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Enhancer Function and Evolutionary Roles of Human Accelerated Regions.

Sean Whalen1, Katherine S Pollard1,2,3

  • 1Gladstone Institute of Data Science and Biotechnology, San Francisco, California, USA; email: sean.whalen@gladstone.ucsf.edu, kpollard@gladstone.ucsf.edu.

Annual Review of Genetics
|September 7, 2022
PubMed
Summary
This summary is machine-generated.

Human accelerated regions (HARs) are rapidly evolving DNA sequences. HARs act as gene enhancers, particularly in neurodevelopment, with many showing distinct functions compared to chimpanzee versions.

Keywords:
enhancerepigeneticsevolutionhuman accelerated regionmachine learningreporter assay

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Area of Science:

  • Genomics
  • Evolutionary Biology
  • Neuroscience

Background:

  • Human accelerated regions (HARs) are the fastest-evolving sequences in the human genome.
  • Initial understanding of HAR function was limited due to poor noncoding genome annotation.
  • Emerging evidence links HARs to gene regulation, especially in neurodevelopment.

Purpose of the Study:

  • To quantitatively assess the enhancer activity of thousands of HARs.
  • To model nucleotide-level contributions to gene expression within HARs.
  • To investigate functional divergence of HARs between humans and chimpanzees.

Main Methods:

  • High-throughput measurement of HAR enhancer activity.
  • Computational modeling of nucleotide effects on gene expression.
  • Comparative analysis of HARs in human and chimpanzee genomes.

Main Results:

  • HARs function as gene regulatory enhancers, with notable enrichment in neurodevelopmental genes.
  • Quantitative assays reveal differential enhancer activity for many human HARs compared to chimpanzee orthologs.
  • Individual nucleotide changes within HARs can have opposing effects, suggesting compensatory evolution.

Conclusions:

  • HARs play a significant role in human evolution, particularly in shaping neurodevelopment.
  • Functional divergence at the nucleotide level contributes to species-specific gene regulation.
  • Further research across diverse cell types and developmental stages is needed to fully elucidate HAR roles.