# In vivo transition in chromatin accessibility during differentiation of deep-layer excitatory neurons in the neocortex

## TL;DR

This study tracks how chromatin accessibility changes during the development of deep-layer neurons in the mouse brain, showing early preparation for mature neuronal functions.

## Contribution

A new method for tracing neuronal differentiation in vivo combined with RNA-seq and DNase-seq to study chromatin accessibility.

## Key findings

- Genomic regions linked to mature neuronal functions become accessible during the embryonic stage.
- Bivalent marks and genes Dmrt3 and Dmrta2 regulate chromatin accessibility during neuronal differentiation.
- Chromatin regulation is crucial for timely activation of neuronal genes during maturation.

## Abstract

During neuronal differentiation, gene transcription patterns change in response to both intrinsic and extrinsic cues. Chromatin regulation at regulatory elements plays a key role in this process. However, how chromatin accessibility evolves in vivo in cortical neurons remains unclear. Here, we established a method for labeling differentiating neurons with specific birthdates. Using this method, we traced the 4-day differentiation process of in vivo deep-layer excitatory neurons in the mouse embryonic cortex and examined changes in the genome-wide transcription pattern and chromatin accessibility using RNA sequencing and DNase sequencing, respectively. We found that genomic regions of genes linked to mature neuronal functions, including deep layer-specific and stimulus-responsive genes, became accessible even at the embryonic stage. Additionally, our results indicated the involvement of bivalent marks in neural precursor/stem cells and Dmrt3 and Dmrta2 in the regulation of chromatin accessibility during neuronal differentiation. These findings highlight the importance of chromatin regulation in embryonic neurons, enabling the timely activation of neuronal genes during maturation.

Summary: A neuronal differentiation tracing method combined with RNA-seq and DNase-seq analyses reveals the potential role of chromatin accessibility in preparing the activation of mouse neuronal genes in mature neurons.