WT and DNMT TKO cells (blue colored heat map) [25]. Enrichment of ZFP57, KAP1 and H3K9me3 in ZFP57 KO ES cells (red) at the same regions. Figure S11. ZFP57 maintains H3K9me3 methylation during preimplantation development. H3K9me3 methylation level dynamics during preimplantation development at non-DMR regions methylated in both germ lineages (left) and oocyte-specific germline DMRs (right). Light colored boxes show non-ZFP57 bound (n = 100 randomly selected regions) versus those targeted by ZFP57 (darker colored). Known maternally methylated ICRs are shown as hatched boxes for comparison. ICM, inner cell mass. ns, not significant, *P < 0.05, **P < 0.01, ***P < 0.001; Mann–Whitney U Test