Chromatin and Single-Cell RNA-Seq Profiling Reveal Dynamic Signaling and Metabolic Transitions during Human Spermatogonial Stem Cell Development.
Chromatin and Single-Cell RNA-Seq Profiling Reveal Dynamic Signaling and Metabolic Transitions during Human Spermatogonial Stem Cell Development.
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DOI：
10.1016/j.stem.2017.09.003
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发表时间：
2017-10-05
期刊：
影响因子：
23.9
通讯作者：
Cairns BR
中科院分区：
文献类型：
--
作者：
Guo J;Grow EJ;Yi C;Mlcochova H;Maher GJ;Lindskog C;Murphy PJ;Wike CL;Carrell DT;Goriely A;Hotaling JM;Cairns BR
人成体精原干细胞（hSSCs）必须平衡自我更新和分化。为了理解这是如何实现的，我们分析了SSEA4+ hSSCs中的DNA甲基化和开放染色质（ATAC-seq），分析了SSEA4+ hSSCs和分化的c-KIT+精原细胞中的大量和单细胞RNA转录组（RNA-seq），并通过免疫荧光进行了验证研究。首先，胚胎发育基因的DNA低甲基化支持其在hsc中用于未来/胚胎表达的表观遗传“定位”，而核心多能基因（OCT4和NANOG）在转录和表观遗传上受到抑制。有趣的是，hsc中的开放染色质在先锋因子（NFYA/B、DMRT1和激素受体）的结合位点上显著富集。值得注意的是，单细胞RNA-seq聚类分析确定了hSSC分化过程中的四种细胞/发育状态，包括细胞周期和转录调控因子、剪接和信号因子以及葡萄糖/线粒体调控因子的主要转变。总体而言，我们的研究结果概述了hsc中运行的动态染色质/转录景观，并确定了伴随从静止到增殖和分化转变的关键分子途径。人类精原干细胞的分化涉及四个连续的细胞/发育状态，关键的转变涉及细胞周期、转录因子、信号传导和代谢。Cairns和他的同事表明，人类精原干细胞（hSSCs）具有独特的DNA甲基化和开放的染色质景观，这可能促进适当的发育、生态位反应和“平衡”的多能性。有趣的是，单细胞转录组和免疫荧光分析揭示了四种细胞状态，从静止的hsc到增殖、代谢活跃、分化的精原细胞。
Human adult spermatogonial stem cells (hSSCs) must balance self-renewal and differentiation. To understand how this is achieved, we profiled DNA methylation and open chromatin (ATAC-seq) in SSEA4+ hSSCs, analyzed bulk and single-cell RNA transcriptomes (RNA-seq) in SSEA4+ hSSCs and differentiating c-KIT+ spermatogonia, and performed validation studies via immunofluorescence. First, DNA hypomethylation at embryonic developmental genes supports their epigenetic “poising” in hSSCs for future/embryonic expression, while core pluripotency genes (OCT4 and NANOG) were transcriptionally and epigenetically repressed. Interestingly, open chromatin in hSSCs was strikingly enriched in binding sites for pioneer factors (NFYA/B, DMRT1, and hormone receptors). Remarkably, single-cell RNA-seq clustering analysis identified four cellular/developmental states during hSSC differentiation, involving major transitions in cell-cycle and transcriptional regulators, splicing and signaling factors, and glucose/mitochondria regulators. Overall, our results outline the dynamic chromatin/transcription landscape operating in hSSCs and identify crucial molecular pathways that accompany the transition from quiescence to proliferation and differentiation. Open chromatin in hSSCs correlates with pioneer factors and hormone receptors hSSC differentiation involves four sequential cellular/developmental states Key transitions involve the cell cycle, transcription factors, signaling, and metabolism Cairns and colleagues show that human spermatogonial stem cells (hSSCs) bear unique DNA methylation and open chromatin landscapes, which may enable proper development, niche responsiveness, and “poised” pluripotency. Interestingly, single-cell transcriptome and immunofluorescence analyses reveal four cellular states, spanning from quiescent hSSCs to proliferating, metabolically active, differentiating spermatogonia.
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DOI：
10.1038/nrm3772
发表时间：
2014-04
期刊：
Nature reviews. Molecular cell biology
影响因子：
--
作者：
通讯作者：
--
影响因子：
64.5
作者：
Gkountela S;Zhang KX;Shafiq TA;Liao WW;Hargan-Calvopiña J;Chen PY;Clark AT
通讯作者：
Clark AT
影响因子：
23.9
作者：
Hara, Kenshiro;Nakagawa, Toshinori;Enomoto, Hideki;Suzuki, Mikiko;Yamamoto, Masayuki;Simons, Benjamin D.;Yoshida, Shosei
通讯作者：
Yoshida, Shosei
影响因子：
64.5
作者：
Gifford CA;Ziller MJ;Gu H;Trapnell C;Donaghey J;Tsankov A;Shalek AK;Kelley DR;Shishkin AA;Issner R;Zhang X;Coyne M;Fostel JL;Holmes L;Meldrim J;Guttman M;Epstein C;Park H;Kohlbacher O;Rinn J;Gnirke A;Lander ES;Bernstein BE;Meissner A
通讯作者：
Meissner A
人类原始生殖细胞的转录组和 DNA 甲基化组景观
影响因子：
64.5
作者：
Guo, Fan;Yan, Liying;Qiao, Jie
通讯作者：
Qiao, Jie