# A single-cell multiomics roadmap of zebrafish spermatogenesis reveals regulatory principles of male germline formation

## TL;DR

This study maps zebrafish spermatogenesis using multiomics data to reveal how chromatin and gene regulation change during sperm cell development.

## Contribution

The study provides a high-resolution single-cell multiomics atlas of zebrafish spermatogenesis, revealing regulatory dynamics and epigenetic inheritance mechanisms.

## Key findings

- Chromatin transitions from compact in early spermatogonia to accessible in spermatocytes, then condenses in spermatids.
- Zebrafish spermatogenesis lacks global DNA methylation reprogramming, unlike mammals, with only localized methylation changes.
- Unmethylated CpG-rich regions in elongated spermatids retain open chromatin, suggesting a role in intergenerational regulatory inheritance.

## Abstract

Spermatogenesis is the biological process by which male sperm cells (spermatozoa) are produced in the testes. Beyond facilitating the transmission of genetic information, spermatogenesis also provides a potential framework for inter- and transgenerational inheritance of gene-regulatory states. While extensively studied in mammals, our understanding of spermatogenesis in anamniotes remains limited. Here we present a comprehensive single-cell multiomics resource, combining single-cell RNA sequencing (scRNA-seq) and single-cell chromatin accessibility (scATAC-seq) profiling, with base-resolution DNA methylome (WGBS) analysis of sorted germ cell populations from zebrafish (Danio rerio) testes. We identify the major germ cell types involved in zebrafish spermatogenesis as well as key drivers associated with these transcriptional states. Moreover, we describe localised DNA methylation changes associated with spermatocyte populations, as well as local and global changes in chromatin accessibility leading to chromatin compaction in spermatids. Notably, we identify loci that evade global chromatin compaction, and which remain accessible, suggesting a potential mechanism for the intergenerational transmission of gene-regulatory states. In summary, this high-resolution atlas of zebrafish spermatogenesis provides a valuable resource for studying vertebrate germ cell development and epigenetic inheritance, while offering a robust framework for comparative analyses across diverse models of germ cell biology.

A multiomics study of zebrafish spermatogenesis integrating scRNA-seq, scATAC-seq, and base-resolution DNA methylomes defines the chromatin and transcriptional states of germ cells, revealing the regulatory dynamics of this continuous process.

Progressive transcriptional downregulation was observed during spermatogenesis, consistent with global chromatin condensation.Chromatin transitions from a more compact state in early spermatogonia to increased accessibility peaking in spermatocytes, followed by progressive condensation in spermatids.Unlike mammals, which undergo extensive genome-wide DNA methylation reprogramming during spermatogenesis, zebrafish show no such global reprogramming, with only localized methylation changes detected in spermatocytes.Unmethylated CpG-rich regions frequently retain open chromatin in elongated spermatids, supporting a potential role for these loci in maintaining regulatory information across generations.

Progressive transcriptional downregulation was observed during spermatogenesis, consistent with global chromatin condensation.

Chromatin transitions from a more compact state in early spermatogonia to increased accessibility peaking in spermatocytes, followed by progressive condensation in spermatids.

Unlike mammals, which undergo extensive genome-wide DNA methylation reprogramming during spermatogenesis, zebrafish show no such global reprogramming, with only localized methylation changes detected in spermatocytes.

Unmethylated CpG-rich regions frequently retain open chromatin in elongated spermatids, supporting a potential role for these loci in maintaining regulatory information across generations.

A multiomics study of zebrafish spermatogenesis integrating scRNA-seq, scATAC-seq, and base-resolution DNA methylomes defines the chromatin and transcriptional states of germ cells, revealing the regulatory dynamics of this continuous process.