Giulia Nicoletto, Marianna Terreri, Ilaria Maurizio, Emanuela Ruggiero, Filippo M Cernilogar, Christine A Vaine, Maria Vittoria Cottini, Irina Shcherbakova, Ellen B Penney, Irene Gallina, David Monchaud, D Cristopher Bragg, Gunnar Schotta, Sara N Richter
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We next showed that highly stable G4s can form and stop polymerase amplification at the SVA region from patient-derived fibroblasts and neural progenitor cells. Using chromatin immunoprecipitazion (ChIP) with an anti-G4 antibody coupled to sequencing or quantitative PCR, we showed that XDP SVA G4s are folded even when embedded in a chromatin context in patient-derived cells. Using the G4 ligands BRACO-19 and quarfloxin and total RNA-sequencing analysis, we showed that stabilisation of the XDP SVA G4s reduces TAF1 transcripts downstream and around the SVA, and increases upstream transcripts, while destabilisation using the G4 unfolder PhpC increases TAF1 transcripts. 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引用次数: 0
摘要
G-quadruplexes (G4s) 是在富含鸟嘌呤 (G) 的基因组区域形成的非经典核酸结构。X-连锁肌张力障碍性帕金森病(XDP)是一种遗传性神经退行性疾病,在这种疾病中,一个SINE-VNTR-Alu(SVA)反转座子插入到RNA聚合酶II的关键伙伴TAF1的编码序列中,该反转座子的特点是富含G的重复扩增。XDP SVA改变了TAF1的表达,但在XDP中造成这种结果的原因仍不清楚。为了评估 G4 是否在 XDP SVA 中形成并影响 TAF1 的表达,我们首先对生物信息学预测的 XDP SVA G4 进行了体外鉴定。接下来,我们从患者来源的成纤维细胞和神经祖细胞中发现,高度稳定的 G4s 可以在 SVA 区域形成并阻止聚合酶扩增。通过使用抗 G4 抗体进行染色质免疫沉淀(ChIP),并结合测序或定量 PCR,我们发现 XDP SVA G4 即使嵌入患者来源细胞的染色质中也会折叠。通过使用 G4 配体 BRACO-19 和 quarfloxin 以及总 RNA 序列分析,我们发现稳定 XDP SVA G4s 会减少 SVA 下游和周围的 TAF1 转录本,并增加上游转录本,而使用 G4 解除older PhpC 破坏稳定则会增加 TAF1 转录本。我们的数据表明,XDP SVA 中 G4 的形成是 TAF1 表达异常的主要原因,这为开发 G4 的解稳策略和潜在的靶向疾病开辟了道路。
G-quadruplexes in an SVA retrotransposon cause aberrant TAF1 gene expression in X-linked dystonia parkinsonism
G-quadruplexes (G4s) are non-canonical nucleic acid structures that form in guanine (G)-rich genomic regions. X-linked dystonia parkinsonism (XDP) is an inherited neurodegenerative disease in which a SINE–VNTR–Alu (SVA) retrotransposon, characterised by amplification of a G-rich repeat, is inserted into the coding sequence of TAF1, a key partner of RNA polymerase II. XDP SVA alters TAF1 expression, but the cause of this outcome in XDP remains unknown. To assess whether G4s form in XDP SVA and affect TAF1 expression, we first characterised bioinformatically predicted XDP SVA G4s in vitro. We next showed that highly stable G4s can form and stop polymerase amplification at the SVA region from patient-derived fibroblasts and neural progenitor cells. Using chromatin immunoprecipitazion (ChIP) with an anti-G4 antibody coupled to sequencing or quantitative PCR, we showed that XDP SVA G4s are folded even when embedded in a chromatin context in patient-derived cells. Using the G4 ligands BRACO-19 and quarfloxin and total RNA-sequencing analysis, we showed that stabilisation of the XDP SVA G4s reduces TAF1 transcripts downstream and around the SVA, and increases upstream transcripts, while destabilisation using the G4 unfolder PhpC increases TAF1 transcripts. Our data indicate that G4 formation in the XDP SVA is a major cause of aberrant TAF1 expression, opening the way for the development of strategies to unfold G4s and potentially target the disease.
期刊介绍:
Nucleic Acids Research (NAR) is a scientific journal that publishes research on various aspects of nucleic acids and proteins involved in nucleic acid metabolism and interactions. It covers areas such as chemistry and synthetic biology, computational biology, gene regulation, chromatin and epigenetics, genome integrity, repair and replication, genomics, molecular biology, nucleic acid enzymes, RNA, and structural biology. The journal also includes a Survey and Summary section for brief reviews. Additionally, each year, the first issue is dedicated to biological databases, and an issue in July focuses on web-based software resources for the biological community. Nucleic Acids Research is indexed by several services including Abstracts on Hygiene and Communicable Diseases, Animal Breeding Abstracts, Agricultural Engineering Abstracts, Agbiotech News and Information, BIOSIS Previews, CAB Abstracts, and EMBASE.