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. 2019 Feb 27;8:e43738. doi: 10.7554/eLife.43738

Figure 6. Coordinated upregulation of the meiotic prophase I gene expression program by STRA8.

(A) Volcano plot depicting gene expression differences between high-STRA8 and Stra8 KO preleptotene cells. Shown are 103 genes associated with meiotic prophase I in the fetal ovary (Soh et al., 2015), with 76 STRA8-bound genes shaded light blue. (B) Comparison of expression levels of meiotic prophase genes in high-STRA8 and KO preleptotene cells. The light gray region identifies genes that are not expressed in the KO. (C) Input-subtracted STRA8 ChIP-seq signal at promoters of key meiotic genes. Sequencing reads were pooled from three Stra8FLAG/FLAG ChIP replicates. Red arrows mark the TSS. (D) Lack of STRA8 ChIP-seq signal at Rec8 gene. (E) STRA8 ChIP-seq signal at its own promoter. (F) STRA8 ChIP-seq signal at promoters of Meioc and Ythdc2..

Figure 6—source data 1. Source data for CNCCTCAG motif enrichment at meiotic genes.
elife-43738-fig6-data1.xlsx (11.4KB, xlsx)
DOI: 10.7554/eLife.43738.024

Figure 6.

Figure 6—figure supplement 1. Taf7l2 (4933416C03Rik) is a functional retrogene of Taf7l.

Figure 6—figure supplement 1.

(A) Comparison of the gene structures of the mouse Taf7, Taf7l, and 4933416C03Rik (now called Taf7l2) genes. Coding regions are colored, and the 5’ and 3’ untranslated regions are shown in white. Shown are the percent identities, in the coding region, of the nucleotide (nt) and amino acid (aa) sequences. Taf7 is a known functional retrogene of Taf7l (Cheng et al., 2007), and Taf7l2 also appears to be a retrogene of Taf7l. The Taf7l sequence is more similar to that of Taf7l2 than to the Taf7 sequence. (B) Maximum likelihood phylogenetic tree showing evolutionary relationships among genes of the Taf7l family in human, mouse, rat, and hamster. The rodent Taf7l2 genes cluster with rodent Taf7l genes, and no Taf7l2 ortholog was found in human, indicating that Taf7l2 arose from a retrotransposition event in the rodent lineage. (C) Expression level, in TPM units, of Taf7, Taf7l, and Taf7l2 genes in sorted mouse preleptotene cells. All three genes are robustly expressed.
Figure 6—figure supplement 2. Enrichment and conservation of STRA8 (CNCCTCAG) motifs at promoters of meiotic genes.

Figure 6—figure supplement 2.

(A) The fraction of genes with at least one STRA8 motif (CNCCTCAG) at the promoter, at meiotic prophase I genes (Soh et al., 2015) and at all other genes. In both mouse and human, the majority of meiotic genes have CNCCTCAG motifs (exact match) at their promoters. Only genes with known 1:1 orthologs between mouse and human are shown. (B) Comparison of distributions of promoter STRA8 motifs between meiotic prophase I genes and all other genes, in mouse and in human. Meiotic genes are significantly enriched for CNCCTCAG motifs (p<3.5×10−16 and 1.1×10−8 in mouse and human, respectively). P-values between groups were determined by two-tailed Mann-Whitney U tests.