MOESM3 of Transient reduction of DNA methylation at the onset of meiosis in male mice

Additional file 3: Figure S3. Transcript abundance of select genes in individual MPI germ cells using RNA-seq, expressed as RPKM. Prominent transcripts from (A) testicular somatic cells, including Sertoli, Leydig and Macrophage cells, were examined to assess the level of contamination and included Amh, Ccl2, Cd9, Cyp11a1, Cyp17a1, Fn1, Fshr, Gap43, Gata1, Gata4, Gpc3, Lhcgr, Lum, Mmp12, Mmp9, Pla2g4a, Rlf, Star, Tead2 and Vcam1. Meiosis-specific gene Mlh3 is used for relative comparison. Transcript abundance of genes associated with (B) differentiated (blue) and undifferentiated (beige) Spg, (C) meiosis-specific synaptonemal complex (SC) formation, (D) meiotic onset (Stra8), meiosis-specific sister chromatid cohesion complex (Smc1b, Rec8, Rad21l and Stag3), recognition of meiotically programmed DSBs (H2afx) and other early meiosis-associated genes (e.g., Mei1), (E–F) DSB formation and repair and recombination were evaluated. (G-H) Replication-dependent histone variant genes are highly expressed and enriched in PL spermatocytes. Twelve replication-dependent histone variant genes with high transcript abundance are shown. Selected are whose genes that are known to be highly enriched in early spermatocytes at 9-dpp testis, but not 2-dpp (gonocytes), 25-dpp (enriched in round spermatids) or 60-dpp (enriched in haploid cells). (I) Two genes, H3f3a and H3f3b, encoding replication-independent histone H3.3 were examined