Single-cell multi-omics sequencing reveals the epigenomic landscapes in human spermatogenesis [STRT-seq; scCOOL-seq]

Human spermatogenesis is a well-ordered dynamic process, which ensures the long-term production of functional spermatozoa; however, the roles of DNA methylation and chromatin accessibility in this process remain largely unknown. Here, by simultaneously investigating the chromatin accessibility, DNA methylome and transcriptome landscapes of human spermatogenesis using the modified single-cell chromatin overall omic-scale landscape sequencing approach (Modified scCOOL-seq), we revealed that the transcriptional changes throughout human spermatogenesis were correlated with the dynamic alternations of chromatin accessibility; particularly, several potential transcription factors and a set of regulatory elements involved in such process were identified. Remarkably, a round of DNA demethylation was uncovered upon meiosis initiation in human spermatogenesis, which was associated with male meiotic recombination and conserved between human and mouse. And aberrant DNA hypermethylation at recombination hotspots could be detected in leptotene spermatocytes of certain nonobstructive azoospermia patients. Functionally, the intervention of DNA demethylation affected male meiotic recombination. Collectively, this study provides multi-omics landscapes of human spermatogenesis at single-cell resolution, and offers insights into the association between DNA demethylation and male meiotic recombination. In total, we analyzed 1097 scCOOL-seq data of normal human adult testicular cells and 306 scCOOL-seq data of testicular cells from one nonobstructive azoospermia (NOA) donor. Samples 1-32 are RNA-seq data (RNA part), samples 33-1435 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)***