Alison D. Tang, Colette Felton, Eva Hrabeta-Robinson, Roger Volden, Christopher Vollmers, Angela N. Brooks
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引用次数: 0
摘要
RNA-seq 在 RNA 处理畸变方面有重大发现,这些 RNA 变异与多种疾病有关。事实证明,RNA 中的异常剪接和单核苷酸变异(SNV)会改变转录本的稳定性、定位和功能。特别是,ADAR(一种介导腺苷酸-肌苷酸编辑的酶)的上调与肺腺癌细胞侵袭性的增加有关,也与剪接调控有关。尽管研究剪接和SNVs具有重要的功能意义,但短线程RNA-seq的使用限制了研究界同时研究这两种形式的RNA变异的能力。我们采用长线程测序技术获取全长转录本序列,在单分子水平上阐明变异对剪接变化的顺式效应。我们开发了一种计算工作流程,它增强了 FLAIR(一种调用长线程数据中表达的同工酶模型的工具)的功能,将 RNA 变异调用与携带变异的相关同工酶整合在一起。我们从有无敲除 ADAR 的 H1975 肺腺癌细胞中生成了具有高序列准确性的纳米孔数据。我们应用我们的工作流程来确定关键肌苷酸同工酶,以帮助阐明 ADAR 在肿瘤发生中的重要作用。最终,我们发现长读方法为描述 RNA 变体与剪接模式之间的关系提供了宝贵的见解。
Detecting haplotype-specific transcript variation in long reads with FLAIR2
RNA-seq has brought forth significant discoveries regarding aberrations in RNA processing, implicating these RNA variants in a variety of diseases. Aberrant splicing and single nucleotide variants (SNVs) in RNA have been demonstrated to alter transcript stability, localization, and function. In particular, the upregulation of ADAR, an enzyme that mediates adenosine-to-inosine editing, has been previously linked to an increase in the invasiveness of lung adenocarcinoma cells and associated with splicing regulation. Despite the functional importance of studying splicing and SNVs, the use of short-read RNA-seq has limited the community’s ability to interrogate both forms of RNA variation simultaneously. We employ long-read sequencing technology to obtain full-length transcript sequences, elucidating cis-effects of variants on splicing changes at a single molecule level. We develop a computational workflow that augments FLAIR, a tool that calls isoform models expressed in long-read data, to integrate RNA variant calls with the associated isoforms that bear them. We generate nanopore data with high sequence accuracy from H1975 lung adenocarcinoma cells with and without knockdown of ADAR. We apply our workflow to identify key inosine isoform associations to help clarify the prominence of ADAR in tumorigenesis. Ultimately, we find that a long-read approach provides valuable insight toward characterizing the relationship between RNA variants and splicing patterns.
Genome BiologyBiochemistry, Genetics and Molecular Biology-Genetics
CiteScore
21.00
自引率
3.30%
发文量
241
审稿时长
2 months
期刊介绍:
Genome Biology stands as a premier platform for exceptional research across all domains of biology and biomedicine, explored through a genomic and post-genomic lens.
With an impressive impact factor of 12.3 (2022),* the journal secures its position as the 3rd-ranked research journal in the Genetics and Heredity category and the 2nd-ranked research journal in the Biotechnology and Applied Microbiology category by Thomson Reuters. Notably, Genome Biology holds the distinction of being the highest-ranked open-access journal in this category.
Our dedicated team of highly trained in-house Editors collaborates closely with our esteemed Editorial Board of international experts, ensuring the journal remains on the forefront of scientific advances and community standards. Regular engagement with researchers at conferences and institute visits underscores our commitment to staying abreast of the latest developments in the field.