从RNAseq输入中预测可转移元素 (TE) 插入和TE对Drosophila大脑转录组中的RNA剪接和基因表达的影响
Md Fakhrul Azad1, Tong Tong2, Nelson C Lau3,4,5
1Department of Biochemistry and Cell Biology, Boston University Chobanian & Avedisian School of Medicine, Boston, MA, 02118, USA.
Mobile DNA
|October 10, 2024
概括
内子中的可转移元素 (TE) 很少被拼接成mRNA. 实验验证表明,大多数预测的TE-mRNA融合是内子保留,而不是外离,突出了对 TE 分析改善生物信息学工具的需求.
科学领域:
- 遗传学 遗传学 是一个
- 分子生物学分子生物学
- 生物信息学是一种生物信息学.
背景情况:
- 可转移元素 (TE) 是移动DNA序列.
- 内子中的TEs可能会通过剪接影响基因表达.
- 之前的研究表明,TE经常被外化成mRNA.
研究的目的:
- 重新检查TEs在蛋白质编码基因转录中的异能化频率.
- 用RNA测序 (RNAseq) 数据验证TE插入的生物信息学预测.
- 评估转子子插入和消耗分析仪 (TIDAL) 程序的准确性.
主要方法:
- 对Drosophila RNAseq数据集 (昼夜节律和中脑) 的分析.
- 应用TIDAL程序用于TE插入预测.
- 使用基因组DNA-PCR (gDNA-PCR) 和RT-PCR对预测的TE-mRNA融合的验证.
主要成果:
- 泰达尔预测了几次TE插入,其中一些与之前的研究一致.
- 在TIDAL预测和实验验证之间发现了显著的差异.
- 在23人中只有9人 (约. 40%) 预测的TE插入被gDNA-PCR验证.
- 经过验证的TE插入主要导致了内部保留,而不是嵌合式mRNA形成.
- 具有内在TEs的基因与没有的基因相比,表达明显更高.
结论:
- 从RNAseq数据中预测TE外化的生物信息需要进一步优化.
- 由 TE 拼接成转录产生的化学 TE-mRNA 似乎不常见.
- 实验验证对于确认TE插入及其功能影响至关重要.
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