Recent detailed comparisons of human and chimpanzee DNA differences have identified important differences related to gene expression including human accelerated regions (HARs) (Pollard et al., 2006a, 2006b) or conserved noncoding sequences (CNSs) (Prabhakar et al., 2006), genomic neighborhood differences (De et al., 2009), copy number variations (CNVs) (Gazave et al., 2011; Perry et al., 2008), and promoter and enhancer variations (Haygood et al., 2007; Planas
and Serrat, 2010) that could contribute substantially to differences in phenotype. In addition to these DNA studies, several previous studies have directly examined human-chimpanzee differences PI3K inhibitor in gene expression in the brain using microarrays to measure RNA transcript levels (Cáceres et al., 2003; Enard et al., 2002a; Khaitovich et al., 2004a). While these studies were an important first step in uncovering human-specific patterns of gene expression in the brain, microarray technology has several limitations that are especially germane to evolutionary comparisons. First, PARP inhibitor microarray analysis
relies on a priori knowledge of the sequence of the sample being measured, which precludes identifying unannotated transcripts. The dynamic range of microarrays is also narrow compared to that of new sequencing technologies (Asmann et al., 2009; Feng et al., 2010). Perhaps most importantly, with respect to cross-species comparisons, is the tremendous loss of usable probes due to sequence divergence (Preuss et al., 2004). To avoid these limitations, we utilized Parvulin next-generation
sequencing (NGS) (Metzker, 2010) to compare gene expression in the brains of three primates: humans, chimpanzees, and rhesus macaques, employing 3′ digital gene expression (DGE) tag-based profiling to assess levels of mRNA expression. DGE has been shown to be both highly sensitive and reproducible when assessing gene expression from human brain (Asmann et al., 2009). Importantly, the present study included rhesus macaques as an outgroup, which provides a basis for inferring whether differences between humans and chimpanzees occurred in the human lineage or the chimpanzee lineage. With a few exceptions (Brawand et al., 2011; Cáceres et al., 2003; Liu et al., 2012; Somel et al., 2009, 2011), previous microarray or NGS studies have not included an outgroup or only investigated one brain region (Babbitt et al., 2010; Cáceres et al., 2003; Enard et al., 2002a; Khaitovich et al., 2004a, 2005; Liu et al., 2011; Marvanová et al., 2003; Somel et al., 2009; Uddin et al., 2004; Xu et al., 2010a). We examine three brain regions representing different developmental origins within the telencephalon: subpallial (caudate), allocortical (hippocampus), and neocortical (frontal pole). Frontal pole is of particular interest because it was enlarged and structurally modified in human evolution (Semendeferi et al.