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Fig. 5 | Epigenetics & Chromatin

Fig. 5

From: Genome-wide analysis of gene regulation mechanisms during Drosophila spermatogenesis

Fig. 5

Mip40 shows highly dynamic chromatin binding during spermatogenesis. a Mip40 binding profiles in spermatogonia (bam mutants), in aly mutant testes (no tMAC), can mutant testes (no tTAFs), as well as in the wild-type testes. b Basic types of changes in Mip40 binding to the genes. The genes having Mip40 peaks within 300 bp around TSS were identified in each genotype and sub-classified to six groups (I–VI) reflecting the main trends of Mip40 binding across the genotypes tested: group I was associated with Mip40 in all four genotypes, group II was bound by Mi40 only in spermatogonia of bam mutants, and so on (see the main text for details). c Mip130 coincides with Mip40 binding sites devoid of Can or Comr and is absent from the sites of Mip40 colocalization with Comr or Can. d Mip130 occupancy in the gene groups showing dynamic binding of Mip40 (Fig. 5B). Mip130 DamID signal was categorized by the significance of DamID signal: no Mip130 binding; − log(P) = {0..1}—nonsignificant binding; − log(P) = {1..3}—medium significance peaks; − log(P) > 3—highly significant Mip130 peaks. Mip130 strongly marks the genes in groups I (Chi-square test, P < 10−300), II (Chi-square test, P = 1.8 × 10−155), V (Chi-square test, P = 5.9 × 10−161), and VI (Chi-square test, P = 3.4 × 10−163). Groups III and VI show Mip130 presence similar to random expectation. e Enrichment or depletion in testis-specific genes (blue) and ovary-specific genes (orange) in the six gene sets (***P < 10−31; **P < 10−6; *P < 10−2, Chi-square test). f Distribution of Mip40 around the transcripts showing greater than fourfold difference in gene expression (in mip40 vs. wild-type testes) according to DamID in bam, aly, and can mutants. For each transcript, the distance between its TSS and the closest Mip40 peak was calculated and plotted in 1 kb bins within 10 kb around the TSS. Asterisks indicate that the differences among the groups of transcripts showing greater than fourfold changes in expression are statistically significant. Binding of Mip40 in spermatogonia, as well as in the absence of tTAFs and tMAC, is predominantly associated with gene repression. g Ratios of repressed and activated genes in the groups of genes shown in Fig. 5b. Mip40-bound gene targets in spermatogonia tend to be up-regulated in mip40 mutants (groups I, II, V, and VI). The genes that acquire Mip40 binding following spermatocyte differentiation via tMAC activity (groups III and IV) show overall decreased expression in mip40 mutants, i.e., Mip40 in this case is needed for their activation (***P < 10−30; **P < 10−10; *P < 10−3, Chi-square test). h Presence of Comr protein in the promoters of the genes from the six groups of genes in Fig. 5b. Comr binding in wild-type testes was categorized by the significance of DamID signal: no Comr binding; − log(P) = {0..1}—nonsignificant binding; − log(P) = {1..3}—medium significance peaks; − log(P) > 3—highly significant Comr peaks. High and medium significance peaks of Comr are overrepresented in the groups III (Chi-square test, P = 1.3 × 10−96) and IV (Chi-square test, P = 1.2 × 10−110)

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