Transcriptional consequences of XPA disruption in human cell lines
Transcriptional consequences of XPA disruption in human cell lines
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DOI：
10.1016/j.dnarep.2017.06.028
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发表时间：
2017-09-01
期刊：
影响因子：
3.8
通讯作者：
Wood, Richard D.
中科院分区：
文献类型：
--
作者：
Manandhar, Mandira;Lowery, Megan G.;Wood, Richard D.
哺乳动物细胞中的核苷酸切除修复（NER）需要着色性干皮病A组蛋白（XPA）作为核心因子。值得注意的是，通过染色质免疫沉淀在一些活性启动子处检测到XPA和其他NER蛋白，并且有报道称NER缺乏会影响选定基因的激活转录。然而，XPA对人类细胞转录的整体影响尚未确定。我们通过RNA测序（RNA- seq）分析了人类转录组。我们首先证实，即使在没有外部DNA损伤的情况下，XPA也被限制在细胞核内，与之前报道的XPA通常存在于细胞质中，并在DNA损伤后输入。然后，我们分析了四个基因匹配的人类细胞系对缺乏或精通XPA。在每个细胞系中转录的14000个基因中，325个基因（2%）在基因表达上有显著的依赖xpa的方向性变化，这在所有四对中都是共同的（错误发现率为0.05）。这些基因在维持线粒体的途径中富集。只有27个普通基因的差异超过1.5倍。影响最大的是与类固醇激素代谢有关的AKR1C1和AKR1C2。AKR1C2蛋白在所有永生化xpa缺陷细胞中均较低。视黄酸治疗导致一些具有转录相关功能的基因适度的xpa依赖性激活。我们得出结论，XPA状态不影响人类基因转录的全局。然而，XPA显著影响一小部分对线粒体功能和类固醇激素代谢重要的基因的表达。结果可能有助于解释神经功能缺陷和不育的个体与着色性干皮病。
Nucleotide excision repair (NER) in mammalian cells requires the xeroderma pigmentosum group A protein (XPA) as a core factor. Remarkably, XPA and other NER proteins have been detected by chromatin immunoprecipitation at some active promoters, and NER deficiency is reported to influence the activated transcription of selected genes. However, the global influence of XPA on transcription in human cells has not been determined. We analyzed the human transcriptome by RNA sequencing (RNA-Seq). We first confirmed that XPA is confined to the cell nucleus even in the absence of external DNA damage, in contrast to previous reports that XPA is normally resident in the cytoplasm and is imported following DNA damage. We then analyzed four genetically matched human cell line pairs deficient or proficient in XPA. Of the 14,000 genes transcribed in each cell line, 325 genes (2%) had a significant XPA-dependent directional change in gene expression that was common to all four pairs (with a false discovery rate of 0.05). These genes were enriched in pathways for the maintenance of mitochondria. Only 27 common genes were different by more than 1.5-fold. The most significant hits were AKR1C1 and AKR1C2, involved in steroid hormone metabolism. AKR1C2 protein was lower in all of the immortalized XPA-deficient cells. Retinoic acid treatment led to modest XPA-dependent activation of some genes with transcription-related functions. We conclude that XPA status does not globally influence human gene transcription. However, XPA significantly influences expression of a small subset of genes important for mitochondrial functions and steroid hormone metabolism. The results may help explain defects in neurological function and sterility in individuals with xeroderma pigmentosum.