Binary partitioning of human brain organization due to divergent human cytoskeletal evolution

CHRFAM7A is a biallelic uniquely human fusion gene present in 99.3% of humans. The direct and inverted alleles likely emerged independently in Africa and East Asia. We uncovered that the inverted allele regulates ULK4 expression through genetic epistasis. The increase in long to short ULK4 isoform ratio enhances α-tubulin acetylation leading to microtubule (MT) cytoskeleton phenotypes (cell body: microtubule rich projections; neurite: de-bundling; growth cone: fanning with MT invasion). The MT cytoskeleton gain of function enhances neuronal arborization and functional connectivity in the human brain. Considering that the previously reported direct allele leads to actin cytoskeleton gain of function, we propose that CHRFAM7A alleles represent binary human genetic background through divergent evolution of the cytoskeleton. In the human brain the two alleles represent distinct brain organization: the direct allele enhances microstructure as measured by diffusion tensor imaging while the inverted allele increases functional connectivity with increased small world propensity. The two types of brain organization likely represent different susceptibility to neuropsychiatric disease and may underlie the allelic disease associations.