Multimodal profiling of the transcriptional regulatory landscape of the developing mouse cortex identifies Neurog2 as a key epigenome remodeler

Florian Noack,Silvia Vangelisti,Boyan Bonev,Madalena Carido,Jeisimhan Diwakar,Faye Chong,Gerald Raffl

doi:10.1038/s41593-021-01002-4

Abstract

How multiple epigenetic layers and transcription factors (TFs) interact to facilitate brain development is largely unknown. Here, to systematically map the regulatory landscape of neural differentiation in the mouse neocortex, we profiled gene expression and chromatin accessibility in single cells and integrated these data with measurements of enhancer activity, DNA methylation and three-dimensional genome architecture in purified cell populations. This allowed us to identify thousands of new enhancers, their predicted target genes and the temporal relationships between enhancer activation, epigenome remodeling and gene expression. We characterize specific neuronal transcription factors associated with extensive and frequently coordinated changes across multiple epigenetic modalities. In addition, we functionally demonstrate a new role for Neurog2 in directly mediating enhancer activity, DNA demethylation, increasing chromatin accessibility and facilitating chromatin looping in vivo. Our work provides a global view of the gene regulatory logic of lineage specification in the cerebral cortex.

Highlights

How multiple epigenetic layers and transcription factors (TFs) interact to facilitate brain development is largely unknown
We identify thousands of new cell-type-specific enhancer–gene pairs (EGPs) and show that enhancer activation appears to precede gene expression, only a subset of enhancers bound by specific TFs acts as truly lineage priming
Using integrated analysis and in vivo validation, we identify a new role for the TF Neurog[2] in directly mediating enhancer activity, DNA demethylation, as well as leading to increased chromatin accessibility and chromatin looping in vivo

Summary

Introduction

How multiple epigenetic layers and transcription factors (TFs) interact to facilitate brain development is largely unknown. To systematically map the regulatory landscape of neural differentiation in the mouse neocortex, we profiled gene expression and chromatin accessibility in single cells and integrated these data with measurements of enhancer activity, DNA methylation and three-dimensional genome architecture in purified cell populations. This allowed us to identify thousands of new enhancers, their predicted target genes and the temporal relationships between enhancer activation, epigenome remodeling and gene expression. To comprehensively assess how coordinated epigenome remodeling governs cell fate decisions in the developing neocortex in vivo, we integrated single-cell transcriptomic and chromatin accessibility data with cell-type-specific massive parallel reporter assay (MPRA), DNA methylation and 3D genome architecture. The generated data are freely available at https://shiny.bonevlab.com/ for interactive visualization

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