Gene

Biology

Mutation

Regulation of gene expression

DNA methylation

Rett syndrome

Genetics

Mutant

MECP2

Gene expression

Phenotype

Nature Neuroscience

In females with X-linked genetic disorders, wild-type and mutant cells coexist within brain tissue because of X-chromosome inactivation, posing challenges for interpreting the effects of X-linked mutant alleles on gene expression. We present a single-nucleus RNA sequencing approach that resolves mosaicism by using single-nucleotide polymorphisms in genes expressed in cis with the X-linked mutation to determine which nuclei express the mutant allele even when the mutant gene is not detected. This approach enables gene expression comparisons between mutant and wild-type cells within the same individual, eliminating variability introduced by comparisons to controls with different genetic backgrounds. We apply this approach to mosaic female mouse models and humans with Rett syndrome, an X-linked neurodevelopmental disorder caused by mutations in the gene encoding the methyl-DNA-binding protein MECP2, and observe that cell-type-specific DNA methylation predicts the degree of gene upregulation in MECP2-mutant neurons. This approach can be broadly applied to study gene expression in mosaic X-linked disorders. The authors develop a single-cell RNA-seq approach to distinguish cells expressing wild-type or mutant genes in mosaic individuals with X-linked disorders and find that cell-type-specific DNA methylation predicts gene misregulation in Rett syndrome.

Characterization of human mosaic Rett syndrome brain tissue by single-nucleus RNA sequencing