背景:人类加速区(HARs)是短的保守基因组序列,在与黑猩猩的分化后,已经获得了比人类谱系中预期的显着更多的核苷酸取代。HARs的快速进化可能反映了它们在人类特定性状起源中的作用。最近的一项研究报道了大脑专有人类加速增强子(BE-HAEs)hs1210(前脑)中积极选择的单核苷酸变体(SNV),hs563(后脑)和hs304(中脑/前脑)。通过包括来自古人类的数据,这些SNV被证明是智人特异性的,驻留在SOX2(hs1210)的转录因子结合位点(TFBS)内,RUNX1/3(hs563),和FOS/JUND(hs304)。尽管这些发现表明,TFBS中预测的修饰可能在当今的大脑结构中起着一定的作用,需要工作来验证这些变化转化为功能变化的程度。
结果:要开始填补这一空白,我们调查了SOX2SNV,在人类中同时具有前脑表达和强烈的正选择信号。我们证明了SOX2的HMG盒在体外与智人特异性衍生的A等位基因和携带BE-HAEhs1210中DNA位点的祖先T等位基因结合。分子对接和模拟分析表明,与携带祖先T等位基因的位点相比,HMG盒与含衍生A等位基因的DNA位点的结合非常有利。
结论:这些结果表明,在智人的进化史中,BE-HAEhs1210和其他HAR增强子中TF亲和力的过继性变化可能。已经带来了基因表达模式的变化,并对前脑的形成和进化产生了功能影响。
方法:本研究采用电泳迁移率变化测定(EMSA)和分子对接和分子动力学模拟方法。
BACKGROUND: Human accelerated regions (HARs) are short conserved genomic sequences that have acquired significantly more nucleotide substitutions than expected in the human lineage after divergence from chimpanzees. The fast evolution of HARs may reflect their roles in the origin of human-specific traits. A recent study has reported positively-selected single nucleotide variants (SNVs) within brain-exclusive human accelerated enhancers (BE-HAEs) hs1210 (forebrain), hs563 (hindbrain) and hs304 (midbrain/forebrain). By including data from archaic hominins, these SNVs were shown to be Homo sapiens-specific, residing within transcriptional factors binding sites (TFBSs) for SOX2 (hs1210), RUNX1/3 (hs563), and FOS/JUND (hs304). Although these findings suggest that the predicted modifications in TFBSs may have some role in present-day brain structure, work is required to verify the extent to which these changes translate into functional variation.
RESULTS: To start to fill this gap, we investigate the SOX2 SNV, with both forebrain expression and strong signal of positive selection in humans. We demonstrate that the HMG box of SOX2 binds in vitro with Homo sapiens-specific derived A-allele and ancestral T-allele carrying DNA sites in BE-HAE hs1210. Molecular docking and simulation analysis indicated highly favourable binding of HMG box with derived A-allele containing DNA site when compared to site carrying ancestral T-allele.
CONCLUSIONS: These results suggest that adoptive changes in TF affinity within BE-HAE hs1210 and other HAR enhancers in the evolutionary history of Homo sapiens might. have brought about changes in gene expression patterns and have functional consequences on forebrain formation and evolution.
METHODS: The present study employ electrophoretic mobility shift assays (EMSA) and molecular docking and molecular dynamics simulations approaches.