Transcription Factors Bind Negatively Selected Sites within Human mtDNA Genes
Transcription Factors Bind Negatively Selected Sites within Human mtDNA Genes
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DOI：
10.1093/gbe/evu210
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发表时间：
2014-10-01
影响因子：
3.3
通讯作者：
Mishmar, Dan
中科院分区：
文献类型：
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作者：
Blumberg, Amit;Sailaja, Badi Sri;Mishmar, Dan
线粒体DNA(MtDNA)编码基因的转录被认为是由几个专门的转录因子(TF)调控的，这表明mtDNA基因是从细胞核单独调控的。然而，一些已知具有核活性的转录因子被发现与线粒体DNA结合并调节线粒体转录。此外，线粒体DNA转录调控元件，在体外被证明是重要的，被隐藏在通常在健康个体中分离的缺失。因此，线粒体DNA的转录调控比人们想象的要复杂得多。在这里，通过分析ENCODE染色质免疫沉淀测序(CHIP-SEQ)数据，我们在人类mtDNA蛋白编码基因中发现了三个真正的核转录因子(c-Jun、Jun-D和CEBPB)的强结合位点。我们通过芯片定量聚合酶链式反应(c-Jun和Jun-D)验证了两个转录因子的结合，并通过电子显微镜和亚细胞分裂显示了它们的线粒体定位。作为研究这些转铁蛋白结合位点(TFBS)功能的一步，我们评估了选择的签名。通过分析涵盖所有主要全球种群的9868个人类mtDNA序列，我们记录了TFBS中mtDNA系统发育的尖端和节点的遗传变异。接下来，我们计算了变体对结合基序预测分数的影响。最后，将预测的TFBS与CHIP-SEQ阳性TFBS(CPR)的mtDNA变异模式进行比较。C-Jun、Jun-D和CEBPB的CPR中的基序要么只含有TIP变体，要么含有较高的节点变体，保留了较高的基序预测分数。这反映了mtDNA CPR中的负选择，从而支持了它们的功能。因此，人类线粒体DNA编码序列可能具有双重作用，即编码基因，但也可能具有调节潜力。
Transcription of mitochondrial DNA (mtDNA)-encoded genes is thought to be regulated by a handful of dedicated transcription factors (TFs), suggesting that mtDNA genes are separately regulated from the nucleus. However, several TFs, with known nuclear activities, were found to bind mtDNA and regulate mitochondrial transcription. Additionally, mtDNA transcriptional regulatory elements, which were proved important in vitro, were harbored by a deletion that normally segregated among healthy individuals. Hence, mtDNA transcriptional regulation is more complex than once thought. Here, by analyzing ENCODE chromatin immunoprecipitation sequencing (ChIP-seq) data, we identified strong binding sites of three bona fide nuclear TFs (c-Jun, Jun-D, and CEBPb) within human mtDNA protein-coding genes. We validated the binding of two TFs by ChIP-quantitative polymerase chain reaction (c-Jun and Jun-D) and showed their mitochondrial localization by electron microscopy and subcellular fractionation. As a step toward investigating the functionality of these TF-binding sites (TFBS), we assessed signatures of selection. By analyzing 9,868 human mtDNA sequences encompassing all major global populations, we recorded genetic variants in tips and nodes of mtDNA phylogeny within the TFBS. We next calculated the effects of variants on binding motif prediction scores. Finally, the mtDNA variation pattern in predicted TFBS, occurring within ChIP-seq negative-binding sites, was compared with ChIP-seq positive-TFBS (CPR). Motifs within CPRs of c-Jun, Jun-D, and CEBPb harbored either only tip variants or their nodal variants retained high motif prediction scores. This reflects negative selection within mtDNA CPRs, thus supporting their functionality. Hence, human mtDNA-coding sequences may have dual roles, namely coding for genes yet possibly also possessing regulatory potential.