Single nucleus multi-omics regulatory atlas of the murine pituitary [scRNA-Seq]

The pituitary regulates growth, reproduction and other endocrine systems. To investigate transcriptional network epigenetic mechanisms in this gland, we generated paired single nucleus (sn) transcriptome and chromatin accessibility profiles in single mouse pituitaries, and genome-wide sn methylation datasets. Our analysis provided insight into cell type epigenetics, regulatory circuit and gene control mechanisms. Latent variable transcriptome and accessibility data representation resolved both inter-sexual and inter-individual variation in gene control programs. Multi-omics analysis of cell type-specific gene regulatory networks distinguished distinct mechanisms. Particularly, the FoxL2 gonadotrope network is controlled both by FoxL2 expression and by target gene epigenetic status. Co-accessibility analysis comprehensively identified putative regulatory regions, including a region that overlapped the fertility-linked rs11031006 human polymorphism. In vitro CRISPR-deletion at this locus increased Fshb levels, supporting this domain's predicted regulatory role. The public pituitary atlas [link] is a resource for elucidating cell-type specific gene regulatory mechanisms and principles of transcription circuit control. Single cell transcriptome profiling of adult mouse pituitaries by single cell GEM RNA-seq, using Illumina垂体（pituitary）调控生长、生殖及其他内分泌系统。为探究该腺体中转录网络的表观遗传机制，我们在单只小鼠垂体中生成了配对的单细胞核转录组（single nucleus transcriptome, sn）与染色质开放性图谱，以及全基因组单细胞核甲基化数据集。本研究的分析为细胞类型表观遗传学、调控回路及基因调控机制提供了重要见解。基于潜变量的转录组与染色质开放性数据表征，解析了基因调控程序中的性别间与个体间差异。针对细胞类型特异性基因调控网络的多组学分析，区分出了多种不同的调控机制。其中，FoxL2促性腺激素细胞网络同时受FoxL2自身表达水平与靶基因表观遗传状态的共同调控。共开放性分析全面鉴定出了潜在调控区域，其中包括一个与人类生育力相关的rs11031006多态性位点重叠的区域。在该位点开展体外CRISPR敲除实验可上调Fshb的表达水平，验证了该结构域的预测调控功能。公开可用的垂体图谱[链接]可作为解析细胞类型特异性基因调控机制与转录回路调控原则的重要资源。本研究采用Illumina平台的单细胞GEM RNA测序技术，完成了成年小鼠垂体的单细胞转录组谱型分析。