Gene expression variability in human and chimpanzee populations share common determinants

  1. Benjamin Jung Fair  Is a corresponding author
  2. Lauren E Blake
  3. Abhishek Sarkar
  4. Bryan J Pavlovic
  5. Claudia Cuevas
  6. Yoav Gilad  Is a corresponding author
  1. University of Chicago, United States
  2. University of California, San Francisco, United States

Abstract

Inter-individual variation in gene expression has been shown to be heritable and is often associated with differences in disease susceptibility between individuals. Many studies focused on mapping associations between genetic and gene regulatory variation, yet much less attention has been paid to the evolutionary processes that shape the observed differences in gene regulation between individuals in humans or any other primate. To begin addressing this gap, we performed a comparative analysis of gene expression variability and expression quantitative trait loci (eQTLs) in humans and chimpanzees, using gene expression data from primary heart samples. We found that expression variability in both species is often determined by non-genetic sources, such as cell-type heterogeneity. However, we also provide evidence that inter-individual variation in gene regulation can be genetically controlled, and that the degree of such variability is generally conserved in humans and chimpanzees. In particular, we found a significant overlap of orthologous genes associated with eQTLs in both species. We conclude that gene expression variability in humans and chimpanzees often evolves under similar evolutionary pressures.

Data availability

RNA-Seq data available under GEO accession number GSE151397. Raw whole genome sequencing data under SRA accession PRJNA635393. Processed whole genome sequencing data available as variant calls at European variation archive, EVA accession PRJEB39475.

The following data sets were generated
The following previously published data sets were used

Article and author information

Author details

  1. Benjamin Jung Fair

    Section of Genetic Medicine, Department of Medicine, University of Chicago, Chicago, United States
    For correspondence
    bjf79@uchicago.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-6296-5703
  2. Lauren E Blake

    Department of Human Genetics, University of Chicago, Chicago, United States
    Competing interests
    The authors declare that no competing interests exist.
  3. Abhishek Sarkar

    Human Genetics, University of Chicago, Chicago, United States
    Competing interests
    The authors declare that no competing interests exist.
  4. Bryan J Pavlovic

    Department of Neurology, University of California, San Francisco, San Francisco, United States
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0002-7751-5315
  5. Claudia Cuevas

    Department of Human Genetics, University of Chicago, Chicago, United States
    Competing interests
    The authors declare that no competing interests exist.
  6. Yoav Gilad

    Department of Medicine, University of Chicago, Chicago, United States
    For correspondence
    gilad@uchicago.edu
    Competing interests
    The authors declare that no competing interests exist.
    ORCID icon "This ORCID iD identifies the author of this article:" 0000-0001-8284-8926

Funding

National Institute of General Medical Sciences (R35GM131726)

  • Yoav Gilad

The funders had no role in study design, data collection and interpretation, or the decision to submit the work for publication.

Reviewing Editor

  1. Hunter B Fraser, Stanford University, United States

Publication history

  1. Received: June 12, 2020
  2. Accepted: October 20, 2020
  3. Accepted Manuscript published: October 21, 2020 (version 1)
  4. Version of Record published: November 5, 2020 (version 2)

Copyright

© 2020, Fair et al.

This article is distributed under the terms of the Creative Commons Attribution License permitting unrestricted use and redistribution provided that the original author and source are credited.

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  1. Benjamin Jung Fair
  2. Lauren E Blake
  3. Abhishek Sarkar
  4. Bryan J Pavlovic
  5. Claudia Cuevas
  6. Yoav Gilad
(2020)
Gene expression variability in human and chimpanzee populations share common determinants
eLife 9:e59929.
https://doi.org/10.7554/eLife.59929

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