Unraveling spermatogenesis: A single-cell genomics perspective.

Spermatogenesis is a highly coordinated male developmental process essential for passing on genetic information and fertility. The process features a series of complex cellular and genomic transitions. The main objective of this review is to provide a synthesis of changes single-cell genomics have brought to the male germline. This review begins with an account of the journey from rudimentary, low resolution, and throughput microarray technologies to the advanced and sophisticated, high throughput single-cell RNA sequencing (scRNA-seq) technologies that have provided the means for the generation of extensive and comprehensive "cell atlases" of the testis. The review focuses on the resolution of long-standing controversies associated with the spermatogonial stem cells (SSCs) niche regarding continuum of germ cell differentiation, and germ cell differentiation and stem cell specification. The frontiers of single-cell based DNA techniques such as Single-Cell Assay for Transposase-Accessible Chromatin using sequencing (scATAC-seq) and single-cell DNA methylation will then be discussed. We focus on the perinatal period crucial for the epigenetic priming of the foundational stem cell pool and chromatin remodeling that facilitates the histone-to-protamine transition. The regenerative capacity of the germline and the single-cell identified subsets and metabolic gates that are capable of restoring the ability to conceive post-injury tissues are also explored. Finally, we will go over the prospective views on the use of multi-omics and new spatial transcriptomics. These tools not only provide molecular components of interest within the cells, but also the cellular constituents of the seminiferous tubule and their spatial location within the tubule. This novel information will help translate the molecular discovery into potential clinical applications for male infertility treatment.