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. Author manuscript; available in PMC: 2018 Oct 30.
Published in final edited form as: Nat Struct Mol Biol. 2018 Apr 30;25(5):394–404. doi: 10.1038/s41594-018-0058-0

Figure 7. Defective de novo DNA methylation is associated with deregulated gene expression in Miwi2-/- and Dnmt3l-/- undifferentiated spermatogonia.

Figure 7

(a) Expression scatterplots showing relative average expression (arbitrary unit (AU)) between wild-type (WT) and Miwi2-/- juvenile (P14) undifferentiated spermatogonia of ENSEMBLE annotated genes (right) and transcripts identified by de novo transcriptome assembly (left). Indicated in the figure is the methylation status in Miwi2-/- juvenile (P14) undifferentiated spermatogonia of the loci giving rise to the respective transcripts. (b) Percentage of significantly upregulated ENSEMBLE annotated genes and upregulated transcripts identified by de novo transcriptome assembly in Miwi2-/- juvenile (P14) undifferentiated spermatogonia that overlap DMRs is presented as “observed” genes in light blue. A percentage of a 10,000 randomly generated size-matched transcript cohorts that overlap DMRs is presented as “random” genes in dark blue. Error bars represent a standard deviation of the mean. *** indicates a p value of < 0,0001. (c) Expression scatterplots showing relative average expression between WT and Dnmt3l-/- juvenile (P14) undifferentiated spermatogonia of ENSEMBLE annotated genes (right) and transcripts identified by de novo transcriptome assembly (left) as presented in panel a. (d) Percentage of significantly upregulated ENSEMBLE annotated genes and upregulated transcripts identified by de novo transcriptome assembly in Dnmt3l-/- juvenile (P14) undifferentiated spermatogonia that overlap DMRs as presented in panel b. (e) Representative examples of a DMR overlapping a transcription start site of IAP element in a case of class I, II and III gene expression upregulation. The percentage of DMR methylation in WT, Miwi2-/- and Dnmt3l-/- juvenile (P14) undifferentiated spermatogonia is indicated. Significance in b and d was assessed using two-sided t-test.