Time-series single-cell transcriptomics reveals pervasive daily rhythmicity and nocturnal spermatogenesis in the zebrafish testis

Jun 12, 2026Science advances

Daily gene activity patterns and nighttime sperm production in zebrafish testis revealed by single-cell analysis

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Abstract

The adult zebrafish testis exhibits robust oscillations in key circadian clock genes across various cell types.

Sertoli cells, spermatogonia, and spermatids show significant daily fluctuations in circadian clock gene expression.
Leydig cells and spermatocytes mainly display rhythmic expression of functional genes rather than circadian genes.
Daily rhythmic intercellular communication networks are present in the testis.
Germ cell progression demonstrates a distinct preference for activity at night.
Constant light exposure disrupts circadian rhythms, leading to reduced germ cell numbers and fertility issues.
Genetic modifications affecting circadian genes can significantly impair spermatogenesis and meiotic cell development.

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The vertebrate testis has long been regarded as lacking strong cellular daily rhythmicity. Here, we use time-series single-cell RNA sequencing to construct a temporal atlas of the adult zebrafish testis. We identify previously unknown cell-type-specific markers and previously unidentified testicular subtypes and reveal that Sertoli cells, spermatogonia, and spermatids exhibit robust oscillations in key circadian clock genes. In contrast, Leydig cells and spermatocytes primarily exhibit rhythmic expression of key functional genes. We show that intercellular communication networks also exhibit daily rhythmicity. Pseudotime trajectory analysis demonstrates a notable nocturnal preference for germ cell progression. Disrupting circadian input via constant light reduced germ cell numbers and impaired fertility. Genetic ablation ofarrests spermatogonial differentiation, whereas mutation of the rhythmic spermatocyte genesubstantially reduces meiotic cells. Together, our findings redefine the testis as a highly rhythmic organ in which a precisely timed, nocturnally coordinated cellular symphony drives spermatogenesis. clock1a hmgb1a

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Time-series single-cell transcriptomics reveals pervasive daily rhythmicity and nocturnal spermatogenesis in the zebrafish testis

Abstract

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