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epidecodeR:一种功能性探索工具,用于表观遗传学和表观转录学调节
Kandarp Joshi1, Dan O Wang1,2,3
1Institute for Integrated Cell-Material Sciences (iCeMS), Kyoto University, Yoshida Ushinomiya-cho, Sakyo-ku, Kyoto, 606-8501, Japan.
Briefings in bioinformatics
|January 25, 2024
概括
科学家们开发了epidecodeR,这是一个R包,可以将表观遗传标记 (epi-marks) 与基因表达联系起来. 该工具有助于探索DNA和RNA的修改如何影响生物过程,并预测治疗的有效性.
科学领域:
- 表观遗传学和表观转录学.
- 生物信息学和计算生物学
- 基因规则 基因规则
背景情况:
- 高通量测序产生了大量的表观遗传学和表观转录学数据.
- 现有的in silico方法可以识别和量化修饰部位,但很难将它们与基因表达联系起来.
- 在将特定的表观遗传修饰 ('epi-marks') 与生物环境中的基因表达联系起来时,存在一个关键的差距.
研究的目的:
- 开发一个计算工具,epidecodeR,以促进探索表观基因组/表观基因组状态和基因表达之间的关系.
- 让生物学家能够快速评估"epi标记"对基因表达反应的潜在影响.
- 为分析大规模表观遗传数据集提供一个用户友好的R包.
主要方法:
- 在R中实现epidecodeR,使用累积分布函数和差异基因表达分析.
- 根据相关"epi标记"的数量对基因进行分组,以评估统计学意义.
- 该工具的应用用于分析基因组修饰 (H3K9ac,H3K27ac) 和N6-甲基氨酸 (m6A) 修饰.
主要成果:
- epidecodeR成功预测了H3K9ac和H3K27ac在脱乙酶倒置后的基因表达中的作用.
- 该工具在将N6-甲基-腺酸修饰与读者蛋白敲击后的基因表达联系起来时证明了实用性.
- 应用epidecodeR来研究FTO抑制剂和组织蛋白修饰在药物滥用动物模型中的影响.
结论:
- epidecodeR对于生物学家来说是一个有价值的工具,可以快速调查和理解表观遗传学和表观转录学修饰对基因表达的影响.
- 该套餐有助于将特定的"epi-mark"与细胞和生物过程联系起来,加速生命科学领域的研究.
- epidecodeR提供了一种新的方法来探索潜在的治疗点和治疗疗效,正如药物滥用研究所证明的那样.
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