A developmentally regulated long-range enhancer-promoter contact mediates human neural development

Area of Science:

• Developmental Biology
• Genetics
• Stem Cell Biology

Background:

• SOX2 is a key pluripotency factor in human embryonic stem cells (hESCs).
• SOX2 expression is maintained in neuroectoderm during differentiation.
• Mechanisms controlling SOX2 transcription during development are not fully understood.

Purpose of the Study:

• To investigate the regulatory mechanisms of SOX2 transcription during human development.
• To identify and characterize regulatory elements controlling SOX2 expression in neural stem cells (NSCs).
• To understand the role of long-range interactions in SOX2 gene regulation.

Main Methods:

• CRISPR-Cas9 gene editing to excise a distant enhancer and a CTCF motif.
• Analysis of SOX2 transcription in human embryonic stem cells (hESCs) and neural stem cells (NSCs).
• Assessment of neuroectodermal differentiation and forebrain specification in teratomas and cerebral organoids.

Main Results:

• A distant enhancer, 550 kb from the SOX2 locus, is selectively activated in NSCs.
• Enhancer deletion in NSCs reduces SOX2 transcription and impairs neuroectodermal differentiation and forebrain development.
• Disruption of a CTCF motif near the enhancer affects chromatin looping and SOX2 transcription, partially mimicking enhancer deletion phenotypes.

Conclusions:

• A developmentally regulated, long-range enhancer interaction controls SOX2 expression in the developing human nervous system.
• This enhancer-gene communication is essential for neuroectodermal differentiation and forebrain specification.
• CTCF-mediated looping plays a role in facilitating this long-range regulatory interaction.