通过混合测序来检测来自非同线性拼接接口的内基因跨拼接事件
Yu-Chen Chen1, Chia-Ying Chen1, Tai-Wei Chiang1
1Genomics Research Center, Academia Sinica, Taipei, Taiwan.
Nucleic acids research
|July 27, 2023
概括
转接RNAs (ts-RNAs),非同线性转录,使用一种新的生物信息学管道准确地识别. 这项研究澄清了ts-RNA生物发生和功能,将它们与圆形RNA (circRNA) 区分开来.
科学领域:
- 分子生物学分子生物学
- 生物信息学是一种生物信息学.
- 基因组学就是基因组学.
背景情况:
- 转接RNAs (ts-RNAs) 是非同线性转录,由于人工物,循环RNAs (circRNAs) 和遗传重组,因此难以检测.
- 在RNA测序数据分析中,内部ts-RNAs经常被误认为circRNAs.
研究的目的:
- 开发一个强大的生物信息管道 (NCLscan-hybrid) 以准确检测ts-RNA.
- 为了区分内部ts-RNAs和circRNAs,使用集成的短和长RNA-seq读取.
- 研究t-RNAs在生物通路中的作用及其形成机制.
主要方法:
- 开发NCLscan-hybrid生物信息管道,整合短和长RNA-seq读数.
- 使用外循环和滚动循环的长读数来进行ts-RNA和circRNA的区分.
- 采用基于CRISPR的基因组修饰和实验验证,用于ts-RNA的表征.
主要成果:
- 在NCLscan混合管道成功地减少了ts-RNA检测中的假阳性.
- 以前被确定为circRNAs的四个非同线性事件被证实为ts-RNAs.
- 克里斯普尔实验揭示了侧面的内基补充序列促进了ts-RNA的形成.
- 发现一种特定的ts-RNA,ts-ARFGEF1,在乳腺癌细胞中通过PERK/eIF2a/ATF4/CHOP通路的p53-介导亡中起着至关重要的作用.
结论:
- 该研究提供了经过验证的生物信息学和实验方法,用于严格的ts-RNA表征.
- 这些发现扩大了对ts-RNA识别,生物发生和功能作用的理解.
- 这项工作提供了有关ts-RNA参与癌症相关信号通路的见解.
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