2018.08.02
Human-specific features of spatial gene expression and regulation in eight brain regions
（Genome Res. 2018 Jun 13. doi: 10.1101/gr.231357.117. [Epub ahead of print]）
Xu C1, Li Q1, Efimova O2, He L1, Tatsumoto S3, Stepanova V2, Oishi T4, Udono T5, Yamaguchi K6, Shigenobu S6,7, Kakita A8, Nawa H8, Khaitovich P2,9,10,11, Go Y3,7,12.
1CAS Key Laboratory of Computational Biology, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, University of Chinese Academy of Sciences, Chinese Academy of Sciences, China.
2Skolkovo Institute of Science and Technology, Russia.
3Cognitive Genomics Research Group, Exploratory Research Center on Life and Living Systems, National Institutes of Natural Sciences, Japan.
4Primate Research Institute, Kyoto University, Japan.
5Kumamoto Sanctuary, Wildlife Research Center, Kyoto University, Japan.
6NIBB Core Research Facilities, National Institute for Basic Biology, Japan.
7School of Life Science, SOKENDAI (The Graduate University for Advanced Studies), Japan.
8Brain Research Institute, Niigata University, Japan.
9Center for Excellence in Animal Evolution and Genetics, Chinese Academy of Sciences, China.
10Comparative Biology Laboratory, CAS-MPG Partner Institute for Computational Biology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, China.
11School of Life Science and Technology, ShanghaiTech University, China.
12Department of Physiological Sciences, National Institute for Physiological Sciences, Japan.
Abstract
Molecular maps of the human brain alone do not inform us of the features unique to humans. Yet, the identification of these features is important for understanding both the evolution and nature of human cognition. Here, we approached this question by analyzing gene expression and H3K27ac chromatin modification data collected in eight brain regions of humans, chimpanzees, gorillas, a gibbon, and macaques. An analysis of spatial transcriptome trajectories across eight brain regions in four primate species revealed 1851 genes showing human-specific transcriptome differences in one or multiple brain regions, in contrast to 240 chimpanzee-specific differences. More than half of these human-specific differences represented elevated expression of genes enriched in neuronal and astrocytic markers in the human hippocampus, whereas the rest were enriched in microglial markers and displayed human-specific expression in several frontal cortical regions and the cerebellum. An analysis of the predicted regulatory interactions driving these differences revealed the role of transcription factors in species-specific transcriptome changes, and epigenetic modifications were linked to spatial expression differences conserved across species.
