Fast-Evolving Human Genome Sequences Found to Have Brain-Related Regulatory Roles

NEW YORK – A team led by investigators at Harvard Medical School has demonstrated that regulatory enhancers involved in human neurodevelopment are particularly common in fast-evolving parts of the human genome.

Dubbed human accelerated regions (HARs), these areas contain genes that have evolved quickly in humans compared to other animals and are thought to have contributed to the evolution of the cerebral cortex.

“Our data suggest that evolution of the human brain involved changes in dozens or perhaps even hundreds of sites in the genome, rather than just a single key gene,” senior author Christopher Walsh, a genetics and genomics researcher affiliated with the Allen Discovery Center for Human Brain Evolution at Boston Children’s Hospital and Harvard Medical School, said in a statement.

As they reported in Neuron on Thursday, the researchers turned to a capture-based massively parallel reporter assays (caMPRA) — combined with RNA sequencing, chromatin immunoprecipitation sequencing, chromatin conformation capture-based interaction profiling, DNaseI-seq, and other approaches — to look at enhancer element activity for nearly 3,200 known HARs in human and chimpanzee genomic DNA samples and in mouse or human neural cell lines.

Along with available data from efforts such as the Roadmap Epigenomics Consortium, the team performed a series of regulatory and chromatin experiments, cell cycle and growth assays, and other analyses on neural progenitor cells and maturing neurons isolated from fetal brain tissues, as well as mouse primary cortical neurosphere models, ferret and rhesus macaque brain tissues, and cell lines. Results from the study have been pulled together in an online collection known as HARHub on the Genome Browser of the University of California, Santa Cruz.

We knew going into this study that many HARs were likely to function as regulators of gene expression in the brain, but we knew very little about which cell types in the brain they worked in, where, or at what time in the human lifespan,” co-first author Ellen DeGennaro, a researcher in Walsh’s lab, said in a statement.

“Our goal was to fill in these gaps of knowledge about which HARs had important roles in the brain, and how,” DeGennaro added, “so that we and other researchers could take the most important ‘brain HARs’ and perform deeper tests of their evolutionary function.”

Close to half of the 3,171 HARs analyzed showed signs of neurodevelopmental enhancer activity, the team reported, noting that regulatory features associated with HARs also seemed to differ by neuronal differentiation stage. Just a fraction of the histone modifications at HAR sites were shared in the neural progenitor cells and maturing neurons, for example, and distinct pathways and processes turned up when investigators looked at HAR-related regulatory elements in these cell types.

Within a subset of HARs that showed neurodevelopmental enhancer activity in both their in vitro and in vivo analyses, the researchers focused in on a cerebral cortex-related gene called PPP1R17 that appeared to have undergone speedy expression shifts and cell type roles during evolution, differing not only between humans and non-human primates, but also between primates and other animals. Their results hint that PPP1R17 is particularly important when it comes to the regulation of neural progenitor cells, stretching out cell cycle progression in those cells in a manner that has been linked to large primate brain development.

“By interrogating the epigenetic landscape of more than 3,100 HARs during human neurodevelopment, we demonstrate that nearly half of all HARs act as neurodevelopmental enhancers and that the cis-regulatory architecture of these HARs has undergone extensive human-specific rewiring,” the authors wrote, adding that “human-specific sequence changes within HARs largely augment their enhancer activity within neuronal cells, further establishing HARs as human-specific neurodevelopmental enhancers.”

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