结合TSS-MPRA和敏感的TSS配置不相似度评分,研究转录启动的序列决定因素
Carlos Guzman1,2, Sascha Duttke1, Yixin Zhu1
1Department of Medicine, Division of Endocrinology, U.C. San Diego School of Medicine, La Jolla, CA 92093, USA.
Nucleic acids research
|July 5, 2023
概括
大规模并行报告员测试 (MPRA) 可以准确地捕获大约60%的发起者的转录开始地点 (TSS) 配置文件. 开发了一种新的TSS-MPRA协议和WIP评分方法,以评估MPRA对研究基因调节的忠实性.
科学领域:
- 遗传学 遗传学 是一个
- 分子生物学分子生物学
- 表观遗传学 在表观遗传学中,表观遗传学是指表观遗传学.
背景情况:
- 互联调节元件 (Cis-regulatory elements,简称CREs) 具有不同的转录开始地点 (TSS) 配置文件,表明了调节机制.
- 大规模并行报告员测定 (MPRA) 广泛用于CRE研究,但它们复制内源性TSS配置文件的能力尚不清楚.
研究的目的:
- 开发和验证一个低输入的MPRA协议 (TSS-MPRA) 用于测量插曲性和染色化的报告者TSS配置文件.
- 创建一个新的不相似性评分算法 (WIP评分) 来进行MPRA和内源TSS配置文件的敏感比较.
- 评估MPRA在复制内源TSS配置文件中的忠实性,并评估插入尺寸和染色化的影响.
主要方法:
- 开发一个低输入的TSS-MPRA协议.
- 创建一个新的WIP得分算法用于TSS配置文件比较.
- 应用TSS-MPRA和WIP评分到500个独特的记者插件.
- 将MPRA TSS配置文件与内源配置文件进行比较,包括lentiviral染色化和不同插入长度的影响.
主要成果:
- 短 (153 bp) MPRA促销者插入复制的内源性TSS模式大约60%的促销者.
- 伦氏病毒记者染色化没有提高TSS-MPRA启动模式的忠实性.
- 在MPRA中插入尺寸的增加往往导致活体中不存在的外部TSS的激活.
结论:
- TSS-MPRA和WIP评分提供了一种敏感的方法来比较MPRA和内生TSS配置文件.
- 特别是在短插件的MPRA可以复制大量内源TSS模式,但存在局限性.
- 研究结果强调了使用MPRA研究转录机制和监管元素的关键考虑因素.
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