Ptbp2 Controls an Alternative Splicing Network Required for Cell Communication during Spermatogenesis

Abstract

Alternative splicing has essential roles in development. Remarkably, spermatogenic cells express more alternatively spliced RNAs compared to most whole tissues; however, regulation of these RNAs remains unclear. Here, we characterize the alternative splicing landscape during spermatogenesis and reveal an essential function for the RNA-binding protein Ptbp2 in this highly regulated developmental program. We found that Ptbp2 controls a network of genes involved in cell adhesion, migration, and polarity, suggesting that splicing regulation by Ptbp2 is critical for germ cell communication with Sertoli cells (multifunctional somatic cells necessary for spermatogenesis). Indeed, Ptbp2 ablation in germ cells resulted in disorganization of the filamentous actin (F-actin) cytoskeleton in Sertoli cells, indicating that alternative splicing regulation is necessary for cellular crosstalk during germ cell development. Collectively, the data delineate an alternative splicing regulatory network essential for spermatogenesis, the splicing factor that controls it, and its biological importance in germ-Sertoli communication.

Keywords: RNA networks; alternative splicing; cell-cell communication; post-transcriptional regulation; spermatogenesis.

Figure 1

Identification of stage-specific AS changes in spermatogenesis. (A) Top: Schematic of the three pairwise comparisons of cell types (transitions) examined. Bottom: Violin plots showing the distribution of ΔPSI values (FDR<0.05 and p<0.05) for each AS category in transition 1, 2, and 3 (left, center, and right, respectively). Dashed lines are positioned at ΔPSI=±20%. AS type is indicated at the bottom. (B) Pie chart showing the distribution of AS changes detected in each transition. (C) Number and overlap in genes with AS changes in one or more transitions. (D) Number and overlap in individual AS exons with changes in one or more transitions. (E) Clustered heatmaps showing PSI values of AS exons regulated in more than one transition (overlapping events from panel D), indicated by the blue/red color scale. Each column represents a single cell type in the transitions that are being compared, while each row represents an overlapping AS exon. Black dots represent an AS exon that undergoes a unidirectional, continuous splicing change. (F) Representative examples of RT-PCR validation of splicing changes measured in triplicate in P6 and P19 testes. (G) Bar chart showing the number of AS changes (ΔPSI=±20%) for each AS category in each transition. Color code for each AS type is indicated in A. (H) Distribution of absolute ΔPSI values in T1, T2, and T3. Dashed line represents ΔPSI>±20%. See also Figures S1,2; Tables S1,3; Files S1,4.

Figure 2

Identification of AS differences between WT and cKO testes. (A) Violin plots showing the distribution of ΔPSI values for each splicing category. (B) 257 AS changes with ΔPSI>20 in 217 genes, binned according to the splicing categories indicated at left. Color-coding reflects ΔPSI value, according to the gradient shown in A. Pearson correlation coefficients (R) are shown at right for RPKM comparisons in WT and cKO for genes with AS changes in each category. (C) Representative examples of RT-PCR analysis of AS isoforms measured in replicate WT and cKO testes at P25. (D) Comparison of RPKM values for the 217 genes with ΔPSI=±20% AS changes in WT and cKO testes. (E) Distribution of absolute fold change fold change values for genes with RNA increases or decreases in cKO testes (black and red lines, respectively). Dashed line is positioned at absolute fold change of 2. Inset shows relative number of genes with RNA increases (grey) or decreases (red). (F) Comparison of fold change values for the 792 RNAs that shared 2-fold or greater differences (p<0.01) in analysis of both WT versus cKO (x-axis) and meiotic versus post-meiotic cells (y-axis). Values in each corner correspond to the percentage of data points in each quadrant. (G) Representative example of RT-PCR validation of an AS event that is stage-specific and Ptbp2-dependent, with postnatal age of tissue indicated at top. See also Figure S3; Tables S2,3; Files S1,2

Figure 3

Ptbp2 regulates AS temporally (A) Intersection of AS cassette exons identified in T1 and in WT versus cKO datasets. (B) Distribution of ΔPSI values for 250 co-regulated cassette exons indicated in A. (C) Intersection of AS cassette exons identified in T3 and in WT versus cKO datasets. (D) Distribution of ΔPSI values for 51 co-regulated cassette exons indicated in C.

Figure 4

Identification of Ptbp2 binding sites in the germ cell transcriptome. (A) Autorad of nitrocellulose membrane containing cross-linked and radiolabelled Ptbp2-RNA complexes immunopurified from lysates treated with either a high (1:1,000) or low (1:20,000) concentration of RNAse. Assays were performed in parallel using UV-irradiated and non-irradiated testes (UV+ and UV-, respectively). Arrow denotes position of Ptbp2. Open bracket indicates region of membrane excised for library preparation. (B) Distribution of BR3 clusters in intergenic and genic regions. CDS corresponds to exonic coding sequences, while ambiguous BR3 clusters are those that map to sequences with more than one annotation. (C) Distribution of z-scores following tetramer-enrichment analysis for BR3 clusters. (D) Motifs with the top 5 z-scores are shown at top, with the percentage of BR3 clusters containing each motif indicated. Pie chart indicates the percentage of clusters that contain one or more of the top 5 motifs. See also Figure S6; File S3

Figure 5

Analysis of Ptbp2-RNA interactions near cassette exons. Distribution of binding sites in 20 nt windows relative to the splice sites of the Ptbp2-enhanced (A, red boxes) and Ptbp2-repressed (D, blue boxes) cassette exons and the 5’ and 3’splice sites of the upstream and downstream constitutively spliced exons, respectively. Each row in A and D represents a cassette exon region, with some rows empty due to the absence of a Ptbp2-RNA interaction within the intervals included in the figure. Metagene summaries of the data in A and D are shown in panels B and E, wherein thick dots indicate number of binding events relative to the indicated splice sites, and the dotted lines represent the number of regions that have exons or introns of the indicated size. (C) Distribution of PhastCons scores for Ptbp2-RNA interactions in regions associated with Ptbp2-enhanced (red) and Ptbp2-repressed cassette exons. (F) Metagene analysis of Ptbp2 binding events in a control set of 100 randomly selected internal coding exons, with 35 containing BR2 or BR3 sites. Black line represents the number of Ptbp2 binding events relative to the indicated splice sites, while grey lines represent the number of regions that have exons or introns of the indicated size. See also File S3

Figure 6

Enriched gene ontology terms associated with RNAs that are mis-spliced in Ptbp2-deficient testes. (A) Hierarchical view of parent-child relationships for the enriched GO terms associated with genes with altered AS in cKO testis. Seven different groups were identified and outlined to match colors assigned to each group indicated at bottom. Circle sizes reflect the number of genes in each enriched term, while circle color reflects enrichment p value. (B) Clustering of genes based on co-occurrence in the enriched GO terms, with color-coded GO terms indicated at the top. (C) Higher magnification view of two boxed regions (dotted lines) from B. See also Figure S4; File S4

Figure 7

Ptbp2-loss in germ cells results in disorganization of the Sertoli cell actin cytoskeleton. Fluorescence microscopy to detect F-actin (phalloidin, green), acrosome (PNA, red), and DNA (DAPI, blue). A-D shows a representative seminiferous tubule from a P36 WT mouse, with panels C and D showing high magnification views of the dotted box in A and B which contains elongated spermatids. E-G shows a representative example from a P36 cKO seminiferous tubules. H-J and K-M show representative examples of seminiferous tubules from P24 WT and cKO mice, respectively. Open arrows indicate elongated spermatids, closed arrows indicate early round spermatids, and arrowheads indicate polarized F-actin filaments. Scale bar is 25 µM. See also Figure S5