Single-cell-resolution transcriptome map of human, chimpanzee, bonobo, and macaque brains
- Ekaterina Khrameeva1,11,
- Ilia Kurochkin1,11,
- Dingding Han2,11,
- Patricia Guijarro3,
- Sabina Kanton4,
- Malgorzata Santel4,
- Zhengzong Qian3,
- Shen Rong3,
- Pavel Mazin1,5,
- Marat Sabirov6,
- Matvei Bulat1,
- Olga Efimova1,
- Anna Tkachev1,5,
- Song Guo1,3,
- Chet C. Sherwood7,
- J. Gray Camp8,
- Svante Pääbo4,
- Barbara Treutlein9 and
- Philipp Khaitovich1,3,4,10
- 1Skolkovo Institute of Science and Technology, Moscow, 143028, Russia;
- 2Guangzhou Institute of Pediatrics, Guangzhou Women and Children's Medical Center, Guangzhou Medical University, Guangzhou, 510623, China;
- 3CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai, 200031, China;
- 4Max Planck Institute for Evolutionary Anthropology, Leipzig, 04103, Germany;
- 5Kharkevich Institute for Information Transmission Problems, Russian Academy of Sciences, Moscow, 127051, Russia;
- 6Center for Precision Genome Editing and Genetic Technologies for Biomedicine, Institute of Gene Biology, Russian Academy of Sciences, Moscow, 119334, Russia;
- 7Department of Anthropology and Center for the Advanced Study of Human Paleobiology, The George Washington University, Washington, DC 20052, USA;
- 8Institute of Molecular and Clinical Ophthalmology, Basel, 4057, Switzerland;
- 9Department of Biosystems Science and Engineering, Swiss Federal Institute of Technology in Zurich, Basel, 4058, Switzerland;
- 10Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, Kunming, 650223, China
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↵11 These authors contributed equally to this work.
Abstract
Identification of gene expression traits unique to the human brain sheds light on the molecular mechanisms underlying human evolution. Here, we searched for uniquely human gene expression traits by analyzing 422 brain samples from humans, chimpanzees, bonobos, and macaques representing 33 anatomical regions, as well as 88,047 cell nuclei composing three of these regions. Among 33 regions, cerebral cortex areas, hypothalamus, and cerebellar gray and white matter evolved rapidly in humans. At the cellular level, astrocytes and oligodendrocyte progenitors displayed more differences in the human evolutionary lineage than the neurons. Comparison of the bulk tissue and single-nuclei sequencing revealed that conventional RNA sequencing did not detect up to two-thirds of cell-type-specific evolutionary differences.
Footnotes
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[Supplemental material is available for this article.]
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Article published online before print. Article, supplemental material, and publication date are at http://www.genome.org/cgi/doi/10.1101/gr.256958.119.
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Freely available online through the Genome Research Open Access option.
- Received September 10, 2019.
- Accepted April 30, 2020.
This article, published in Genome Research, is available under a Creative Commons License (Attribution-NonCommercial 4.0 International), as described at http://creativecommons.org/licenses/by-nc/4.0/.
