MicroRNA Expression and Regulation in Human, Chimpanzee, and Macaque Brains

Hai Yang Hu,Svante Pääbo,Song Guo,Philipp Khaitovich,Corinna Menzel,Rong Zeng,Ning Fu,Min Zhao,Hongyu Liang,Xiaoyu Zhang,Wei Chen,Hongyi Yang,Zheng Yan,Jiang Xi

doi:10.1371/journal.pgen.1002327

Abstract

Among other factors, changes in gene expression on the human evolutionary lineage have been suggested to play an important role in the establishment of human-specific phenotypes. However, the molecular mechanisms underlying these expression changes are largely unknown. Here, we have explored the role of microRNA (miRNA) in the regulation of gene expression divergence among adult humans, chimpanzees, and rhesus macaques, in two brain regions: prefrontal cortex and cerebellum. Using a combination of high-throughput sequencing, miRNA microarrays, and Q-PCR, we have shown that up to 11% of the 325 expressed miRNA diverged significantly between humans and chimpanzees and up to 31% between humans and macaques. Measuring mRNA and protein expression in human and chimpanzee brains, we found a significant inverse relationship between the miRNA and the target genes expression divergence, explaining 2%–4% of mRNA and 4%–6% of protein expression differences. Notably, miRNA showing human-specific expression localize in neurons and target genes that are involved in neural functions. Enrichment in neural functions, as well as miRNA–driven regulation on the human evolutionary lineage, was further confirmed by experimental validation of predicted miRNA targets in two neuroblastoma cell lines. Finally, we identified a signature of positive selection in the upstream region of one of the five miRNA with human-specific expression, miR-34c-5p. This suggests that miR-34c-5p expression change took place after the split of the human and the Neanderthal lineages and had adaptive significance. Taken together these results indicate that changes in miRNA expression might have contributed to evolution of human cognitive functions.

Highlights

Phenotypic differences between species, including humanspecific features such as language and tool-making, are thought to have arisen, to a large extent, through changes in gene expression [1]
We tested this notion by studying expression divergence of a specific type of regulatory RNA, microRNA, and its effect on gene expression profiles in brains of humans, chimpanzees, and rhesus macaques
Our results indicate that changes in miRNA expression have played a considerable role in the establishment of gene expression divergence between human brains and brains of nonhuman primates at both mRNA and protein expression levels

Summary

Introduction

Phenotypic differences between species, including humanspecific features such as language and tool-making, are thought to have arisen, to a large extent, through changes in gene expression [1]. Humans and the closest living primate relatives, chimpanzees, display substantial gene expression divergence in all tissues including the brain [2,3]. Previous studies focusing on transcription factors (TFs) have indicated an excess of human-specific expression divergence for several TFs in the liver [4] and the brain [5] These findings suggest that changes in TF expression might explain some of human-chimpanzee gene expression divergence. The predominant mechanism of miRNA-mediated gene silencing employs complementary base-pairing between the miRNA seed region and the mRNA 39 UTR region [9,10] This interaction guides RISC to target transcripts, which are degraded, destabilized or translationally inhibited, causing an inverse expression relationship between miRNA and its cognate targets [8,9,10,11,12]. The roles of miRNA in determining gene expression divergence between species and, in particular, their contribution to expression differences specific to the human brain remains, largely unknown

Author Summary

Findings

Materials and Methods