Single-nucleus multiomics reveals the gene-regulatory networks underlying sex determination of murine primordial germ cells

Reviewer #1 (Public Review):

Summary:

This study uses single nucleus multiomics to profile the transcriptome and chromatin accessibility of mouse XX and XY primordial germ cells (PGCs) at three time-points spanning PGC sexual differentiation and entry of XX PGCs into meiosis (embryonic days 11.5-13.5). They find that PGCs can be clustered into sub-populations at each time point, with higher heterogeneity among XX PGCs and more switch-like developmental transitions evident in XY PGCs. In addition, they identify several transcription factors that appear to regulate sex-specific pathways as well as cell-cell communication pathways that may be involved in regulating XX vs XY PGC fate transitions. The findings are important and overall rigorous. The study could be further improved by a better connection to the biological system, including the addition of experiments to validate the 'omics-based findings in vivo and putting the transcriptional heterogeneity of XX PGCs in the context of findings that meiotic entry is spatially asynchronous in the fetal ovary. Overall, this study represents an advance in germ cell regulatory biology and will be a highly used resource in the field of germ cell development.

Strengths:

(1) The multiomics data is mostly rigorously collected and carefully interpreted.

(2) The dataset is extremely valuable and helps to answer many long-standing questions in the field.

(3) In general, the conclusions are well anchored in the biology of the germ line in mammals.

Weaknesses:

(1) The nature of replicates in the data and how they are used in the analysis are not clearly presented in the main text or methods. To interpret the results, it is important to know how replicates were designed and how they were used. Two "technical" replicates are cited but it is not clear what this means.

(2) Transcriptional heterogeneity among XX PGCs is mentioned several times (e.g., lines 321-323) and is a major conclusion of the paper. It has been known for a long time that XX PGCs initiate meiosis in an anterior-to-posterior wave in the fetal ovary starting around E13.5. Some heterogeneity in the XX PGC populations could be explained by spatial position in the ovary without having to invoke novel sub-populations.

(3) There is essentially no validation of any of the conclusions. Heterogeneity in the expression of a given marker could be assessed by immunofluorescence or RNAscope.

(4) The paper sometimes suffers from a problem common to large resource papers, which is that the discussion of specific genes or pathways seems incomplete. An example here is from the analysis of the regulation of the Bnc2 locus, which seems superficial. Relatedly, although many genes and pathways are nominated for important PGC functions, there is no strong major conclusion from the paper overall.

Reviewer #2 (Public Review):

Summary:

This manuscript by Alexander et al describes a careful and rigorous application of multiomics to mouse primordial germ cells (PGCs) and their surrounding gonadal cells during the period of sex differentiation.

Strengths:

In thoughtfully designed figures, the authors identify both known and new candidate gene regulatory networks in differentiating XX and XY PGCs and sex-specific interactions of PGCs with supporting cells. In XY germ cells, novel findings include the predicted set of TFs regulating Bnc2, which is known to promote mitotic arrest, as well as the TFs POU6F1/2 and FOXK2 and their predicted targets that function in mitosis and signal transduction. In XX germ cells, the authors deconstruct the regulation of the premeiotic replication regulator Stra8, which reveals TFs involved in meiosis, retinoic acid signaling, pluripotency, and epigenetics among predictions; this finding, along with evidence supporting the regulatory potential of retinoic acid receptors in meiotic gene expression is an important addition to the debate over the necessity of retinoic acid in XX meiotic initiation. In addition, a self-regulatory network of other TFs is hypothesized in XX differentiating PGCs, including TFAP2c, TCF5, ZFX, MGA, and NR6A1, which is predicted to turn on meiotic and Wnt signaling targets. Finally, analysis of PGC-support cell interactions during sex differentiation reveals more interactions in XX, via WNTs and BMPs, as well as some new signaling pathways that predominate in XY PGCs including ephrins, CADM1, Desert Hedgehog, and matrix metalloproteases. This dataset will be an excellent resource for the community, motivating functional studies and serving as a discovery platform.

Weaknesses:

My one major concern is that the conclusion that PGC sex differentiation (as read out by transcription) involves chromatin priming is overstated. The evidence presented in the figures includes a select handful of genes including Porcn, Rimbp1, Stra8, and Bnc2 for which chromatin accessibility precedes expression. Given that the authors performed all of their comparisons between XX versus XY datasets at each timepoint, have they missed an important comparison that would be a more direct test of chromatin priming: between timepoints for each sex? Furthermore, it remains possible that common mechanisms of differentiation to XX and XY could be missing from this analysis that focused on sex-specific differences.

Reviewer #3 (Public Review):

Summary:

Alexander et al. reported the gene-regulatory networks underpinning sex determination of murine primordial germ cells (PGCs) through single-nucleus multiomics, offering a detailed chromatin accessibility and gene expression map across three embryonic stages in both male (XY) and female (XX) mice. It highlights how regulatory element accessibility may precede gene expression, pointing to chromatin accessibility as a primer for lineage commitment before differentiation. Sexual dimorphism in these elements and gene expression increases over time, and the study maps transcription factors regulating sexually dimorphic genes in PGCs, identifying sex-specific enrichment in various transcription factors.

Strengths:

The study includes step-wise multiomic analysis with some computational approach to identify candidate TFs regulating XX and XY PGC gene expression, providing a detailed timeline of chromatin accessibility and gene expression during PGC development, which identifies previously unknown PGC subpopulations and offers a multimodal reference atlas of differentiating PGC clusters. Furthermore, the study maps a complex network of transcription factors associated with sex determination in PGCs, adding depth to our understanding of these processes.

Weaknesses:

While the multiomics approach is powerful, it primarily offers correlational insights between chromatin accessibility, gene expression, and transcription factor activity, without direct functional validation of identified regulatory networks.