RNA-seq and ChIP-seq for human-specific regulation of neural maturation identified by cross-primate transcriptomics

Brain development is exceptionally delayed in humans compared to nonhuman primates (NHPs), a finding often termed neoteny. Signatures of neoteny, including a protracted proliferation of apical and basal progenitors as well as a delay in physiological activity of mature neurons, have been revealed in part through the use of induced pluripotent stem cell (iPSC) modeling of primate neurogenesis. IPSC modeling is particularly useful when examining the molecular drivers of a cellular phenotype such as gene transcription. It has long been proposed that phenotypic differences between closely related species may be driven, in part, by divergent transcriptional regulation rather than novel protein-coding sequence, however, how these regulatory mechanisms play a role in the protracted maturation process in human neurons remains largely unknown.Here we show that the transcription factor GATA3 directly regulates the rate of physiological maturity in human neurons. We modeled neurogenesis across 5 primate species consisting of 4 genera and 2 families and assessed the differences in transcriptional dynamics. We discovered that GATA3, a pioneer transcription factor, exhibited a unique up-regulation during human neurogenesis and was highly correlated with species-specific transcription. Strikingly, we also found that down-regulating GATA3 generated a gain-of-function, speeding up the rate of physiological maturity in human neurons. These findings indicate that the rate of physiological maturity in human neurons can be directly controlled by modulating a single, conserved transcription factor, providing evidence for the divergence of gene regulation as a major contributor to human neoteny.

相较于非人类灵长类（NHPs），人类大脑发育的延迟程度极为显著，这一现象通常被称为幼态延续（neoteny）。幼态延续的特征包括顶侧祖细胞与基侧祖细胞的增殖期延长，以及成熟神经元的生理活动延迟，这些特征部分通过灵长类神经发生的诱导多能干细胞（iPSC）模型得以揭示。诱导多能干细胞（iPSC）模型在探究细胞表型的分子驱动因素（如基因转录）时尤为实用。长期以来，学界提出，近缘物种间的表型差异部分可能由转录调控的分化而非新的蛋白质编码序列所驱动，但这类调控机制如何参与人类神经元的持续成熟过程，目前仍知之甚少。本研究中，我们证实转录因子GATA3可直接调控人类神经元的生理成熟速率。我们对涵盖4个属、2个科的5种灵长类的神经发生过程进行了建模，并评估了其转录动态差异。研究发现，作为先锋转录因子（pioneer transcription factor）的GATA3在人类神经发生过程中呈现独特的上调表达模式，且与物种特异性转录高度相关。令人意外的是，我们还发现下调GATA3可诱导功能获得性（gain-of-function）表型，加快人类神经元的生理成熟速率。上述研究结果表明，人类神经元的生理成熟速率可通过调控单个保守转录因子直接调控，为基因调控分化是人类幼态延续的主要驱动因素之一提供了直接实验证据。