Single-cell multi-omics sequencing reveals the epigenomic landscapes in human spermatogenesis [CUT&Tag]. Single-cell multi-omics sequencing reveals the epigenomic landscapes in human spermatogenesis [CUT&Tag]

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. Overall design: To evaluate if DNA demethylation could affect the binding of PRDM9, the binding sites of PRDM9 were examined in HEK293T cells with DNA methylation inhibitor (Decitabine) treatment followed by transfection of hPRDM9-Flag. Submitters declare that raw data related to human is submitted to the National Genomics Data Center, China National Center for Bioinformation (CNCB-NGDC) due to the Regulations of the People's Republic of China on the Management of Human Genetic Resources. *** All the raw fastq data have been uploaded to GSA for Human as access controlled data under accession HRA004922: https://ngdc.cncb.ac.cn/gsa-human/browse/HRA004922