Human-specific DNA enhancer linked to brain development and neuron proliferation microbiologystudy

Duke University Medical Center-led research has identified a human-specific DNA enhancer that regulates neural progenitor proliferation and cortical size. Small genetic changes in HARE5 amplify a key developmental pathway, resulting in increased cortical size and neuron number in experimental models. Findings have implications for understanding the genetic mechanisms underlying neurodevelopmental disorders.

Humans possess a significantly larger and more complex cerebral cortex compared to other species, contributing to advanced cognitive functions. Comparative genomics research has identified Human Accelerated Regions (HARs), segments of non-coding DNA with human-specific genetic changes. Many HARs are located near genes associated with brain development and neural differentiation.

Because thousands of HARs have been identified and linked to brain-related genes, the next critical step is to investigate how these regulatory elements actively shape human brain features.

HARE5, a specific HAR located on chromosome 10, functions as an enhancer for FZD8, a receptor gene involved in the WNT signaling pathway. Regulatory modifications in HARE5 are associated with cortical development, but the molecular mechanisms by which human-specific nucleotide changes influence neural progenitor behavior remain unclear.

In the study, “A human-specific enhancer fine-tunes radial glia potency and corticogenesis,” published in Nature, researchers employed a series of genome-editing techniques to examine how human-specific nucleotide changes in HARE5 affect cortical development.

Mouse models were generated with genome-edited versions of HARE5, including human, chimpanzee, and mouse sequences. Human embryonic stem cells and chimpanzee induced pluripotent stem cells were edited to express either human or chimpanzee HARE5.

Human and chimpanzee neural progenitor cells and cortical organoids were analyzed to assess enhancer activity and cell proliferation.

Genome editing was employed to generate mouse models expressing human, chimpanzee, or mouse HARE5 sequences. CRISPR interference (CRISPRi) targeted HARE5 to assess its regulatory effect on the expression of FZD8 in neural progenitor cells.

Live imaging, single-cell RNA sequencing, and lineage tracing were performed to evaluate neural progenitor proliferation and differentiation.

Functional analyses of cortical size, neuron number, and neural progenitor dynamics were conducted using wide-field calcium imaging in mice. Cortical organoids derived from genome-edited human and chimpanzee stem cells were analyzed to assess HARE5 enhancer activity and cell proliferation.

Quantitative PCR and bulk RNA sequencing were utilized to measure gene expression levels of FZD8 and associated signaling pathway components.

Human HARE5 knock-in mice exhibited increased cortical size and neuron number compared to controls. Quantification of mature neurons revealed a significant increase, particularly in the upper cortical layers.

Live imaging and lineage tracing demonstrated enhanced proliferation and self-renewal of radial glial cells during early developmental stages, followed by expanded neurogenic potential during mid-neurogenesis. Four specific human nucleotide substitutions in HARE5 collectively drove increased enhancer activity, with Variants I and II accounting for approximately 80% of the effect.

Autism spectrum disorder-associated mutations adjacent to Variant I significantly reduced enhancer activity, correlating with decreased neural progenitor proliferation. Conditional knockout of mouse HARE5 reduced cortical size, confirming the enhancer’s necessity in cortical development. CRISPR interference confirmed the specificity of HARE5’s regulatory effect on Fzd8 expression.

Increased functional independence between cortical regions was observed through wide-field calcium imaging in HARE5 knock-in mice, suggesting broader network-level implications.

Researchers demonstrated that small genetic changes in a human-specific DNA enhancer can significantly alter neural development. Findings offer insight into how regulatory DNA sequences influence brain structure and suggest potential pathways through which evolutionary changes in DNA can contribute to neurodevelopmental disorders.

Identifying how specific nucleotide variations in HARE5 drive increased cortical size and neuron production provides a framework for investigating genetic factors underlying brain complexity.

Future studies may explore how similar DNA sequences impact neural function and cognitive development, with implications for understanding conditions such as autism spectrum disorder.

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