Characterization of the noncoding regulatory landscape within human-specific duplicated regions
Human-specific segmental duplications (HSDs, or regions >1 kbp at >98% sequence identity), which arose uniquely in the human lineage, are known drivers of evolution and diversity based on their ability to create novel genes with innovative functions. HSDs also contribute to ‘genomic hotspots’—by sensitizing regions to deletions and duplications—which can cause neurodevelopmental disease, including autism spectrum disorder (ASD), epilepsy, schizophrenia, and intellectual disability. Until recently, many HSDs were erroneously assembled in human reference builds due to high sequence similarities. Considerable effort has gone into identifying novel genes created by these duplications, while noncoding elements, that can alter expression of multiple genes, have largely been ignored. To address this, we performed targeted assessment in HSD regions of the chromatin marks H3K27ac and H3K4me1 as well as enhancer-associated transcripts using publicly available ChIP-seq and RNA-seq datasets from human, chimpanzee and rhesus macaque lymphoblasts and three brain regions. By comparing with non-human primates we distinguished ancestral regulatory signals with novel ones from human duplications. We identified over 200 enhancers within HSDs originally dismissed in the public datasets, including cerebellum-specific enhancer of neuronally-implicated SRGAP2. We increased in nine-fold the overall enhancer discovery rate and confirmed that regulatory elements are duplicated along with HSD genes. Interestingly, duplication of such elements was seen in regions associated to neurodevelopmental disorders and ASD, including Williams-Beuren syndrome, Dup15q, 1q21.1, 2q21.1 and other loci. Using a capture Hi-C method in human and non-human primate cells, we identified differences of novel regulatory elements with genome-wide contacts between ape species, and are correlating results with public RNA-seq data. We premise that HSD regulatory elements have affected the expression of nearby genes contributing to novel human neurobehavioral traits when these duplications arose in our hominin ancestors. Such findings will allow us to understand how chromatin states were shaped upon duplications, and moreover, to identify novel candidate pathways altered in neurological disorders.