Fig. 3: Transcriptome changes in Mov10l1^–/– oocytes.

a, MA plot of differentially expressed protein-coding genes (DESeq2, P < 0.01). The red and blue points depict genes of which the transcripts were present at significantly higher or lower levels in fully-grown Mov10l1^–/– oocytes, respectively. The full DEG list is provided in Supplementary Table 5. b, Composition of an 18–32-nucleotide segment of RNA-seq libraries from fully grown Mov10l1^+/+ and Mov10l1^–/– oocytes. The abundance of small RNAs in the wild-type control corresponds to the RPM of 18–32-nucleotide reads (average value from two libraries). The Mov10l1^–/– library was normalized to the amount of maternal miRNAs. c, Reduced levels of different classes of piRNAs in Mov10l1^–/– oocytes. The abundance of reads of different sizes mapping to annotated oocyte piRNA clusters (Supplementary Table 6) is shown. Mov10l1^–/– values were scaled by miRNA abundance. Read sizes were divided into categories to separate putative PIWIL3-bound piRNAs (18–20 nucleotides), Dicer products (21–23 nucleotides), and smaller and longer piRNAs (24–27 nucleotides and 28–31 nucleotides). d, Reduction of LTR retrotransposon-derived piRNAs in Mov10l1^–/– oocytes. e, Changes in RNAs from L1 and IAP families and subfamilies. The RPMs of RNAs mapping to L1 or IAP elements (all), active subfamilies and FLI only are shown. Data are the mean values of two (Mov10l1^+/+) and three (Mov10l1^–/–) biological replicates. f, LTR retrotransposon groups ranked by the highest transcript upregulation in Mov10l1^–/– oocytes. Data are the mean values from two (Mov10l1^+/+) and three (Mov10l1^–/–) replicates. g, DNA methylation of intact IAPs. The vertical bars represent methylation (black portion) observed for the indicated 5′ CpG dinucleotides covered by at least ten sequence reads; the analysed region corresponds to the central and 3′ part of the 5′ LTR, as indicated in the IAP scheme and by CpG position. Data are from a single genome-wide bisulfite sequencing experiment.

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