Evolution and Comprehensive Analysis of DNaseI Hypersensitive Sites in Regulatory Regions of Primate Brain-Related Genes.

Yueer Lu,Bangwei Chen,Wei Wang,Chongyin Han,Xiao Wang,Zhiqiang Jiang,Hang Yu,Fei Ling,Weidong Tian,Chunbo Chen,Yueqi Lu,Lizhen Huang,Ying Ouyang,Jianlin Li

doi:10.3389/fgene.2019.00152

Abstract

How the human brain differs from those of non-human primates is largely unknown and the complex drivers underlying such differences at the genomic level remain unclear. In this study, we selected 243 brain-related genes, based on Gene Ontology, and identified 184,113 DNaseI hypersensitive sites (DHSs) within their regulatory regions. To performed comprehensive evolutionary analyses, we set strict filtering criteria for alignment quality and filtered 39,132 DHSs for inclusion in the investigation and found that 2,397 (~6%) exhibited evidence of accelerated evolution (aceDHSs), which was a much higher proportion that DHSs genome-wide. Target genes predicted to be regulated by brain-aceDHSs were functionally enriched for brain development and exhibited differential expression between human and chimpanzee. Alignments indicated 61 potential human-specific transcription factor binding sites in brain-aceDHSs, including for CTCF, FOXH1, and FOXQ1. Furthermore, based on GWAS, Hi-C, and eQTL data, 16 GWAS SNPs, and 82 eQTL SNPs were in brain-aceDHSs that regulate genes related to brain development or disease. Among these brain-aceDHSs, we confirmed that one enhanced the expression of GPR133, using CRISPR-Cas9 and western blotting. The GPR133 gene is associated with glioblastoma, indicating that SNPs within DHSs could be related to brain disorders. These findings suggest that brain-related gene regulatory regions are under adaptive evolution and contribute to the differential expression profiles among primates, providing new insights into the genetic basis of brain phenotypes or disorders between humans and other primates.

Highlights

Human-specific social and cognitive behaviors, including language, civilization, society, as well as some mental disorders, are rooted in the complex human brain; the mechanisms underlying human-specific neurodevelopment remain unclear
To focus on regulatory regions correlated with brain development and minimize the influence of constitutive genes in the acceleration analysis, we first filtered out those reported to be housekeeping genes, which are extensively expressed in many tissues and required for basic cellular functions (Eisenberg and Levanon, 2003; Zhu et al, 2008)
To identify brain-related DNaseI hypersensitive sites (DHSs) under accelerated evolution, we considered local ancient repeat elements (AREs) to be neutrally evolving (Dong et al, 2016); AREs served as a neutral model for assessing brain-related DHSs with evidence of accelerated evolution

Summary

Introduction

Human-specific social and cognitive behaviors, including language, civilization, society, as well as some mental disorders, are rooted in the complex human brain; the mechanisms underlying human-specific neurodevelopment remain unclear. Unlike coding region variations, which usually lead to loss or gain of gene product function, mutations within non-coding regions can influence the binding affinity of transcription factors or the recruitment of transcriptional elements, thereby affecting the expression of downstream genes. Several human genomic regions with evidence of accelerated evolution are associated with neurodevelopment, cognition, social behavior, and even brain disorders (Reilly et al, 2015; Doan et al, 2016; Brandler et al, 2018). These findings represent strong evidence of the importance of non-coding regions in primate brain development and divergence, as well as human brain diseases. A more comprehensive analysis should be conducted to determine how brain-related regulatory regions participate in primate brain evolution and what biological functions they serve

Methods

Results

Conclusion