应激扰动基因表达研究中的严重并发症：以紫外线照射的p53突变型小鼠胚胎成纤维细胞为例。
Serious complications in gene-expression studies with stress perturbation: An example of UV-exposed p53-mutant mouse embryonic fibroblasts.
作者信息
Bruning Oskar, Yuan Xiaolian, Rodenburg Wendy, Bruins Wendy, van Oostrom Conny T, Rauwerda Han, Wittink Floyd Ra, Jonker Martijs J, de Vries Annemieke, Breit Timo M
机构信息
MicroArray Department and Integrative Bioinformatics Unit (MAD-IBU); Swammerdam Institute for Life Sciences; Faculty of Science; University of Amsterdam (UvA); Amsterdam, The Netherlands.
出版信息
Transcription. 2010 Nov;1(3):159-164. doi: 10.4161/trns.1.3.13487. Epub 2010 Aug 30.
Abstract
Reanalysis of our UV study of p53-mutant mouse embryonic fibroblasts revealed an intriguing orchestration of massive transcriptome responses. However, close scrutiny of the data uncovered an affected mRNA/rRNA ratio, effectively inhibiting valid data analysis. UV-dose range-finding showed low-dose UV specific- and high-dose stress-related responses, which represent a plea for UV dose range-finding in experimental design.
摘要
对我们关于p53突变型小鼠胚胎成纤维细胞的紫外线研究进行重新分析后发现，大量转录组反应呈现出一种有趣的协同作用。然而，对数据的仔细审查发现mRNA/rRNA比例受到影响，这实际上阻碍了有效的数据分析。紫外线剂量范围测定显示出低剂量紫外线特异性反应和高剂量应激相关反应，这表明在实验设计中进行紫外线剂量范围测定是很有必要的。
相似文献
1
Serious complications in gene-expression studies with stress perturbation: An example of UV-exposed p53-mutant mouse embryonic fibroblasts.应激扰动基因表达研究中的严重并发症：以紫外线照射的p53突变型小鼠胚胎成纤维细胞为例。
Transcription. 2010 Nov;1(3):159-164. doi: 10.4161/trns.1.3.13487. Epub 2010 Aug 30.
2
The absence of Ser389 phosphorylation in p53 affects the basal gene expression level of many p53-dependent genes and alters the biphasic response to UV exposure in mouse embryonic fibroblasts.p53中Ser389磷酸化的缺失会影响许多p53依赖性基因的基础基因表达水平，并改变小鼠胚胎成纤维细胞对紫外线照射的双相反应。
Mol Cell Biol. 2008 Mar;28(6):1974-87. doi: 10.1128/MCB.01610-07. Epub 2008 Jan 14.
3
Cryptochrome deletion in p53 mutant mice enhances apoptotic and anti-tumorigenic responses to UV damage at the transcriptome level.p53 突变小鼠中隐色素的缺失增强了转录组水平对 UV 损伤的凋亡和抗肿瘤反应。
Funct Integr Genomics. 2019 Sep;19(5):729-742. doi: 10.1007/s10142-019-00680-5. Epub 2019 May 1.
4
Mutational status of the p53 gene modulates the basal level of jun N-terminal kinase and its inducibility by ultraviolet irradiation in A1-5 rat fibroblasts.p53基因的突变状态可调节A1-5大鼠成纤维细胞中Jun氨基末端激酶的基础水平及其对紫外线照射的诱导性。
Mol Carcinog. 1999 Aug;25(4):262-72. doi: 10.1002/(sici)1098-2744(199908)25:4<262::aid-mc5>3.0.co;2-u.
5
Apoptosis in UV-C light irradiated p53 wild-type, apaf-1 and p53 knockout mouse embryonic fibroblasts: interplay of receptor and mitochondrial pathway.紫外线C照射的p53野生型、凋亡蛋白酶激活因子-1和p53基因敲除小鼠胚胎成纤维细胞中的细胞凋亡：受体和线粒体途径的相互作用
Apoptosis. 2005 Dec;10(6):1295-304. doi: 10.1007/s10495-005-1392-3.
6
Human tumor p53 mutations are selected for in mouse embryonic fibroblasts harboring a humanized p53 gene.在携带人源化p53基因的小鼠胚胎成纤维细胞中选择了人类肿瘤p53突变。
Proc Natl Acad Sci U S A. 2004 Mar 2;101(9):2963-8. doi: 10.1073/pnas.0308607101. Epub 2004 Feb 19.
7
Abrogation of p53 function affects gadd gene responses to DNA base-damaging agents and starvation.p53功能的缺失影响gadd基因对DNA碱基损伤剂和饥饿的反应。
DNA Cell Biol. 1996 Oct;15(10):805-15. doi: 10.1089/dna.1996.15.805.
8
9
Telomerase-immortalized human fibroblasts retain UV-induced mutagenesis and p53-mediated DNA damage responses.端粒酶永生化的人成纤维细胞保留紫外线诱导的诱变作用和p53介导的DNA损伤反应。
DNA Repair (Amst). 2006 Jan 5;5(1):61-70. doi: 10.1016/j.dnarep.2005.07.005. Epub 2005 Sep 1.
10
Fen1 is induced p53 dependently and involved in the recovery from UV-light-induced replication inhibition.Fen1 由 p53 依赖性诱导，并参与紫外线诱导的复制抑制的恢复过程。
Oncogene. 2005 Dec 15;24(56):8304-13. doi: 10.1038/sj.onc.1208994.
引用本文的文献
1
Allele-specific wild-type TP53 expression in the unaffected carrier parent of children with Li-Fraumeni syndrome.李-弗劳梅尼综合征患儿未受影响的携带致病基因的亲代中，等位基因特异性野生型TP53的表达
Cancer Genet. 2017 Feb;211:9-17. doi: 10.1016/j.cancergen.2017.01.001. Epub 2017 Jan 9.
2
Confounding Factors in the Transcriptome Analysis of an In-Vivo Exposure Experiment.体内暴露实验转录组分析中的混杂因素
PLoS One. 2016 Jan 20;11(1):e0145252. doi: 10.1371/journal.pone.0145252. eCollection 2016.
3
Valuable lessons-learned in transcriptomics experimentation.转录组学实验中获得的宝贵经验教训。
Transcription. 2015;6(3):51-5. doi: 10.1080/21541264.2015.1064195.
4
A range finding protocol to support design for transcriptomics experimentation: examples of in-vitro and in-vivo murine UV exposure.一种支持转录组学实验设计的预实验方案：体外和体内小鼠紫外线照射示例
PLoS One. 2014 May 13;9(5):e97089. doi: 10.1371/journal.pone.0097089. eCollection 2014.
本文引用的文献
1
Regulation of human skin pigmentation in situ by repetitive UV exposure: molecular characterization of responses to UVA and/or UVB.反复紫外线照射对人皮肤色素沉着的原位调控：对 UVA 和/或 UVB 反应的分子特征。
J Invest Dermatol. 2010 Jun;130(6):1685-96. doi: 10.1038/jid.2010.5. Epub 2010 Feb 11.
2
Finding transcriptomics biomarkers for in vivo identification of (non-)genotoxic carcinogens using wild-type and Xpa/p53 mutant mouse models.利用野生型和Xpa/p53突变小鼠模型寻找用于体内鉴定（非）基因毒性致癌物的转录组学生物标志物。
Carcinogenesis. 2009 Oct;30(10):1805-12. doi: 10.1093/carcin/bgp190. Epub 2009 Aug 20.
3
Phosphorylation of eukaryotic translation initiation factor 2alpha coordinates rRNA transcription and translation inhibition during endoplasmic reticulum stress.真核生物翻译起始因子2α的磷酸化在内质网应激期间协调核糖体RNA转录和翻译抑制。
Mol Cell Biol. 2009 Aug;29(15):4295-307. doi: 10.1128/MCB.00260-09. Epub 2009 May 26.
4
DNA damage regulates alternative splicing through inhibition of RNA polymerase II elongation.DNA损伤通过抑制RNA聚合酶II的延伸来调控可变剪接。
Cell. 2009 May 15;137(4):708-20. doi: 10.1016/j.cell.2009.03.010.
5
Bioinformatics enrichment tools: paths toward the comprehensive functional analysis of large gene lists.生物信息学富集工具：通向大型基因列表全面功能分析的途径
Nucleic Acids Res. 2009 Jan;37(1):1-13. doi: 10.1093/nar/gkn923. Epub 2008 Nov 25.
6
Transcriptional changes in trichothiodystrophy cells.毛发硫营养不良细胞中的转录变化。
DNA Repair (Amst). 2008 Aug 2;7(8):1364-71. doi: 10.1016/j.dnarep.2008.05.002. Epub 2008 Jun 24.
7
The absence of Ser389 phosphorylation in p53 affects the basal gene expression level of many p53-dependent genes and alters the biphasic response to UV exposure in mouse embryonic fibroblasts.p53中Ser389磷酸化的缺失会影响许多p53依赖性基因的基础基因表达水平，并改变小鼠胚胎成纤维细胞对紫外线照射的双相反应。
Mol Cell Biol. 2008 Mar;28(6):1974-87. doi: 10.1128/MCB.01610-07. Epub 2008 Jan 14.
8
Rat toxicogenomic study reveals analytical consistency across microarray platforms.大鼠毒理基因组学研究揭示了不同微阵列平台间的分析一致性。
Nat Biotechnol. 2006 Sep;24(9):1162-9. doi: 10.1038/nbt1238.
9
The MicroArray Quality Control (MAQC) project shows inter- and intraplatform reproducibility of gene expression measurements.微阵列质量控制（MAQC）项目展示了基因表达测量在不同平台间和同一平台内的可重复性。
Nat Biotechnol. 2006 Sep;24(9):1151-61. doi: 10.1038/nbt1239.
10
Performance comparison of one-color and two-color platforms within the MicroArray Quality Control (MAQC) project.微阵列质量控制（MAQC）项目中单色和双色平台的性能比较。
Nat Biotechnol. 2006 Sep;24(9):1140-50. doi: 10.1038/nbt1242.
Zotero 插件