Fig. 3: H3K4me3, H3K9me3 and SPIN1 mark young LINE1 elements before de novo genome methylation.
From: Two-factor authentication underpins the precision of the piRNA pathway
a,b, Metaplot and heat map for different transposon families of H3K4me3 (a) and H3K9me3 (b) ChIP signal in reads per million (RPM) from fetal gonocytes at the indicated time points during mouse development. Data are merged from n = 2 biological replicates, reanalysed from ref. 24. c, SPIN1 (green) and DAPI (blue) staining of wild-type fetal testis sections from the indicated developmental time points. Images are representative of n = 3 biological replicates. Scale bars, 2 μm. d, Volcano plot showing enrichment (log2(mean label-free quantification ratio of anti-HA immunoprecipitates from Spocd1HA/HA/wild-type)) and statistical confidence (−log10(P-value of two-sided Student’s t-test)) of proteins co-purifying with HA-SPOCD1 from E14.5 fetal testes; n = 3. e–i, CUT&Tag data for H3K4me3, H3K9me3 and SPIN1 from E14.5 fetal germ cells. Data are merged from two (H3K4me3, H3K9me3) and three (SPIN1) biological replicates. In e–g, metaplot and heatmaps of signal over elements of different transposon families (e) are shown as well as young and old copies in the L1Md_T (f) and L1Md_A (g) families. Columns adjacent to the heatmaps show statistically significant peaks called for SPIN1 and the indicated histone modifications. In e, the overlap of H3K4me3 and H3K9me3 peaks with SPIN1 peaks is significant for L1Md_A (P = 0.0099, Z-score = 1,052), L1Md_T (P = 0.0099, Z-score = 1,398) and L1Md_Gf (P = 0.0099, Z-score = 2,007) by one-tailed permutation tests. In f and g, enrichment of overlapping H3K4me3 and H3K9me3 peaks with SPIN1 peaks is significantly different between young and old L1Md_A (adjusted P < 2.2 × 10−16) and L1Md_T (adjusted P < 2.2 × 10−16) copies, as observed by two-tailed Fisher’s exact test. In h and i, charts show overlap analysis of H3K4me3 and H3K9me3 peaks (h) and SPIN1 peaks (i) with the indicated genomic features. P-values and Z-scores from one-tailed permutation tests to assess the statistical significance of overlaps of CUT&TAG peaks with LINE1 elements are shown.
