Single-Cell Multi-Omics Sequencing Reveals the Dynamic Epigenome Landscape of Human Adult Spermatogenesis

Stepwise and sequential cell fate transition accomplished by global transcriptional changes occurs across human spermatogenesis, but the epigenome roadmap and regulatory networks underlying this process have not been established. Here, we explore a single-cell multi-omics landscape of human adult testicular cells using the single-cell chromatin overall omic-scale landscape sequencing (scCOOL-seq) technique, deriving an unbiased multi-omics reference map of human adult spermatogenesis. The initial commitment to meiosis coincides with a novel dramatic DNA demethylation process in non-coding regions that highly overlapped with crossover and double strand break (DSB) hotspots. Chromatin accessibility mainly accounts for the global expression dynamics in human spermatogenesis. Further studies identify the cis- regulatory elements of several key regulators such as STRA8, ID3, HMGA1 and TEX29 in human spermatogenesis. Thus, our data characterize the regulatory networks orchestrating gene expression and chromatin configuration under the state of normal human spermatogenesis and its perturbation imposed by disease lesion, providing novel insights into the association of epigenome with germ cell development and male infertility. In total, we analyzed 1097 scCOOL-seq data of normal human adult testicular cells and 176 scCOOL-seq data of testicular cells from one nonobstructive azoospermia (NOA) donor. Samples 1-29 are RNA-seq data (UMI barcode RNA part), samples 30-1302 are scCOOL-seq data (DNA part). *** All the raw fastq data have been uploaded to GSA for Human as access controlled data under accession HRA000148 (https://bigd.big.ac.cn/gsa-human/browse/HRA000148).