An ancient transcription factor initiates the burst of piRNA production during early meiosis in mouse testes

Abstract

Animal germ cells produce PIWI-interacting RNAs (piRNAs), small silencing RNAs that suppress transposons and enable gamete maturation. Mammalian transposon-silencing piRNAs accumulate early in spermatogenesis, whereas pachytene piRNAs are produced later during postnatal spermatogenesis and account for >95% of all piRNAs in the adult mouse testis. Mutants defective for pachytene piRNA pathway proteins fail to produce mature sperm, but neither the piRNA precursor transcripts nor the trigger for pachytene piRNA production is known. Here, we show that the transcription factor A-MYB initiates pachytene piRNA production. A-MYB drives transcription of both pachytene piRNA precursor RNAs and the mRNAs for core piRNA biogenesis factors including MIWI, the protein through which pachytene piRNAs function. A-MYB regulation of piRNA pathway proteins and piRNA genes creates a coherent feedforward loop that ensures the robust accumulation of pachytene piRNAs. This regulatory circuit, which can be detected in rooster testes, likely predates the divergence of birds and mammals.

Figure 1. piRNA Precursors are RNA Pol II Transcripts

(A) Strategy to assemble the mouse testis transcriptome. Round-corner rectangles, input or output data; rectangles, processes. Decisions are shown without boxing. (B) Aggregated data for piRNA-producing transcripts (5% trimmed mean). Oxidized small RNA (>23 nt) sequencing data was used to detect piRNAs; transcript abundance was measured using total RNA depleted of rRNA (RNA-seq). RNA pol III data was from SRA001030. Dotted lines show the transcriptional start site (Start) and site of polyadenylation (End). See also Figure S1 and Table S1.

Figure 2. Three Classes of piRNA-Generating Loci

(A) Normalized piRNA density (rpkm) for each piRNA-producing gene is shown as a heat map across the developmental stages. Hierarchical clustering divided the genes into three classes. Arrowheads mark seven pachytene piRNA genes that were not classified as pachytene according to the change in the abundance of their precursor RNAs from 10.5 to 17.5 dpp. (B) Top, box plots present piRNA density per gene as spermatogenesis progresses (here and elsewhere, pre-pachytene in yellow and pachytene in purple). Middle, expression of A-Myb, B-Myb, Mili, and Miwi was measured by RNA-seq. Bottom, box plots present piRNA precursor expression per gene, measured by RNA-seq, from 10.5 to 20.5 dpp. See also Figure S2 and Table S2.

Figure 3. Examples of Pachytene piRNA Genes

Previous cluster boundaries are from Lau et al. (2006; gray) and Girard et al. (2006; dark gray). See also Figure S3.

Figure 4. A-MYB Binds the Promoters of Pachytene piRNA Genes

(A) Top, MEME identified a sequence motif (top) in the bidirectional promoters of the 15 pairs of divergently transcribed pachytene piRNA genes. E-value computed by MEME measures the statistical significance of the motif. Middle, Myb motif from the mouse UniPROBE database. Bottom, MEME-reported motif for the top 500 (by peak score) A-MYB ChIP-seq peaks from adult mouse testes. (B) A-MYB ChIP-seq data for the common promoter of the divergently transcribed pachytene piRNA genes 17-qA3.3-27363.1 and 17-qA3.3-26735.1. (C) The distance from the annotated transcription start site (TSS) of each piRNA gene to the nearest A-MYB peak. See also Figure S4.

Figure 5. Pachytene piRNA and Precursors Decrease in A-Myb Mutant Testes

The change in transcript or piRNA abundance per gene in A-Myb (n = 3) and Miwi (n = 1) mutants compared to heterozygotes in testes isolated at 14.5 and 17.5 dpp. See also Figure S5

Figure 6. Examples of the Effect of the A-Myb Mutant on piRNA Expression

Transcript and piRNA abundance in heterozygous (Het) and homozygous A-Myb (Mut) point mutant testes is shown for four illustrative examples at 14.5 and 17.5 dpp. Also shown is the abundance of piRNA sequencing reads that map to the exon-exon junctions. Gene 11-qE1-9443 does not have an intron. Exons, blue boxes; splice junctions, gaps; the last exon is compressed and not to scale. See also Figure S6

Figure 7. A-MYB Regulates Expression of mRNAs Encoding piRNA Pathway Proteins

(A) mRNA abundance in A-Myb mutant versus heterozygous testes. The 407 genes with a significant (q <0.05) change in steady-state mRNA levels are shown as red circles. The 203 with A-MYB peaks within 500 bp of their transcription start site are filled. (B) A-MYB ChIP-seq signal at the transcription start sites of A-Myb and genes implicated in RNA silencing pathways. For each, the figure reports the change in mRNA abundance between 17.5 and 10.5 dpp in wild-type testes and the mean change between A-Myb mutant and heterozygous testes at 14.5 dpp (mean ± S.D.; n = 3). (C) A model for the regulation of pachytene piRNA biogenesis by A-MYB. See also Figure S7 and Table S3

Figure 8. Feed-Forward Regulation of piRNA Biogenesis by A-MYB is Conserved in Rooster

(A) Length distributions of total roster testis small RNAs (black) and miRNAs (gray). (B) Sequence logo showing the nucleotide composition of piRNA reads and species. (C) The 5′-5′ overlap between piRNAs from opposite strands was analyzed to determine if rooster piRNAs display Ping-Pong amplification. The number of pairs of piRNA reads at each position is reported. Z-score indicates that a significant ten-nucleotide overlap (“Ping-Pong”) was detected. Z-score >1.96 corresponds to p-value < 0.05. (D) MEME-reported motif of the top 500 (by peak score) A-MYB ChIP-seq peaks from adult rooster testes. (E) A-MYB, H3K4me3, and input ChIP-seq signals at the transcription start sites of rooster PIWIL1, TDRD1, and TDRD3. See also Figure S8.