ZBTB16/PLZF regulates juvenile spermatogonial stem cell development through an extensive transcription factor poising network

Main

Murine spermatogonia (SPG)-derived stem cells continuously balance self-renewal and differentiation, orchestrated by multiple transcription factors (TFs). In the mouse adult testis, undifferentiated SPG (uSPG) have mesenchymal stem cell (MS cell)-like properties and forage for limited cytokines^1,2,3,4. In vitro systems to study uSPG include primary cultures of uSPG (PC-uSPG) that, at low frequency, lose MS cell-like cell identity during in vitro expansion and instead acquire embryonic stem cell (ES cell)-like cell properties (with an active pluripotency network)^5,6. Here, we aimed to understand how TF networks regulate uSPG and their differentiation and began our studies with zinc finger and BTB domain-containing protein 16 (ZBTB16; also known as promyelocytic leukemia zinc finger (PLZF)), which is specifically expressed in undifferentiated A-single, A-paired and A-aligned uSPG⁷ and A1 differentiating SPG (dSPG)^8,9. ZBTB16 is not essential for spermatogenesis but rather helps ensure long-term uSPG maintenance, as its absence results in the gradual of depletion of uSPG in a substantial subset of seminiferous tubules, especially during aging^7,10,11. Previous studies used microarrays or small interfering RNA-mediated knockdown to explore ZBTB16 function in uSPG or PC-uSPG^7,12. In both testis and blood development, ZBTB16 functions as both an activator and a repressor^{10,12,13,14,15} but the mechanisms remain incompletely understood. Repression involves ZBTB16 recruiting Polycomb repressive complexes 1 and 2 (PRC1 and PRC2) and interaction between B cell-specific Moloney murine leukemia virus integration site 1 (BMI1) and histone deacetylases (HDACs)^16,17, while activation entails interaction with both chromatin and post-translational modifiers^15,18. Here, we initially examined the relationship between ZBTB16 and two other uSPG TFs, SRY-box TF 3 (SOX3) and Spalt like TF 4 (SALL4), in establishing the chromatin and transcription landscape of uSPG.

Human and mouse spermiogenesis (postmeiotic differentiation) exhibits a chromatin transcription logic that greatly differs from somatic cells. Mitotic SPG and meiotic cells predominantly use ‘typical promoters’ with active chromatin modifications, while spermiogenesis primarily relies on ‘atypical promoters’ that bear repressive chromatin modifications such as DNA methylation (DNAme) and histone 3 methylation (H3K27me3) during their transcription, alongside active modifications such as histone acetylation (H3K27ac)^19,20. Here, we examined the logic and mechanisms underlying the establishment of active chromatin at typical promoters in uSPG. Remarkably, ZBTB16, SALL4 and SOX3, along with several positive epigenetic marks (H3K4me2/3, H3K27ac and DNA hypomethylation), co-occupy >12,000 typical promoters that coincide with open higher-order chromatin architectures in uSPG. This encompasses the genes active in uSPG, as well as the vast majority of genes later activated in dSPG and during meiosis, suggesting that this TF network establishes chromatin poising in uSPG for both differentiation and meiotic activation. We further dovetail our work with recent work of others reporting the presence of paused RNA polymerase II (RNAPol2) at uSPG genes²¹, which we show resides at typical promoters. Functionally, we reveal that ZBTB16 helps activate a portion of typical network genes to help regulate uSPG self-renewal, MS cell-like cell identity and uSPG progression by promoting cell-cycle progression.

Results

Defining ZBTB16-occupied and affected genes in vivo

Prior work characterized ZBTB16-binding sites and affected genes in PC-uSPG rather than in cells directly isolated from the testis¹². To characterize ZBTB16 in vivo, we isolated uSPG directly from the testis and conducted RNA sequencing (RNA-seq) and histone modification chromatin immunoprecipitation followed by deep sequencing (ChIP-seq). ZBTB16 ChIP-seq was also performed from the whole testis as ZBTB16 expression is limited to uSPG at P7 (refs. ^1,7). Using immunomagnetic cell sorting (IMCS) with anti-THY1 and anti-KIT antibodies^1,22, we isolated uSPG and dSPG from wild-type (WT) and Zbtb16^lu/lu (null) mice at P7. Additionally, to study later stages of germ cell development, we used the STA-PUT method^23,24 to isolate pachytene spermatocytes (PSs) and round spermatids (RSs) (Fig. 1a). Our RNA-seq approach involved three replicates with high similarity (Extended Data Fig. 1a). THY1⁺-sorted and KIT⁺-sorted SPG were highly enriched for Thy1 or Kit mRNA, verifying the utility of the IMCS approach (Extended Data Fig. 1b). When comparing THY1⁺ uSPG from WT and null mice, we found 739 genes upregulated and 695 genes downregulated in Zbtb16-deficient THY1⁺ uSPG (Fig. 1b).

ZBTB16/PLZF regulates juvenile spermatogonial stem cell development through an extensive transcription factor poising network — **Fig. 1: Defining the gene targets of ZBTB16.**

We next identified ZBTB16-occupied loci by ChIP-seq, using biological duplicates and two different ZBTB16 antibodies (rabbit or goat), confirmed by immunoblot analysis (Extended Data Fig. 1c). First, the peaks (ChIP signal) occupied by ZBTB16 in the datasets derived from the rabbit and the goat antibodies were numerous and nearly identical (r values ≈ 0.93; Extended Data Fig. 1d). About 40% of ZBTB16-binding sites reside in gene promoters, with another ~40% in distal intergenic regions and ~10% in gene bodies (Extended Data Fig. 1e,f). Although ZBTB16 bound the proximal promoter of 20,116 genes, in our RNA-seq, only 4.7% of ZBTB16-bound genes were affected in Zbtb16-deficient THY1⁺ uSPG. Within the affected genes, ZBTB16 bound 459 of the 695 downregulated genes (66.0%) and 496 of the 739 upregulated genes (67.1%) (Fig. 1c).

Analysis of affected genes by Gene Ontology (GO) using Panther²⁵ identified enriched GO terms related to receptors and TFs for development and cell migration or regulation of locomotion (for genes downregulated in the null cells; Fig. 1d) and terms for meiosis and carboxylic acid biosynthetic process (for genes upregulated in the null cells; Fig. 1e). Notably, ZBTB16 activates itself (Zbtb16; autoactivation), T (Brachyury, a TF important for uSPG maintenance regulated by glial cell-derived neurotrophic factor (GDNF) and Ets variant gene 5 (ETV5))²⁶, Eomes (a TF for long-term uSPG maintenance)¹¹ and Fgfr1 (a receptor important for uSPG maintenance)²⁷ (Fig. 1f). In contrast, ZBTB16 binds and attenuates Krt18, Sycp3 (meiosis), Cth (metabolism) and Rhox10 (gonocyte-to-uSPG conversion²⁸) (Fig. 1g). The genes indirectly regulated by ZBTB16 are linked to immune response (Extended Data Fig. 2a). Overall, ZBTB16 occupies an interesting set of genes but curiously only impacts a small fraction of its occupied promoters, which is explored further below.

ZBTB16 occupancy correlates with broad H3K4me3 and H3K27ac

We then examined chromatin attributes correlated with ZBTB16 occupancy in uSPG. In nontestis cells, ZBTB16 represses genes by recruiting PRC1, PRC2 and HDACs^16,17. Regarding activation, phosphorylation of ZBTB16 promotes transcriptional action, while acetylation of ZBTB16 correlates with repression¹⁸ (Fig. 2a). However, in uSPG, ZBTB16 occupancy at promoters strikingly overlapped with high and broad H3K4me3 (>90% overlap), H3K27ac (~56% overlap) and low DNAme (Fig. 2b–e), regardless of transcriptional status. Overlap with H3K27me3 (~17%) or BMI1 (~7%) was modest and similar between upregulated and downregulated genes (Fig. 2b,d,e and Extended Data Fig. 2b,c). ZBTB16-regulated genes (either upregulated or downregulated) showed no distinct pattern in terms of their initial DNAme or chromatin status (for example, H3K4me3, H3K27me3 or their combination (that is, bivalency)) (Fig. 2d–g). Thus, loss of ZBTB16 does not specifically impact genes bearing a particular chromatin state, including bivalency. Overall, the clear feature in uSPG is that ZBTB16-bound genes uniformly bear high and broad H3K4me3 and lack DNAme and a majority bear H3K27ac.

**Fig. 2: Relationships of ZBTB16 to chromatin modifications.**

ZBTB16 lacks a single consensus DNA-binding site in uSPG

Prior efforts have yielded surprisingly diverse ZBTB16-binding motifs in different cell types^12,13,29. To identify a motif in uSPG, we used MEME-ChIP³⁰ and GEM³¹ analysis on ZBTB16-bound peaks from the regular ChIP-seq and also ZBTB16-bound footprints from our ChIP-nexus approach³². However, MEME-ChIP produced a top-ranked site overlapping with only ~3% of bound peaks, affecting only 15 genes in Zbtb16-deficient uSPG (Extended Data Fig. 2d). Notably, GEM analysis from both datasets yielded a telomere motif (Extended Data Fig. 2e, f) but this observation was absent in MEME-ChIP. Thus, ZBTB16 lacks a single defined binding motif in uSPG and may instead be tethered to the DNA with other protein partners (explored below)¹⁷.

ZBTB16 attenuates particular retrotransposons possessing H3K4me3

Around 40% of ZBTB16-bound regions are associated with distal intergenic areas (Extended Data Fig. 1e,f). Indeed, ZBTB16 repressed long interspersed element (LINE) L1 in the whole testis and bone marrow³³, prompting an examination of transposable elements in the testis. We found that ZBTB16 binds LINEs, as well as particular long terminal repeats (LTRs) and short interspersed elements (SINEs) (Extended Data Fig. 3a). Surprisingly, a high proportion of ZBTB16-occupied LTRs (46.2%), LINEs (48.3%) and SINEs (57.9%) overlapped with broad H3K4me3 and low DNAme, a pattern similar to that seen with ZBTB16 at RefSeq genes, and only rarely overlapped with H3K9me3, H3K27me3 and Piwi-interacting RNA (piRNA) clusters (Fig. 2b and Extended Data Fig. 3b–d). Thus, in uSPG, ZBTB16 attenuates specific retrotransposons independently of H3K9me3, H3K27me3 and DNA hypermethylation. Overall, ZBTB16 appears to have dual functions (activation and repression) at RNAPol2-transcribed protein-coding genes, whereas it only attenuates retrotransposons. Here, we note that our data leave open the possibility of both direct and indirect mechanisms for ZBTB16-dependent repeat element regulation.

Limited overlap of ZBTB16 targets between uSPG and PC-uSPG

We then considered using established in vitro culturing approaches to advance our work but first needed to examine whether there are differences in ZBTB16 binding between in vivo (testis-derived) and PC-uSPG. To test this, we compared our Zbtb16-affected genes in THY1⁺ P7 uSPG to those reported in ITGA6⁺ uSPG¹⁰ and PC-uSPG^12,14. Surprisingly, only about 2% (33 genes) of Zbtb16-affected genes in THY1⁺ uSPG were shared with those impacted in Zbtb16-deficient ITGA6⁺ uSPG (Extended Data Fig. 4a,b). Furthermore, just two of the top ten ZBTB16 targets from PC-uSPG (Zbtb16 and Lhx1) were also affected by ZBTB16 deficiency in vivo. Most genes identified in vitro, such as Etv5, Bcl6b and Uchl1, remained unaffected in Zbtb16-deficient P7 THY1⁺ uSPG (Extended Data Fig. 4c).

Principal component analysis (PCA) revealed striking transcriptome differences between THY1⁺ uSPG and PC-uSPG, with PC-uSPG closely resembling multipotent adult SPG-derived stem cells (MASCs) and ES cells (Extended Data Fig. 5a). Notably, Zbtb16 expression in THY1⁺ uSPG remained unaltered in PC-uSPG but was silenced in MASCs (Extended Data Fig. 5b). We next compared differential ZBTB16 enrichment at gene promoters in uSPG and PC-uSPG¹² by ChIP-seq using a goat anti-ZBTB16 antibody. ZBTB16 bound 16,852 gene promoters in uSPG but only 8,261 gene promoters in PC-uSPG, a subset of those bound in vivo (Extended Data Fig. 5c). However, only 508 of the genes occupied in PC-uSPG were affected in the Zbtb16-null cells (Extended Data Fig. 5c,d). Notably, ZBTB16 occupied and attenuated Utf1 in uSPG while it remained unoccupied in PC-uSPG, correlated with Utf1 upregulation (Extended Data Fig. 6e,f), a result validated by examining UTF1 levels in Zbtb16-deficient LIN28A⁺ uSPG (Extended Data Fig. 6a,b). Additionally, whereas adult uSPG lack pluripotency factors Sox2 and Nanog (ref. ¹⁹), PC-uSPG upregulate these factors, alongside Myc, Lin28a and Klf4 (Extended Data Fig. 6c), suggesting a transition to a more ES cell-like state. Lastly, ZBTB16 indirectly attenuated Pou5f1 (Oct4) expression (Extended Data Fig. 2a).

uSPG are migratory, display MS cell charateristics^1,2 and undergo a mesenchymal-to-epithelial transition at low frequency during uSPG in vitro expansion into PC-uSPG⁶. Indeed, ZBTB16 target genes downregulated in the null were enriched in cell migration categories (Fig. 1d). Moreover, in PC-uSPG, where ZBTB16 occupancy was lowered, cell-migration-related genes were further downregulated (Extended Data Fig. 6d). uSPG appear to migrate by extracellular matrix remodeling, as a subset of LIN28A⁺ uSPG displayed ADAMTS5 metalloproteinase expression (Extended Data Fig. 6e) and cleaved Versican (Versikine) was detected in SOX3⁺ uSPG (Extended Data Fig. 6f). Taken together, ZBTB16-bound sites were greatly reduced and gene expression patterns, including genes for migration, were highly altered in PC-uSPG versus in vivo uSPG. Thus, ZBTB16 occupancy and activity depend on the cell type, developmental stage and growth conditions, requiring investigation of the direct in vivo cellular context.

dSPG decrease in Zbtb16-null mice

Previous studies have suggested that ZBTB16 represses Kit (refs. ^13,34). Although ZBTB16 occupies the Kit promoter in vivo, the loss of Zbtb16 did not affect Kit expression in either THY1⁺ uSPG or KIT⁺ dSPG (Extended Data Fig. 1b). In Zbtb16-null mice testes at P7, THY1⁻/KIT⁺ dSPG were decreased ~2.1-fold while the other two populations of uSPG (THY1⁺/KIT⁻ and THY1⁺/KIT⁺) were not significantly changed (Fig. 3a,b and Extended Data Fig. 7a), implying that ZBTB16 promotes the THY1⁺ uSPG-to-KIT⁺ dSPG transition, and does not inhibit Kit expression or suppress uSPG differentiation. Thus, ZBTB16 promotes the undifferentiated-to-differentiating SPG transition, termed hereafter U–DT.

**Fig. 3: Fewer KIT⁺ dSPG and spermatocytes in *Zbtb16-*null testes.**

ZBTB16 activates neurogen 3 (Neurog3) and cyclin D1 (Ccnd1) for SPG differentiation

To understand how ZBTB16 promotes U–DT and supports progenitor development, we examined genes linked to progenitor initiation and cell-cycle regulation. Notably, ZBTB16 directly activated Neurog3 (Fig. 2h and Extended Data Fig. 7b,c), which promotes uSPG differentiation and is inhibited by high GDNF, thereby preventing uSPG differentiation^35,36,37. Furthermore, ZBTB16 directly activated Ccnd1 (Fig. 3c), which is involved in entry into the cell cycle and G₁–S transition, consistent with previous results in Zbtb16-knockout (KO) mice¹⁰. Thus, these findings imply that ZBTB16 antagonizes GDNF in uSPG to promote U–DT and developmental progression.

Next, we performed flow cytometry analysis to evaluate cell-cycle status as a function of DNA content in P7 testicular cells from Zbtb16-null and littermate control (WT) mice. While THY1⁺/KIT⁻ uSPG were relatively quiescent (72.57% of G₀/G₁ phase cells), THY1⁺/KIT⁺ uSPG (31.20% of G₀/G₁ phase cells) and THY1⁻/KIT⁺ dSPG (58.17% of G₀/G₁ phase cells) displayed increased activity. Furthermore, G₀/G₁ phase cells were enriched in Zbtb16-deficient THY1⁺/KIT⁺ uSPG (~1.3-fold) and THY1^–/KIT⁺ dSPG (~1.4-fold), while fewer G₀/G₁ phase cells were observed in Zbtb16-deficient THY1⁺/KIT⁻ uSPG at P7 (Fig. 3d). These results imply that ZBTB16 ensures a slow cell cycle in self-renewing early uSPG (THY1⁺/KIT⁻) but helps accelerate the cell cycle in late uSPG (THY1⁺/KIT⁺).

Delay in spermatocyte development in Zbtb16-null mice

We next assessed the impact of delayed U–DT on spermatocyte emergence at P14. Zbtb16-null testis growth halted at P56, followed by shrinkage by P70, possibly because of age-related germ cell loss (Extended Data Fig. 7d,e). At P14, testis weight was ~1.6-fold lower in Zbtb16-null mice at P14 (Fig. 3e,f and Extended Data Fig. 7d,e). Immunofluorescence (IF) revealed a ~2.1-fold decrease in spermatocytes and a ~3.2-fold decrease in PSs with the XY body displaying H2AX phosphorylation (γH2AX) in Zbtb16-null mice (Fig. 3g–i). Notably, LIN28A⁺ uSPG were increased ~1.3-fold in Zbtb16-null cells. However, no abnormal γH2AX was detected in Zbtb16-deficient uSPG (Fig. 3g), implying that DNA damage response is not triggered in Zbtb16-deficient uSPG. Together, spermatocyte reduction and the accumulation of SPG appear to be linked to late uSPG transition delay.

Distinct cyclin D (CCND)–cyclin-dependent kinase 4 (CDK4) complexes in early and late uSPG

To better understand cell-cycle regulation in uSPG, we examined CCND family proteins and their catalytic partners CDK4 and CDK6. Analysis of RNA-seq data from Id4–GFP^Bright uSPG, characterized by high transplantation efficiency³⁸, revealed elevated expression of Ccnd2 and Cdk4, which are associated with uSPG self-renewal, in comparison to Ccnd1 and Cdk6. Additionally, Ccnd1 and Cdk6 are known to be dispensable for uSPG self-renewal^38,39,40 (Extended Data Fig. 7f). Intriguingly, the expression pattern of Ccnd, Cdk4 and Cdk6 in uSPG differed from PC-uSPG, primordial germ cells (PGCs), ES cells and hematopoietic stem cells (HSCs), suggesting that cell-cycle acceleration varies in cell types and developmental stages (Extended Data Fig. 7g). Here, we hypothesized that CCND2 and CDK4 promote a more rapid cell cycle in early uSPG, while CCND1 and CDK6 enhance G₀/G₁–S transition in late uSPG. IF in P14 testes confirmed CCND1 expression in uSPG and dSPG while CCND2 was present in a subset of ZBTB16⁺/CCND1⁺ uSPG, marking early uSPG, but absent in ZBTB16⁻/CCND1⁺ dSPG (Extended Data Fig. 7h). Notably, CCND2⁺/CCND1⁺ early uSPG expressed higher ZBTB16 levels than CCND2⁻/CCND1⁺ TA late uSPG (Extended Data Fig. 7i), suggesting that ZBTB16 gradually decreases from early uSPG to late uSPG.

We next explored how uSPG differently use CDK4 and CDK6 for G₀/G₁–S transition. Phosphorylated CDK4 (pCDK4) was detected from uSPG to spermatocytes (Extended Data Fig. 7j). Unexpectedly, pCDK6 was localized in leptotene and PSs but not in SPG (Extended Data Fig. 7k). These results indicate a role of pCDK4 in G₀/G₁–S progression from mitosis to meiosis.

SOX3 promotes SPG differentiation and reduces migration genes

We then returned to the highly unexpected observation above involving ZBTB16 binding at ~20,000 promoters but affecting only a few hundred genes. This prompted consideration of partial redundancy among additional uSPG-specific (for testis) TFs SOX3 and SALL4 (refs. ^41,42). This extension was also prompted by the reported coactivation of Neurog3 by ZBTB16 (Fig. 2f) and SOX3 (refs. ^41,43,44), as well as the reported co-occupancy and antagonistic relationship between ZBTB16 and SALL4 (refs. ^12,34,42).

We first validated prior work^41,42 showing that uSPG express all three TFs (Fig. 4a). We then performed ChIP-seq on SOX3 and SALL4 in whole testis at P7. SOX3 ChIP-seq yielded SOX3 at 19,063 genes and revealed an impressive overlap with ZBTB16 targets (16,953 genes, 88.9% overlap) (Fig. 4b,c). However, only 1,005 of these genes overlapped with SOX3-occupied genes in neural progenitor cells (NPCs) (Fig. 4b), demonstrating cell-type-specific SOX3 occupancy. To define SOX3 impact, we derived germline-specific Sox3-conditional-KO (cKO) mice using Ddx4–Cre mice and conducted RNA-seq analysis from Sox3-deficient THY1⁺ uSPG, which identified 151 differentially expressed genes (DEGs): 65 downregulated and 86 upregulated (Fig. 4d). SOX3 occupied 115 of these genes affected by Sox3, comprising 43 downregulated and 72 upregulated genes in Sox3-deficient THY1⁺ uSPG (Fig. 4e). These findings suggest a dual role of SOX3 in gene regulation of uSPG, akin to ZBTB16. Analysis of upregulated genes in Sox3-null cells enriched GO terms related to cell adhesion and cell differentiation, while there was no significant GO term enriched in downregulated genes (Fig. 4f).

**Fig. 4: SOX3 promotes SPG differentiation.**

To identify shared functions of SOX3 in uSPG and NPCs, we conducted an intersection analysis of ChIP-seq data in uSPG with data from NPCs, revealing only 12 co-occupied genes (Fig. 4g). Examples include Cyp26b1, a retinoic acid (RA)-metabolizing enzyme⁴⁵ that is attenuated by SOX3, suggesting a candidate mechanism to enhance RA responsiveness, leading to uSPG differentiation. Additionally, SOX3 directly activates Lin28a expression, which promotes uSPG differentiation⁴⁶ (Fig. 4g,h). Together, our results raise the possibility that SOX3 promotes cell differentiation through RA signaling and Lin28a, while also tempering cell migration, potentially linked to SPG differentiation.

SALL4 coactivates a subset of ZBTB16 target genes

We next examined the roles of SALL4 in uSPG. First, our data do not support the prior model that SALL4 sequesters or antagonizes ZBTB16 to prevent ZBTB16 activation of Kit (ref. ³⁴). This is because ZBTB16 and SALL4 were coexpressed only in uSPG and early KIT⁺ dSPG, while ZBTB16 was absent in late KIT⁺ dSPG (Fig. 4a and Extended Data Fig. 8a). SALL4 occupied 20,455 genes but only directly regulated 351 genes, constituting only 1.7% of bound genes (Extended Data Fig. 8b). There was remarkable overlap in the genes bound by ZBTB16 and SALL4, encompassing 18,521 genes (90.5% overlap in uSPG) and 5,510 genes (66.7% in PC-uSPG) (Extended Data Fig. 8c,d). However, SALL4 targets yielded certain unique GO terms, suggesting unique functions for SALL4 in uSPG (Fig. 1d,e and Extended Data Fig. 8e,f). SALL4 occupancy was lost at 55.8% of its in vivo target genes in PC-uSPG despite higher Sall4 expression in PC-uSPG compared to THY1⁺ uSPG (Extended Data Fig. 8b,g,h). However, this difference in Sall4 expression was not statistically significant, underscoring variability and potential differences between in vivo and in vitro conditions. Notably, common direct target genes of ZBTB16 and SALL4 showed a positive correlation (Extended Data Fig. 8i–l). Thus, SALL4 and ZBTB16 collaboratively regulate certain targets, challenging prior antagonism models³⁴. Collectively, loss of ZBTB16, SOX3 or SALL4 impacts a distinct and limited subset of genes, indicating limited independent functions.

ZBTB16, SALL4 and SOX3 co-occupy mitotic and meiotic genes

We next explored the contributions of ZBTB16, SALL4 and SOX3 in transcriptional regulation of uSPG. IF analyses showed that the nuclear localization of SALL4 and SOX3 in uSPG was not affected by the absence of Zbtb16 (Extended Data Figs. 6f and 8a). Furthermore, ChIP-seq analysis using testis from WT and Zbtb16-null mice at P7 revealed only a slight reduction in SALL4 occupancy, while SOX3 occupancy remained unchanged in the absence of ZBTB16 (Extended Data Fig. 9a). These findings suggest that SALL4 and SOX3 bind their targets independently of ZBTB16.

Remarkably, ZBTB16, SALL4 and SOX3 co-occupied 16,151 gene promoters (Fig. 5a) and their co-occupancy aligned with active chromatin marks, especially H3K4me3 and H3K27ac in uSPG (Fig. 2c and Extended Data Fig. 9b–e), prompting a deeper exploration for a possible collective role for these three factors in chromatin opening or poising at 16,000 genes. We investigated connections between these three TFs and the temporal stages of gene expression of their occupied genes by examining THY1⁺ uSPG, KIT⁺ dSPG, PSs, RSs and mature sperm. This revealed 21,841 DEGs that were divided into clusters representing the developmental stage of peak expression: mitosis (clusters 1–3), meiosis (clusters 4 and 5) and spermiogenesis (clusters 6 and 7) (Fig. 5b).

**Fig. 5: A ZBTB16, SALL4 and SOX3 TF and chromatin network in uSPG.**

Among these DEGs, 12,708 genes overlapped with promoter binding by the three TFs, while 5,801 genes were unbound (Fig. 5c). Notably, in THY1⁺ uSPG and KIT⁺ dSPG, these factors occupied most genes activated in mitosis and meiosis (clusters 1–5) but only a minority of genes activated in spermiogenesis (clusters 6 and 7) (Fig. 5d). Here, although the fraction of genes bound within these two classes was vastly different, their levels of occupancy at typical promoters across clusters 1–7 were similar (Extended Data Fig. 9f).

Whereas most cobound genes were protein-coding genes, ~50% of unbound genes were noncoding RNAs (Extended Data Fig. 9g). Interestingly, the limited numbers of genes co-occupied by the three TFs in clusters 6 and 7 (spermiogenesis) were mainly associated with splicing and translation in somatic cells (for example, small nuclear RNAs (16 genes), Eif4a2 and small nucleolar RNAs (68 genes)) and, thus, were not exclusive to spermiogenesis (Extended Data Fig. 9h). Conversely, many unbound genes are associated with histone-to-protamine exchange (Extended Data Fig. 9i), which is exclusive to spermiogenesis. Thus, genes co-occupied by ZBTB16, SALL4 and SOX3 were primarily associated with mitotic function in SPG or meiotic processes, whereas a modest number of co-occupied genes activated during spermiogenesis had somatic expression/functions and, therefore, were not germline specific.

ZBTB16, SALL4 and SOX3 distinguish typical from atypical promoters

Our prior work revealed an unexpected chromatin logic during spermatogenesis, where atypical promoters marked by high DNAme and H3K27me3 represent the majority of active promoters during spermiogenesis¹⁹. This contrasts with typical promoters, which are associated with active chromatin modifications (H3K4me3 and H3K27ac), lack DNAme and are active primarily during mitotic and meiotic phases¹⁹. Intriguingly, our analyses here revealed that the target promoters of ZBTB16, SALL4 and SOX3 were strongly associated with typical promoters bearing active chromatin features such as H3K4me2/3, H3K27ac and low DNAme, regardless of the spermatogenesis stage (Fig. 5d). Conversely, genes lacking these three factors exhibited atypical chromatin features, including high DNAme (Fig. 5d). Furthermore, these co-occupied typical promoters maintained consistent enrichment of H3K4me3 and H3K27ac across spermatogenesis. (Fig. 5d and Extended Data Fig. 9j). Chromatin accessibility, measured by assay for transposase-accessible chromatin using sequencing (ATAC-seq)^23,47, was established early in uSPG and remained consistently open in typical genes throughout spermatogenesis. In contrast, atypical genes showed more restricted chromatin openness (only focally open), even during expression in spermiogenesis (Extended Data Fig. 9k).

Interestingly, H3K27me3 was highly enriched at meiotic, spermiogenic and a subset of mitotic typical promoters during expression (Fig. 5d and Extended Data Fig. 9j). Enrichment of H3K27me3 has also been observed at a subset of promoters in ES cells that are undergoing active transcription⁴⁸. These findings suggest that H3K27me3 alone may not be sufficient for strong gene repression, indicating a more complex role in gene regulation. Additionally, atypical genes such as those encoding protamine, gained H3K4me3 in PSs (along with many typical genes) and retained active histone modifications (H3K4me3 and H3K27ac) in mature sperm. In contrast, atypical genes that acquired H3K4me3 and became transcriptionally active in RSs subsequently lost these modifications in mature sperm (Extended Data Fig. 9j).

As ZBTB16 regulates enhancers in hematopoietic progenitors⁴⁹ and MS cells⁵⁰, we then extended our analyses to known super-enhancers (SEs) in spermatogenesis⁵¹. Notably, these three TFs cobound the majority of previously identified mitotic (81/107) and meiotic (260/425) SEs, which were characterized by H3K4me2/3 and H3K27ac marks. Conversely, unbound meiotic SEs were either low or lacking H3K4me2/3 and H3K27ac (Extended Data Fig. 9l). Taken together, uSPG appear to establish a large TF-active chromatin network that opens chromatin at typical promoters and the large majority of meiotic SEs to drive the SPG mitotic program, which may poise the meiotic program for subsequent activation.

Transcription and occupancy interactions between ZBTB16 and reproductive homeobox 10 (RHOX10) in uSPG

To better understand the transcription network regulatory logic, we next sought a TF that might reside and impact only a minor subset of the network targets. We chose the candidate RHOX10, which facilitates the transition from gonocytes to uSPG, in part through indirect activation of Zbtb16 (refs. ^28,52). Strikingly, 99.1% of RHOX10-bound genes in PC-uSPG overlap with ZBTB16-bound genes in uSPG and 82.5% of RHOX10-bound genes overlap with ZBTB16, SALL4 and SOX3. However, only 8.9% of ZBTB16-occupied loci are co-occupied by RHOX10 (Extended Data Fig. 10a). As expected, RHOX10-occupied gene promoters align with the active chromatin marks H3K4me3 and H3K27ac and exclude H3K27me3, implying a role at active genes (Extended Data Fig. 10b,c). Functional analysis (RNA-seq) of Zbtb16 and Rhox10 mutant uSPG revealed only 134 commonly regulated genes (Extended Data Fig. 10d). Among these, only three genes emerged as direct cotargets (Extended Data Fig. 10e). Interestingly, genes indirectly affected by RHOX10 displayed anticorrelation with ZBTB16’s direct target genes, particularly for cell migration genes such as Zeb2 (Extended Data Fig. 10f). Collectively, these results highlight an example of a TF, RHOX10, that binds and activates only a minor subset of the targets within the ZBTB16–SALL4–SOX3 network and specifically impacts cell migration targets in uSPG.

RNAPol2 and TATA-binding protein (TBP) at typical promoters persist in spermatogenesis

Recent interesting work reported the presence of RNAPol2 at meiotic genes in uSPG, even before their peak expression during meiosis²¹, suggesting that paused RNAPol2 primes meiotic genes for rapid activation. To investigate whether this pausing of RNAPol2 is specific to typical promoters or also occurs at atypical promoters, we conducted a series of ChIP-seq experiments focusing on TBP, RNAPol2 and its active forms, marked by C-terminal domain (CTD) Ser5 phosphorylation (transcription initiation) and Ser2 phosphorylation (transcription elongation). These experiments were dovetailed with recent precision run-on sequencing (PRO-seq) data from uSPG, spermatocytes and RSs²¹.

Our ChIP-seq analysis using juvenile testis revealed that both TBP and RNAPol2 consistently occupied typical gene promoters across all stages of spermatogenesis but were notably absent from atypical gene promoters (Fig. 6a). This finding indicates that the transcriptional machinery for meiotic gene expression is poised during the SPG stage and resides within an open and active or poised chromatin landscape. Interestingly, the small number of typical promoters (consisting of genes that are not germline specific) that are active during spermiogenesis are also poised in uSPG.

**Fig. 6: Differential occupancy of RNAPol2 and higher-order chromatin interactions at typical and atypical promoters during spermatogenesis.**

Additionally, we observed that RNAPol2, marked by Ser5 or Ser2 phosphorylation, occupied the promoters of meiotic genes in SPG. The presence of both phosphorylated forms indicates that RNAPol2 was actively engaged in both the initiation and the elongation phases of transcription at these promoters (Fig. 6a). We note that meiotic genes were expressed at low levels in SPG and then highly expressed during meiosis, indicating that RNAPol2 was prerecruited and primed for elevated expression levels specifically during the meiotic phase. This strategic readiness ensures transcriptional machinery preassembly, allowing for rapid and robust activation of critical meiotic genes when the appropriate developmental signals are received.

Strikingly, our analysis of recent PRO-seq data²¹ revealed a nearly complete overlap (86.9% overlap) with typical promoters and no notable overlap (1.1%) with atypical promoters (Fig. 6b). This overlap suggests a specific regulatory strategy where RNAPol2 pausing is linked to the chromatin categorization of promoters. Intriguingly, RNAPol2 remained associated with mitotic and meiotic genes even after these genes were silenced during spermiogenesis, strongly suggesting a mechanism for reimposing pausing at these promoters. In contrast, RNAPol2 ChIP-seq analysis using adult testis⁵³, combined with the PRO-seq data²¹, revealed that atypical genes recruit RNAPol2 in tandem with active transcription during meiosis and especially spermiogenesis, most notably within clusters 6 and 7 (Fig. 6a,b).

Extensive chromatin interactions among typical promoters

To investigate whether the shared TF-active chromatin network revealed above forms a physical higher-order chromatin network in uSPG, we used Hi-C to examine promoter–promoter (P–P) interactions across spermatogenesis. Remarkably, in uSPG, typical promoters, including those with peak expression in meiosis, displayed robust physical interaction with other nearby typical promoters (within ~20 kb), whereas atypical promoters lacked such P–P interactions. Interestingly, in meiotic cells, the interactions involving mitotic gene typical promotors were reduced while the interactions involving typical meiotic and (rarer) spermiogenic promoters remained robust (Fig. 6c).

Furthermore, in uSPG, we found that 56% of CCCTC-binding factor (CTCF)-bound promoters were typical promoters, whereas only 2.9% of CTCF-bound promoters were atypical, mirroring the pattern observed in PSs (Fig. 6d). Thus, these Hi-C results reveal the establishment of a higher-order physically interacting network involving typical promoters in uSPG, which persists at meiotic genes during meiosis but diminishes at mitotic genes as they are silenced and acquire H3K27me3.

Taken together, in uSPG, ZBTB16, SOX3 and SALL4 (and often CTCF) co-occupy >15,000 promoter and enhancer locations that lack DNAme, bear active histone modifications, exhibit open chromatin and (for meiotic genes) contain paused RNAPol2. These factors interact in a higher-order three-dimensional (3D) network that is largely maintained through spermatogenesis. This contrasts with the majority of genes activated in spermiogenesis, which lack these TFs, are marked by DNAme, lack 3D interactions, and recruit RNAPol2 only at the time of expression (Fig. 6e).

Discussion

Our work started with an in-depth examination in the testis of the uSPG-specific TF ZBTB16 and its relationships to other uSPG-specific TFs and chromatin. Our findings indicate that ZBTB16 exerts multifaced roles in different uSPG processes (Fig. 7a). We then broadened the work, which led to the unexpected finding that a set of TFs participates in a higher-order 3D chromatin network in uSPG to presumably poise the subsequent meiotic program, which is separate from the mechanisms and factors that appear to promote the majority of the spermiogenesis program (Fig. 7b).

**Fig. 7: Transcriptional and chromatin regulation during spermatogenesis.**

First, we addressed roles for ZBTB16 in uSPG development, showing that early uSPG maintain a slow cell cycle through high ZBTB16, impeding G₁–S progression (Fig. 7a). This aligns with the accumulation of S-phase eomesodermin-positive early uSPG in Zbtb16-null mice¹¹ and conceptually resembles myeloid cells, where Zbtb16 overexpression decelerates G₁–S progression by suppressing Ccna2 (refs. ^54,55). Notably, the number CCND1⁺ uSPG and dSPG significantly decreased after P14 in Zbtb16-null mice¹⁰, which corresponds with the reduction in testis size observed from P14 onward (Fig. 3d,e and Extended Data Fig. 8d,e). This may partly underlie ZBTB16’s putative role in supporting long-term uSPG maintenance^7,10,11. Although the exact mechanism remains unknown, ZBTB16’s regulation of the cell cycle does not seem to involve S-phase cyclins (Extended Data Fig. 8b). Instead, GDNF drives cyclic expression of CCND2 to trigger early uSPG self-renewal^36,37,40,56 (Fig. 7a). However, for late uSPG, we established that ZBTB16 activates Ccnd1, which leads to the U–DT (Fig. 7a).

Cdk4 promotes early uSPG self-renewal^39,57 and functions in late uSPG, dSPG and spermatocytes. uSPG self-renewal involves cell-cycle progression driven by GDNF and CCND2 (refs. ^36,37,40,56). However, late uSPG use CCND1, driven in part by ZBTB16, to promote cell-cycle progression. Thus, both early and late uSPG deploy pCDK4 but use distinct CCND–CDK4 complexes to guide uSPG progression and both rely on ZBTB16 for effective regulation of CCND1 (Fig. 7a). Overall, murine ZBTB16 appears to finetune uSPG long-term maintenance by balancing self-renewal and progenitor progression. In keeping with reduced testicular size in Zbtb16-null mice, a prepubertal case with a ZBTB16 mutation likewise exhibited reduced testicular size⁵⁸, hinting toward conservation of roles in humans. Furthermore, our work comparing uSPG to PC-uSPG indicates that ZBTB16 exerts roles in supporting MS cells, reinforcing uSPG identity and preventing conversion to an ES cell-like pluripotent state in vitro.

Next, our work provided several lines of evidence supporting an extensive higher-order and interacting network involving TFs and active chromatin in uSPG that encompasses the majority of the uSPG transcriptional program and poises the SPG differentiation and meiosis programs (Fig. 7b). This network involves over 12,000 promoters expressed in germ cells during spermatogenesis and a plethora of meiotic SEs (Extended Data Fig. 9k), which are co-occupied by ZBTB16, SALL4 and SOX3 and bear high and broad H3K4me3 and DNA hypomethylation in uSPG (Fig. 7b). These results may also provide a mechanistic underpinning for the recent observation of paused RNAPol2 at meiotic gene promoters in uSPG²¹. Notably, this co-occupancy and poised chromatin status distinguishes typical (co-occupied) from atypical promoters (unoccupied and DNA methylated), which instead drive most genes during spermiogenesis and recruit RNAPol2 commensurate with transcription. Our Hi-C data reinforce this notion, underscoring a higher-order physical principle aligned with our promoter classifications; typical promoters display robust physical interactions within uSPG, whereas atypical promoters lack such interactions (Fig. 7b). This finding is consistent with the observation that CTCF binding prefers regions with low DNAme^{59,60,61,62,63,64}, which may contribute to the establishment of open chromatin and facilitate promoter interactions. Regarding dynamics, meiotic promoter interactions were maintained during meiotic activation, whereas mitotic promoters were reduced, correlated with their silencing during meiosis. Thus, these extensive higher-order interactions appear to be established in uSPG and to be notably decommissioned as transcription is silenced (clusters 1 and 2; Fig. 6d).

A major question is why spermatogenesis might use such an extensive TF–chromatin physical poising network. Here, we note that cytoplasmic bridges connect male germ cells during spermatogenesis, which enables the sharing of contents, including TFs⁶⁵. This may enable synchronization of the expression of new TFs (stage-specific activators, SSAs; Fig. 7b), which then conduct synchronous activation of the promoters that contain their binding sites, which already reside in poised or open chromatin across the interconnected cells, promoting orderly entry into and progression through the stages of meiosis. Here, we speculate that particular SSAs activate particular subsets of the typical network in SPG differentiation (for example, RHOX10, spermatogenesis and oogenesis specific basic helix–loop–helix 1 and 2 (SOHLH1/2), NEUROG3 and doublesex and mab-3 related TF 1 (DMRT1)) and during meiotic phases (for example, stimulated by retinoic acid 8 (STRA8), cMyb and TF-like 5 (TCFL5)), whereas a largely separate set of SSAs (for example, regulatory factor X2 (RFX2), cyclic adenosine-monophosphate-responsive element modulator (CREM) and activator of CREM (ACT)) activates atypical promoters to execute stages of spermiogenesis (Fig. 7b).

Additional future work would likely focus on determining whether these extensive interactions between typical promoters represent chromatin loops that reside in condensates or hubs that coalesce locally-interacting typical promoters. Notably, this chromatin poising relationship bears some resemblance to the poising logic observed in the pluripotency network of ES cells^{66,67,68,69,70}, which involves hundreds of developmental genes, although the uSPG network revealed here is much larger. In counter distinction, atypical promoters are not occupied by this network and involve genes specific to male germline and spermatogenesis, including the global histone–protamine exchange (for example, Tnp1 and Prm1) during spermiogenesis (third phase in Fig. 7b).

Regarding transcriptional specificity, we found that loss of one factor (Zbtb16, Sall4 or Sox3) impacts only a small subset of the ~16,000 genes occupied by the network, consistent with partial redundancy among these factors, possibly buffered by the higher-order chromatin interaction network and the likely involvement of additional TFs contributing to the network, which were not highlighted in this study. This redundancy for poising is supported by our observation that omission of ZBTB16 only minimally impinges on the binding of SALL4 or SOX3 at network targets in uSPG. Thus, an important issue for future work is to determine whether additional TFs localize to and help define the chromatin state of the entire network versus those that specifically occupy and regulate a smaller subset of the network (for example, RHOX10). Such endeavors would inform both redundancy and specificity within the network. Here, we hypothesize that SSAs stimulate transcription on an already poised or active promoter chromatin landscape at typical promoters during meiosis, while a separate set of SSAs (which can bind methylated DNA) then activate DNA-methylated atypical promoters during spermiogenesis (Fig. 7b). Further studies would need to be directed at understanding the establishment of this TF and higher-order chromatin network in uSPG and its dynamic changes during spermatogenesis.

Methods

Mouse husbandry and genotyping

The mice used in this study were derived from the C57BL/6J (B6) background obtained from Jackson Laboratory (RRID:IMSR_JAX:000664). Zbtb16 (luxoid) mice, described previously⁷, were also procured from Jackson Laboratory (RRID:IMSR_JAX:000100). Genotyping of Zbtb16-null mice was performed using the TaqMan single-nucleotide polymorphism genotyping assay (Thermo Fisher Scientific, 4332075, clone ID: AH7042A) after assessment of the mice for the presence of hind limb defects. Homozygous Zbtb16-deficient (Zbtb16^lu/lu) mice were compared to WT (Zbtb16^+/+) and heterozygous (Zbtb16^+/lu) littermates in all experiments.

Sox3-floxed mice (B6) were previously generated⁷². Ddx4/Vasa–Cre⁷³ (B6, RRID:IMSR_JAX:018980) was purchased from Jackson Laboratory. Sox3-cKO mice (B6), specifically targeting male germ cells, were generated using Ddx4–Cre mice and the cKO mice were genotyped as described previously⁷². All mice were housed in a pathogen-free animal facility and provided with a standard rodent chow diet. The housing facility maintained a controlled temperature (20–25 °C), a 12-h light–dark cycle and a relative humidity of 30–70% to support the mice’s circadian rhythm. The study was conducted in accordance with approved animal use protocols (no. 18-03004 and 00001726) by the Institutional Animal Care and Use Committee at the University of Utah and the National Institutes of Health Guide for the Care and Use of Laboratory Animals.

Protein extracts and immunoblot

Mouse testes were homogenized in lysis buffer containing 20 mM Tris-HCl pH 8.0, 150 mM NaCl, 2 mM EDTA pH 8.0 and 1% Nonidet-P40 (NP-40) with proteinase inhibitors. After centrifugation, the supernatants were diluted with sample buffer and boiled. Then, 100 μg of total proteins per lane were separated on a 10% SDS–PAGE and subsequently transferred to PVDF membranes (GE Healthcare, RPN303F). For immunoblotting, primary antibodies were diluted in 5% nonfat dried milk in 0.1% Tween-20 TBS and incubated overnight at 4 °C. The primary antibodies used for immunoblotting were anti-rabbit ZBTB16 (Santa Cruz, sc-11146; 1:400) and anti-goat ZBTB16 (Santa Cruz, sc-22839; 1:100). After washing, membranes were probed with horseradish peroxidase-conjugated goat anti-rabbit IgG (Bio-Rad, 1706515; 1:10,000) and bovine anti-goat IgG (Santa Cruz, sc-2350; 1:5,000) secondary antibodies.

RNA-seq sample preparation and analysis

Testes from three mice in Zbtb16-null and Sox3-cKO conditions, along with their respective WT littermates, were pooled for each cell isolation experiment. Single cells were isolated from testes at P7 using 0.25% trypsin digestion and resuspended in MACS separation buffer (Miltenyi Biotec, 130-091-221). The harvested cells were used to purify uSPG and dSPG through IMCS. This was achieved using anti-THY1/CD90.2 (Miltenyi Biotec, 130-049-101; 1:10) and anti-KIT/CD117 (Miltenyi Biotec, 130-091-224; 1:5) antibodies conjugated with magnetic microbeads, following previously described protocols^1,22. The purified cells were lysed in TRIzol and RNA was subsequently isolated and purified using a Direct-zol RNA mini-prep kit (Zymo Research, R2061), which included DNase I treatment to remove genomic DNA.

To assess the RNA integrity, high-sensitivity R6K Screen Tapes were used with a 2200 TapeStation instrument (Agilent Technologies, G2991AA) and the RNA integrity number equivalent values were confirmed to be at least 8.1. RNA libraries were prepared using the Illumina TruSeq stranded RNA kit with Ribo-Zero gold for the mouse, which facilitated the removal of ribosomal RNA (New England Biolabs). The library sequencing was performed on an Illumina 2000/2500 platform and each library sequenced up to 74 million fragments using HiSeq 50-cycle single-read sequencing version 4.

The RNA-seq reads from each library were processed and aligned to the Ensembl annotation NCBI38/mm10 using Novoalign (version 4.04.01, http://novocraft.com). Adaptor sequences were trimmed using the following parameters: -o SAM -r all 50 -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA. Processed reads were used to generate FPKM (fragments per kilobase of transcript per million mapped reads) values. The analysis of differential gene expression was performed using the default parameters with the addition of -x 50000000 using USeq8.9.6 packages that included DESeq2 (version 1.42.1)^74,75. Significantly affected genes were defined as those with an adjusted P value ≤ 0.05 and a 1.5-fold absolute change. Adjusted P values were calculated using the Benjamini–Hochberg method to account for multiple comparisons. The volcano plot was generated with these thresholds to highlight significant upregulated and downregulated genes. Published RNA-seq datasets were retrieved from the National Center for Biotechnology Information Gene Expression Omnibus (GEO) and Sequence Read Archive (SRA) using GNU Wget and SRA Toolkit (version 2.10.8) with the fasterq-dump utility for sequence extraction. For consistency and comparability, all datasets were aligned to the mm10 mouse genome using uniform alignment criteria. The following datasets were used: GSE78127 for PC-uSPG, MASCs, ES cells and HSCs; GSE49624 for PSs; SRA097278 for E13.5 male PGC.

ChIP-seq

ChIP-seq experiments were performed following a previously established protocol¹⁹ with some modifications. For TF ChIP-seq, seminiferous tubules were isolated from three mice at P7–P8, after removing the tunica albuginea. For histone modification ChIP-seq, THY1⁺ uSPG were purified from a total of seventy mice, following the same procedure as described in the RNA-seq sample preparation section. The isolated tissues or THY1⁺ uSPG were crosslinked using 1% formaldehyde–PBS for 10 min at room temperature (RT) and then quenched with glycine (final concentration of 0.125 M) for 5 min. The crosslinked tissues and cells were washed twice with PBS and then frozen using liquid nitrogen. Subsequently, they were homogenized with 15 strokes using a KIMBLE Dounce tissue grinder (Millipore Sigma, D8938) with 10 ml of SDS buffer (100 mM NaCl, 50 mM Tris-Cl pH 8.0, 5 mM EDTA, 10% SDS and protease inhibitor cocktail tablet (Millipore Sigma, 4693159001)). The homogenized samples were transferred to 15-ml tubes and lysed at RT for 10 min. The lysates were then centrifuged at 2,400g at 4 °C for 5 min to collect the nuclei, which were subsequently resuspended in IP buffer (100 mM NaCl, 66.6 mM Tris-Cl pH 8.0, 5 mM EDTA, 6.6% SDS, 1.3% Triton X-100 and protease inhibitor cocktail tablet). The nuclear extracts were sheared using a Branson sonifier, with 0.9 s on and 0.1 s off for seven cycles, resulting in an average fragment size of 300–700 bp. The sheared chromatin was then centrifuged at 18,000g at 4 °C for 10 min and the supernatant was subjected to immunoclearing by incubating with 20 μl of Dynabeads Protein A/G (Thermo Fisher Scientific, 10002D and 10004D) at 4 °C for 30 min. After immunoclearance, 2 mg of the sheared chromatin was incubated with the specific antibodies, including rabbit anti-ZBTB16 (Santa Cruz, sc-22839, 5 µg (25 µl)), goat anti-ZBTB16 (Santa Cruz, sc-11146, 5 µg (25 µl)), rabbit anti-SALL4 (Abcam, ab29112, 5 µg), mouse anti-SOX3 (Santa Cruz, sc-101155, 2.5 µg (25 µl)), mouse anti-TBP (EMD Millipore, MAB3658, 1 µl), pan-RNAPol2 (Active motif, 39097, 0.2 µg (1 µl)), RNAPol2 CTD Ser5 (Active Motif, 39233, 5 µg (5 µl)), RNAPol2 CTD Ser2 (Active motif, 61083, 5 µg (5 µl)), H3K4me3 (Active Motif, 39159, 3 µl), H3K9me3 (Active Motif, 39161, 5 µl) and H3K27me3 (EMD Millipore, 07-449, 5 µl), at 4 °C overnight. To precipitate antibody-bound protein–DNA complexes, 50 μl of Dynabeads protein A/G were used and the incubation lasted for 4 h at 4 °C. The beads were then washed as follows: two times with mixed micelle buffer (150 mM NaCl, 20 mM Tris-Cl pH 8.0, 5 mM EDTA, 34% sucrose (w/v), 0.5% Triton X-100 and 0.2% SDS), two times with buffer 500 (500 mM NaCl, 50 mM HEPES pH 7.5, 1 mM EDTA, 0.1% deoxycholic acid and 1% Triton X-100), two times with LiCl detergent solution (250 mM LiCl, 10 mM Tris-Cl pH 8.0, 1 mM EDTA, 0.5% deoxycholic acid and 0.5% NP-40) and one time with Tris–EDTA buffer (10 mM Tris-Cl pH 7.4 and 1 mM EDTA). The washed beads and input were resuspended in 130 μl of ChIP elution buffer (1% SDS, 0.1 M NaHCO₃) and subjected to overnight incubation at 65 °C with 900 rpm using a thermomixer to reverse-crosslink, including RNase and proteinase digestions. The DNA was purified using the MinElute PCR purification kit (Qiagen, 28006).

To identify TF-binding motifs, ChIP-nexus was conducted, following established procedures³². Briefly, the ChIP-exo treatment process, involving lambda exonuclease, was incorporated into the standard ChIP-seq protocol.

For ChIP-seq library preparation, we used the NEBNext ChIP-Seq library prep master mix set (New England Biolabs, E6240L) and the NEBNext Ultra II DNA library prep kit (E7634L). Library sequencing was performed on an Illumina 2000/2500 platform, with up to 33 million fragments for ZBTB16, SALL4, SOX3, H3K4me3, H3K9me3 and H3K27me3 using HiSeq 50-cycle single-read sequencing version 4. Additionally, TBP, RNAPol2, RNAPol2 CTD Ser5 and RNAPol2 CTD Ser2 libraries were sequenced was performed on a NovaSeq X platform, using 150-bp paired-read sequencing.

ChIP-seq peak calling, replicate handing and peak annotation

For ChIP-seq data analysis, the reads were aligned to the mouse reference genome (mm10) using Novoalign (version 4.04.01, https://novocraft.com) with the following parameters: -o SAM -r random -H -a AGATCGGAAGAGCACACGTCTGAACTCCAGTCA, which includes adaptor sequence removal. To ensure fair comparison across all datasets, PCR duplicates and all unmapped reads were removed using Picard MarkDuplicates (version 2.7.1; https://broadinstitute.github.io/picard/) and SAMtools⁷⁶.

Peak calling was performed using USeq8.9.6 packages and MACS (2.1.1) with default parameters^74,77. Peaks with a −10log₁₀(q value) adjusted by false discovery rate (qValFDR) greater than 30 (q < 0.001) for USeq and 20 (q < 0.01) for MACS were considered for downstream analyses. Replicate handing was modified on the basis of a previous approach⁷⁸. Briefly, only peaks from the merged files of two or three replicates overlapped with at least 50% of peaks from the union of biological replicates. This was achieved using BEDTools intersect with parameters -u -f 0.5. Moreover, genomic regions blacklisted in mice were removed from the peaks using BEDTools intersect with the parameter -v (refs. ^79,80).

To annotate the peaks, ChIPseeker (version 1.38.0)⁸¹ was used with the RefSeq gene list for genome version mm10. For ZBTB16, SALL4, SOX3, TBP and RNAPol2, promoters were defined as ±2 kb from the transcription start site (TSS); for histone modification, promoters were defined as ±1 kb from the TSS. Additionally, annotated genes that were excluded from the merged replicates but overlapped with at least two biological replicates were included and bidirectional promoter genes were manually added using BEDTools. The raw ChIP-seq data and relative negative controls from previous publications were obtained and reprocessed using the same criteria. The data sources were as follows: GSE33024, GSE49624, GSE50807, GSE55060, GSE57186, GSE73390, GSE78129, GSE79230, GSE89502, GSE124190, GSE125168, GSE130652, GSE146706 and GSE165372.

Functional classification and pathway analyses

To discern functional insights from the data, we used PANTHER (version 17.0) for GO and pathway analysis, using a statistical overrepresentation test with the default settings⁸². A corrected P-value threshold of <0.05 was applied to establish statistically significant correlations.

piRNAs, CpG islands, DNAme, ATAC-seq and retrotransposons

Mouse piRNA coordinates⁸³ were converted from mm9 to mm10 using the LiftOver tool available on the UCSC genome browser (http://genome.ucsc.edu/cgi-bin/hgLiftOver). The CpG island database was sourced from the UCSC Genome Browser⁸⁴. DNAme data for THY1⁺ uSPG, KIT⁺ dSPG, PSs, RSs and mature sperm were reprocessed for genome version mm10, extracted from GSE49624 (ref. ¹⁹) and GSE62355 (ref. ¹) and processed following a previously described procedure¹. Similarly, ATAC-seq data were reprocessed for genome version mm10, obtained from GSE79230 and GSE102954, using established protocols²³. For the analysis of retrotransposons, mm10 rmsk data were retrieved from the USCS Table Browser (https://genome.ucsc.edu/cgi-bin/hgTables).

Heat map visualizations, graphs and plots

Heat maps and box-and-whisker plots for RNA-seq data were generated using R (version 4.3.2) packages, including ggplot2 (version 3.5.1) and pheatmap (version 1.0.12). Genome browser visualization was prepared using normalized ChIP signals, which were first adjusted to their corresponding inputs using USeq after peak calling⁷⁴. Genome browser snapshots were captured using the Integrative Genomics Viewer browser (version 2.16.2)⁸⁵. For further ChIP-seq data analysis, the deepTools suite was used. The bamCompare module was used to normalize ChIP signals against their input. Heat maps and clustering were generated using the computeMatrix and plotHeatmap modules, using a reference point and scale regions. Spearman correlation between ChIP-seq samples was computed using the plotCorrelation module⁸⁶. For the area-proportional Venn diagram, the BxToolBox (http://apps.bioinforx.com/bxaf7c/app/venn/app_overlap.php) was used, with statistical significances assessed using a hypergeometric test (http://nemates.org/MA/progs/overlap_stats.html).

Statistics and reproducibility

Statistical analyses were conducted to ensure data robustness and reproducibility. For box-and-whisker plots and line graphs, statistical significance was determined using a two-sided Wilcoxon rank-sum test. Exact P values are reported in the figure legends and n values (sample sizes) are explicitly defined for each dataset. Data distribution was assessed using the Shapiro–Wilk normality test.

All data are presented as either the mean ± s.d. or median with interquartile range (IQR), as specified in the legends. Box plots illustrate the minima, maxima, center (median), bounds (first and third quartiles) and whiskers (1.5× the IQR). Individual data points are overlaid for visualization of data distribution and clarity.

Experiments were independently repeated and biological replicates are explicitly stated in the figure legends. Representative images and data reflect consistent outcomes across experiments.

DNA-binding motif analysis

Analysis of DNA-binding motifs was conducted using the GEM (version 2.6) and MEME suite 5.1.1 programs^30,31. For GEM, both ChIP and input SAM files were used to analyze the DNA-binding motifs, applying the default parameters –f SAM –k_min 6 –k_max 13. A fragment size of 100 bp was selected from the summits within all peaks, top 500 peaks and gene promoter regions derived from genes either downregulated or upregulated in Zbtb16-null cells, as identified using MACS2. For further motif analysis, all known motifs were investigated through MEME-ChIP using the HOCOMOCO Mouse (version 11 FULL) motif database. The regions encompassing binding motifs were scanned using Find Individual Motif Occurrences.

Flow cytometry analysis

To perform flow cytometry analysis, single cells were isolated from testes at P7 and resuspended in MACS separation buffer (Miltenyi Biotec, 130-091-221), following the procedure outlined for RNA-seq sample preparation. The collected cells were subsequently stained with anti-THY1/CD90.2–PE–Cy7 (Thermo Fisher Scientific, 25-0902-81; 0.06 µg per test) and anti-KIT/CD117–PE (Thermo Fisher Scientific, 12-1171-81; 0.125 μg per test) antibodies, according to the manufacturer’s instructions, for a duration of 15 min at 4 °C. Following this, the cells were fixed in a solution of 4% formaldehyde–PBS for 20 min on ice. After appropriate washes, the cells were subjected to staining with DAPI solution (0.1% Triton X-100 and 10 μg ml⁻¹ of DAPI in PBS) and incubated overnight at 4 °C. Subsequently, the samples were analyzed using fluorescence-activated cell sorting (FACS) with a FACS Canto Scan (Becton Dickinson) using FACSDiva (version 8.01, BD BioSciences). The acquired data were analyzed for cell population and cell cycle using the FlowJo software (version 9.9, BD BioSciences).

IF and whole-mount staining

For IF analysis, testes from both WT and Zbtb16-null mice were weighed and then fixed using 4% formaldehyde, incubated overnight at 4 °C. Following fixation, tissues were processed for paraffin embedding using standard procedures. The paraffinized testes were sectioned into 5-μm slices, followed by deparaffinization using CitriSolv (1601, Decon Labs). Subsequently, rehydration was performed through a graded ethanol series (2 × 100%, 2 × 95%, 1 × 80%, 1 × 70%) for 2 min each, followed by rinsing in 1× PBS.

To enable antigen retrieval, sections were subjected to boiling in 10 mM sodium citrate (pH 6.0) or Tris–EDTA buffer (pH 9.0) for 20 min and then allowed to cool for 20 min. Afterward, the sections were blocked for 1 h at RT using a blocking buffer containing 3% BSA and 5% normal donkey serum in PBS.

Primary antibodies specific to target proteins were diluted in the blocking buffer and added to the sections for overnight incubation at 4 °C. The following primary antibodies were used: rabbit anti-ADAMTS5 (Thermo Fisher Scientific, PA5-27165; 1:100 (10 µg ml⁻¹)), mouse anti-CCND1 (Santa Cruz Biotechnology, sc-8396; 1:50 (4 µg ml⁻¹)), rat anti-CCND2 (Santa Cruz Biotechnology, sc-452; 1:50 (4 µg ml⁻¹)), rabbit anti-pCDK4 (Thr172) (Thermo Fisher Scientific, 702556; 1:100 (5.0 µg ml⁻¹)), rabbit anti-pCDK6 (Thermo Fisher Scientific, PA537517; 1:100 (10.0 µg ml⁻¹)), rabbit anti-pH2AX (Cell Signaling, 9718; 1:400), goat anti-LIN28A (R&D systems, AF3757; 1:400), rabbit anti-SALL4 (Abcam, ab29112; 1:1,000 (1 µg ml⁻¹)), mouse anti-SOX3 (Santa Cruz, sc-101155; 1:100 (2 µg ml⁻¹)), mouse anti-SYCP3 (Abcam, ab97672; 1:200 (5.0 µg ml⁻¹)), mouse anti-SYCP3 (Santa Cruz Biotechnology, sc-74569; 1:400 (0.5 µg µl⁻¹)), mouse anti-UTF1 (EMD Millipore, MAB4337; 1:100 (10 µg ml⁻¹)), goat anti-ZBTB16 (Santa Cruz Biotechnology, sc-11146; 1:200 (1 µg ml⁻¹)) and rabbit anti-ZBTB16 (Santa Cruz, sc-22839; 1:100 (2 µg ml⁻¹)).

After washing the slides, the sections were then incubated for 1 h at RT with the fluorescent-conjugated secondary antibodies diluted in PBS. Following another wash, the sections were stained with DAPI (1:300 dilution) for 3 min at RT. Subsequently, ProLong gold antifade mountant with DAPI (Thermo Fisher Scientific, P36931) was applied to preserve the fluorescence.

In addition, whole-mount staining of seminiferous tubules was carried out following a previous described protocol⁸⁷. Briefly, seminiferous tubules were dissociated and fixed with 1% formaldehyde for 2 h at 4 °C. Primary antibodies, including goat anti-GATA4 (Santa Cruz, sc-1237; 1:200 (1 µg ml⁻¹)), mouse anti-SOX3 (Santa Cruz, sc-101155; 1:100 (2 µg ml⁻¹)) and rabbit anti-Versican V0, V1 Neo (Thermo Fisher Scientific, PA1-1748A 1:1,000 (2 µg ml⁻¹)), were diluted in the blocking buffer and incubated tubules. Like the previous steps, tubules were subjected to secondary antibody incubation, DAPI staining and mounting using ProLong gold antifade mountant with DAPI.

For visualization, Nikon A1R HF25 confocal and ECLIPSE Ti microscopes were used and the obtained images were using Nikon Elements AR software (www.microscope.healthcare.nikon.com). Quantification was conducted by evaluating a minimum of 100 circular tubule cross-sections per animal from at least three animals, using ImageJ software (version 1.53t)⁸⁸.

Hi-C: pile-up analysis and CTCF ChIP-seq

THY1⁺ and KIT⁺ SPG were purified as describe above. The BSA gravity sedimentation method^23,24 was used to isolate PSs and RSs from the testis of adult male C57BL/6 mice. Hi-C libraries were generated using the Arima Hi-C kit (A410079) and Accel-NGS 2S plus DNA library kit (21024) following the manufacturer’s instructions. Cells used 4 × 10⁵ to 1 × 10⁶ for THY1⁺ uSPG and KIT⁺ dSPG, 3 × 10⁶ for PSs and 4 × 10⁶ for RSs. Paired-end Hi-C libraries were sequenced on Illumina HiSeq4000 and processed with Juicer (version 1.5)⁸⁹ using BWA (version 0.7.3a)⁹⁰ for alignment with Mus musculus mm10. A .hic file, a highly compressed binary file, was created by Juicer Tools Pre. A .hic file was used to create a balanced cool file using cooler (version 0.8.11)⁹¹ that was used for pile-up analysis. Using coolup.py (version 0.9.5)⁹², we visualized the average interaction between TSS positions. For the pile-up analysis depicting interactions among TSS positions, each TSS position underwent analysis using cool files binned at a 10-kb resolution and a BED file displaying TSS positions, with an additional 100 kb of padding. The resulting piled-up data were visualized through plotup.py. CTCF ChIP-seq was performed in THY1⁺ uSPG and PSs using previously described methods⁵¹.

Reporting summary

Further information on research design is available in the Nature Portfolio Reporting Summary linked to this article.