Embryonic Stem Cell-Derived Neurons as a Model System for Epigenome Maturation during Development.

Area of Science:

• Neuroscience
• Epigenetics
• Developmental Biology

Background:

• DNA methylation, particularly in the CH sequence context (mCH), is crucial for neuronal genome regulation and maturation.
• Vertebrate neurons exhibit unique, high levels of mCH during early postnatal brain development, distinct from other tissues.

Purpose of the Study:

• To assess the capacity of in vitro-derived neurons from mouse and human pluripotent stem cells to mimic in vivo DNA methylation patterns.
• To establish a tractable in vitro model for studying neuronal epigenome maturation.

Main Methods:

• Comparison of DNA methylation patterns in human and mouse embryonic stem cell (ESC)-derived neurons cultured in 2D and 3D organoids versus in vivo development.
• Analysis of DNA methyltransferase Dnmt3a expression, postmitotic marker Rbfox3 (NeuN) timing, and localization of mCH deposition.
• Correlation analysis between mCH and gene expression.

Main Results:

• Human ESC-derived neurons failed to accumulate mCH in vitro, irrespective of culture model (2D or 3D).
• Mouse ESC-derived cortical neurons successfully acquired in vivo levels of mCH in vitro, mirroring developmental timing.
• mCH deposition in mouse neurons correlated with Dnmt3a increase, followed Rbfox3 expression, localized to the nuclear lamina, and negatively impacted gene expression.

Conclusions:

• Mouse ESC-derived neurons serve as a viable in vitro model for recapitulating the neuronal DNA methylation landscape, unlike human counterparts.
• This model system enables experimental investigation of epigenome maturation over experimentally tractable timeframes.
• Subtle differences in methylation patterns suggest non-cell autonomous factors influence in vivo neuronal epigenomes.