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标题：Integrated genome and transcriptome analyses reveal the mechanism of genome instability in ataxia with oculomotor apraxia 2
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作者：Radhakrishnan Kanagaraj ; Richard Mitter ; Theodoros Kantidakis 等
期刊名称：Proceedings of the National Academy of Sciences
印刷版ISSN：0027-8424
电子版ISSN：1091-6490
出版年度：2022
卷号：119
期号：4
DOI：10.1073/pnas.2114314119
语种：English
出版社：The National Academy of Sciences of the United States of America
摘要：Significance Ataxia with oculomotor apraxia (AOA) is a progressive neurodegenerative disease characterized by early‐onset autosomal recessive cerebellar ataxia with oculomotor apraxia, peripheral axonal neuropathy, and impaired motor functions. The AOA-2 subgroup results from mutations in an RNA/DNA helicase, Senataxin, which is encoded by the SETX gene. Here, we carried out integrated genome and transcriptome analyses of cell lines derived from individuals with AOA2, as well as CRISPR/Cas9 generated SETX knockouts, and observed genome-wide chromosome fragility. Genome instability was caused by increased transcription stress and the accumulation of RNA/DNA hybrids near gene promotors, resulting in aberrant DNA repair that led to changes in gene-expression profiles. The results indicate that SETX-defective cells exhibit transcription stress that leads to chromosome fragility. Mutations in the SETX gene, which encodes Senataxin, are associated with the progressive neurodegenerative diseases ataxia with oculomotor apraxia 2 (AOA2) and amyotrophic lateral sclerosis 4 (ALS4). To identify the causal defect in AOA2, patient-derived cells and SETX knockouts (human and mouse) were analyzed using integrated genomic and transcriptomic approaches. A genome-wide increase in chromosome instability (gains and losses) within genes and at chromosome fragile sites was observed, resulting in changes to gene-expression profiles. Transcription stress near promoters correlated with high GCskew and the accumulation of R-loops at promoter-proximal regions, which localized with chromosomal regions where gains and losses were observed. In the absence of Senataxin, the Cockayne syndrome protein CSB was required for the recruitment of the transcription-coupled repair endonucleases (XPG and XPF) and RAD52 recombination protein to target and resolve transcription bubbles containing R-loops, leading to genomic instability. These results show that transcription stress is an important contributor to SETX mutation-associated chromosome fragility and AOA2.
关键词：enDNA repair senataxinataxia with oculomotor apraxiatranscription stress