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Fig. 2 | Epigenetics & Chromatin

Fig. 2

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

Fig. 2

DamID profiling of Can, Comr, and Mip40 in the testes of wild-type male flies and identification of Can, Comr, and Mip40 gene targets. a DamID profiles for Can, Comr, and Mip40 proteins in the germline cells of wild-type males. Peak height corresponds to the value of − log10(P), where P is the significance value (P-value) measured using Fisher’s exact test (log10 probability units). Peaks above the x axis correspond to the regions enriched with the protein of interest, and peaks below the x axis denote genomic regions depleted for this protein. Dashed line shows the significance threshold for peak calling that corresponds to a FDR = 0.05. b Analysis of genomic distribution of protein localizations compared to the random distribution in a set of testis-specifically expressed genes. All three proteins tend to localize to gene promoters and in 5′-UTRs (asterisks—binomial test P < 10−3). c Analysis of the interplay between Can, Comr, and Mip40 binding and gene activity. RNA-seq analysis was used to assess gene expression in the testes of can, comr, and mip40 mutants versus wild-type testes. Transcripts showing greater than fourfold difference in gene expression were used in the analysis. For each transcript, the distance between its TSS and the closest Can/Comr/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 (Chi-square test, P = 1.8 × 10−10 in the case of Can and P = 5.7 × 10−5 in case of Comr). Differences were insignificant for Mip40 gene targets. d Gene targets tend to be cooperatively bound by the proteins studied. This is not the case for indirectly controlled genes. Asterisks denote significant differences (Chi-square test, P < 3.6 × 10−7 in all cases), dotted lines—randomly expected values

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