奇梅拉TE:一个管道检测基因和可转移元素衍生的奇梅拉转录
Daniel S Oliveira1,2, Marie Fablet2,3, Anaïs Larue2,4
1São Paulo State University (Unesp), Institute of Biosciences, Humanities and Exact Sciences, São José do Rio Preto, SP, Brazil.
Nucleic acids research
|August 24, 2023
概括
可转移的元素 (TE) 创建嵌合式转录,驱动遗传多样性和适应. ChimeraTE是一个新的管道,可以识别这些关键的TE-基因融合,即使没有参考基因组.
科学领域:
- 基因组学就是基因组学.
- 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:
- 可移植元素 (TE) 是遗传变异的重要驱动因素,可以导致结构变异.
- TE-基因融合转录或嵌合转录与物种适应有关.
- 目前用于识别嵌合体转录的方法受到规模和依赖参考基因组的限制,忽视了多态TE插入.
研究的目的:
- 开发一种新的计算管道,ChimeraTE,用于转录组全方位识别嵌合体转录.
- 为了能够检测出源于参考指导和无参考分析的嵌合式转录.
- 通过嵌合体转录形成来研究TE在产生遗传多样性的作用.
主要方法:
- 开发了ChimeraTE,这是一个利用对结 RNA-seq 阅读的管道,用于嵌合体转录识别.
- 实现了两种模式:用于多态 TE 插入的参考指导方法 (模式 1) 和无参考方法 (模式 2).
- 使用四个Drosophila melanogaster野生型菌株的RNA-seq数据验证了管道.
主要成果:
- 确定大约1.12%的所有基因产生了嵌合体转录,主要涉及TE-exonized序列.
- 发现大约23%的检测到的嵌合体不在参考基因组中,这表明最近或多态TE插入.
- 证明了ChimeraTE在没有参考基因组的情况下发现嵌合体转录的能力.
结论:
- 奇美拉TE是第一个能够自动识别奇美拉转录的管道,而不需要参考基因组.
- 该工具有助于研究TE对转录组可塑性和遗传多样性的贡献.
- 这些发现强调了多态TE在产生新基因融合和潜在适应过程中的重要性.
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