Fig. 8: ZFP541 binds to the gene promoter regions.
a ZFP541-binding sites were classified by the genomic locations as indicated. b Genomic view of ZFP541 ChIP-seq and input DNA data over representative gene loci. Genomic coordinates were obtained from RefSeq. RefSeq IDs for mRNA isoforms are indicated. To specify testis-specific TSS, RNA-seq of the 5′ capped end of the mRNA (CAGE) in P10.5 testis are shown38. c Top 3 sequence motifs enriched in ZFP541 ChIP-seq with E-values. MEME-ChIP E-value estimates the expected number of motifs with similar features that one would find in a similarly sized set of random sequences. d Venn diagram representing the overlap of ZFP541-bound genes (5921 nearest genes), downregulated (751 genes), and upregulated genes (1530 genes) in Zfp541 KO mice. e GO analysis of the ZFP541-bound genes that were upregulated in Zfp541 KO mice (841 genes) (p < 1.0 × 10−6). Top 3 biological processes ranked by log (p-value) are listed. The ZFP541-bound genes that were downregulated in Zfp541 KO (213 genes) showed no GO terms statistically enriched. See Supplementary Data 3 for a complete gene list of the GO analyses. We used the standard parameters to detect over-represented GO terms for biological function, giving Fisher′s exact p-values. f Expression levels (RPKM) of the ZFP541-bound genes that were upregulated in Zfp541 KO spermatocytes (841 genes) are shown by box-whisker plot (whiskers indicate min and max. Bounds of box indicate 25th and 75th percentiles quantile with median). Thy-SG: Thy+ spermatogonia, cKIT-SG: cKIT+ spermatogonia, PS: pachytene spermatocytes, RS: round spermatid. g Heatmaps showing the hierarchical relationship among the clusters of the ZFP541-bound genes that were upregulated in Zfp541 KO spermatocytes across pseudotime of spermatogenesis. Expressions of the genes were assessed by reanalyzing scRNA-seq data of spermatogenic cells as described in Fig. 5e29. Pseudotime (left to right) corresponds to the developmental trajectory of spermatogenesis (undifferentiated spermatogonia to round spermatids). The cluster number is indicated on the right. See Supplementary Data 4 for the complete gene list of clusters 1–6. h Heat map of H3K27me3 levels on the ZFP541-target genes that are upregulated in Zfp541 KO (841 genes). H3K27me3 levels are shown on the genomic regions between −1.0 kb upstream of TSS and +1.0 kb downstream of TES. The color key is shown. Average distributions of H3K27me3 are shown (upper).
