Modern human changes in regulatory regions implicated in cortical development

Abstract

Background: Recent paleogenomic studies have highlighted a very small set of proteins carrying modern human-specific missense changes in comparison to our closest extinct relatives. Despite being frequently alluded to as highly relevant, species-specific differences in regulatory regions remain understudied. Here, we integrate data from paleogenomics, chromatin modification and physical interaction, and single-cell gene expression of neural progenitor cells to identify derived regulatory changes in the modern human lineage in comparison to Neanderthals/Denisovans. We report a set of genes whose enhancers and/or promoters harbor modern human single nucleotide changes and are active at early stages of cortical development.

Results: We identified 212 genes controlled by regulatory regions harboring modern human changes where Neanderthals/Denisovans carry the ancestral allele. These regulatory regions significantly overlap with putative modern human positively-selected regions and schizophrenia-related genetic loci. Among the 212 genes, we identified a substantial proportion of genes related to transcriptional regulation and, specifically, an enrichment for the SETD1A histone methyltransferase complex, known to regulate WNT signaling for the generation and proliferation of intermediate progenitor cells.

Conclusions: This study complements previous research focused on protein-coding changes distinguishing our species from Neanderthals/Denisovans and highlights chromatin regulation as a functional category so far overlooked in modern human evolution studies. We present a set of candidates that will help to illuminate the investigation of modern human-specific ontogenetic trajectories.

Keywords: Chromatin regulation; Modern humans; Neanderthals/Denisovans; Paleogenomics; Regulatory regions; SETD1A/histone methyltransferase complex.

Fig. 1

Regulatory regions characterized in this study. Active enhancers are typically located in regions of open chromatin and nucleosomes in their vicinity are marked by histone modifications H3K27 acetylation and H3K4 mono-methylation. By contrast, H3K4 tri-methylation defines active promoters [10]. We considered signals of active enhancers and promoters, as well as transposase (Tn5)-accessible chromatin regions, in the developing human brain (from 5 to 20 post-conception weeks) that harbor modern human single-nucleotide changes filtering out those regulatory regions that also contain Neanderthal/Denisovan changes. Chromosome conformation capture (Hi-C) data revealed the genes controlled by these regulatory regions

Fig. 2

Cell-type populations at early stages of cortical development. a Apical radial glial cells (RGCs) populate the ventricular zone and prolong one process apically to the ventricular surface and another one to the basal lamina, which serves as a scaffold for neuronal migration. RGCs also proliferate and differentiate to give rise to another RGC, a basal intermediate progenitor (indirect neurogenesis), or a neuron (direct neurogenesis) [28]. Intermediate progenitor cells (IPCs) are basal progenitors lacking of apical-basal cell polarity. IPCs migrate to the subventricular zone and, after a couple of self-renewal divisions, differentiate to give rise to two neurons [28]. b The tSNE plot shows twelve clusters detected analyzing a total of 762 cells. c The violin plots show expression of two markers (PAX6, EOMES) across the different clusters,distinguishing between RGCs and IPCs. d The miniature tSNE plots show the distribution across the clusters of a selection of genes discussed in the main text.IPC: Intermediate progenitor cells; NascentN: Nascent neurons; ExN: Excitatory neurons; Astro:Astrocytes; RGC: Radial glial cells; InN: Interneurons; Oligodendrocyte progenitor cells: OPC;Oligo: Oligodendrocytes; Cl12: Cluster 12 (unidentified cells)

Fig. 3

Progenitor cell-fate decisions shaped by WNT/β-CATENIN signaling. Based on studies in mice, it is hypothesized that early during neurodevelopment, WNT/β-CATENIN signaling promotes neural stem and progenitor cell self-renewal whereas its depletion causes premature neuronal differentiation [–47]; later on, its down-regulation is required for generation of intermediate progenitor cells from radial glial cells [47, 48]. Lastly, WNT/β-CATENIN signaling promotes differentiation of intermediate progenitors to produce neurons [46]