FOXP2 regulates differential transcriptional programs in human subplate

Mammalian brains are highly conserved at both the neuroanatomical and gene expression levels. However, the subplate is a neocortical subregion distinguished by a markedly different developmental trajectory among primates compared to other mammals. Moreover, the molecular mechanisms driving these species differences in subplate development remain mostly unknown. Here, we show that human FOXP2, a transcription factor important for speech and language, regulates gene expression programs consistent with subplate neuron expression patterns. These transcriptional profiles have unique overlaps with in vivo data from human fetal brain. We also distinguish DNA-dependent and DNA-independent mechanisms for human FOXP2 to repress patterns of germinal zone expression and promote excitatory neuron gene expression patterns. We carried out two RNA-sequencing (RNA-seq) experiments and one ATAC-sequencing (ATAC-seq) experiment in proliferating (hNP) and differentiated (hDN) human neural progenitor cells. For the first RNA-seq, four independent replicates of control and FOXP2-WT over-expressing samples were sequenced in hNPs and hDNs. Three replicates were used in the analysis. For the second RNA-seq three independent replicates of control, FOXP2-WT over-expressing, and FOXP2-KE over-expressing samples were used. The ATAC-seq chromatin was collected in parallel with the second RNA-seq experiment. Four independent replicates of replicates of control, FOXP2-WT overexpressing, and FOXP2-KE overexpressing samples were used. ATAC-seq data and data from the second RNA-seq experiment are published here: DOI:https://doi.org/10.1016/j.celrep.2019.04.044.

哺乳动物大脑在神经解剖学与基因表达层面均具有高度保守性。然而，皮质下板（subplate）作为新皮层亚区，相较于其他哺乳动物，灵长类的该亚区发育轨迹存在显著差异。此外，驱动皮质下板发育出现物种差异的分子机制，目前尚未完全明确。本研究表明，参与言语与语言功能的人源转录因子FOXP2，可调控与皮质下板神经元表达模式相符的基因表达程序。这些转录谱与人类胎儿大脑的体内实验数据存在独特的重叠特征。本研究还阐明了人源FOXP2可通过DNA依赖与非DNA依赖两种机制，抑制生发区基因表达模式，并促进兴奋性神经元基因表达程序。本研究在增殖态（hNP）与分化态（hDN）人源神经前体细胞中，开展了两次RNA测序（RNA-seq）实验与一次转座酶可及性测序（ATAC-seq）实验。在首次RNA-seq实验中，我们对hNP与hDN中的对照组、FOXP2野生型（FOXP2-WT）过表达样本进行了测序，每组均包含4个独立生物学重复，最终分析中选用其中3个重复样本。第二次RNA-seq实验则采用了对照组、FOXP2-WT过表达组与FOXP2-KE过表达组的样本，每组均包含3个独立生物学重复。ATAC-seq的染色质样本与第二次RNA-seq实验同步采集。本次ATAC-seq实验采用了对照组、FOXP2-WT过表达组与FOXP2-KE过表达组的样本，每组均包含4个独立生物学重复。ATAC-seq数据与第二次RNA-seq实验数据已发表于：DOI:https://doi.org/10.1016/j.celrep.2019.04.044。