Single-cell ATAC-Seq reveals cell type-specific transcriptional regulation and unique chromatin accessibility in human spermatogenesis

Abstract

During human spermatogenesis, germ cells undergo dynamic changes in chromatin organization/re-packaging and in transcriptomes. In order to better understand the underlying mechanism(s), scATAC-Seq of 5376 testicular cells from 3 normal men were performed. Data were analyzed in parallel with the scRNA-Seq data of human testicular cells. In all, 10 germ cell types associated with spermatogenesis and 6 testicular somatic cell types were identified, along with 142 024 peaks located in promoter, genebody and CpG Island. We had examined chromatin accessibility of all chromosomes, with chromosomes 19 and 17 emerged as the leading chromosomes that displayed high chromatin accessibility. In accessible chromatin regions, transcription factor-binding sites were identified and specific motifs with high frequencies at different spermatogenesis stages were detected, including CTCF, BORIS, NFY, DMRT6, EN1, ISL1 and GLI3. Two most remarkable observations were noted. First, TLE3 was specifically expressed in differentiating spermatogonia. Second, PFN4 was found to be involved in actin cytoskeletal organization during meiosis. More important, unique regions upstream of PFN4 and TLE3 were shown to display high accessibility, illustrating their significance in supporting human spermatogenesis.

In Vivo Dissection of Chamber-Selective Enhancers Reveals Estrogen-Related Receptor as a Regulator of Ventricular Cardiomyocyte Identity

“…Cell type–specific chromatin accessibility is involved in determining and maintaining cellular identity. 17,32 We measured chromatin accessibility of purified neonatal aCMs and vCMs in biological duplicate by ATAC-seq. There was high correlation between the replicate samples (Figure S8A; Extended Data 1 and 3); 59 939 accessible regions were reproducible across the 2 chambers; 4060 were atrium specific and 12 970 were ventricle specific (Figure 3A).…”

Constitutive activation of CTNNB1 results in a loss of spermatogonial stem cell activity in mice

“…The role of engrailed 1 ( En1 , the most highly downregulated gene identified in our RNAseq analysis) in spermatogenesis has not yet been evaluated. However, a recent study showed that the EN1 motif is present at a high frequency in accessible regions of chromatin in human pachytene spermatocytes, but not in differentiating spermatogonia [ 62 ]. En1 regulation by CTNNB1 could therefore help reconcile the results of this study with the results obtained by Kumar et al [ 19 ], as stabilization of CTNNB1 would first antagonize SSC activity and promote entry of spermatogonia into meiosis, but would then block progression through later stages of meiosis by inhibiting En1 .…”

Editorial: Reproductive genomics

“…Recently, considerable efforts have been devoted to achieving better understanding of the molecular networks, regulatory programs, and germline-soma or soma-soma communications during gametogenesis and embryogenesis. In particular, the rapid advancement of highthroughput sequencing technologies and ultra-low-input (or even single-cell) omics approaches have accelerated novel discoveries in reproductive development e.g., (Wang et al, 2018;Qiao et al, 2020;Xu K. et al, 2021;He et al, 2021b;Tyser et al, 2021;Yan et al, 2021;Wu et al, 2022;Xiong et al, 2022). Towards this direction, Qian et al profiled the transcriptomes of 14,315 single testicular cells from adult zebrafish testes by single-cell RNA sequencing (scRNA-seq) using the 10x Genomics Chromium platform, identified ten distinguishable cell types with novelly revealed marker genes, and characterized interactions between somatic cells and germ cells through ligand-receptor analysis.…”

“…Recently, considerable efforts have been devoted to achieving better understanding of the molecular networks, regulatory programs, and germline-soma or soma-soma communications during gametogenesis and embryogenesis. In particular, the rapid advancement of high-throughput sequencing technologies and ultra-low-input (or even single-cell) omics approaches have accelerated novel discoveries in reproductive development e.g., ( Wang et al, 2018 ; Qiao et al, 2020 ; Xu K. et al, 2021 ; He et al, 2021b ; Tyser et al, 2021 ; Yan et al, 2021 ; Wu et al, 2022 ; Xiong et al, 2022 ). Towards this direction, Qian et al .…”