同时捕获单细胞RNA-seq,ATAC-seq和CRISPR扰动,使多原子屏能够识别基因调节关系
Kaivalya Shevade1, Yeqing Angela Yang2, Kevin Feng1
1Laboratory for Genomics Research, San Francisco, CA 94158, USA; Department of Biochemistry and Biophysics, University of California, San Francisco, CA 94158, USA.
Cell reports methods
|November 11, 2025
概括
我们开发了CRISPR和转录组学测试用于转化酶可访问的染色体 (CAT-ATAC),这是一种将基因表达和染色体可访问性与单细胞中的遗传扰乱联系起来的新方法. 这项技术揭示了基因调节网络,驱动细胞对药物的反应.
科学领域:
- 单细胞基因组学 单细胞基因组学
- 分子生物学分子生物学
- 系统生物学 系统生物学
背景情况:
- 了解基因调节网络 (GRNs) 对于破译细胞功能和反应至关重要.
- 现有的单细胞多组学试验缺乏直接将遗传干扰与转录组和染色质可访问性数据联系起来的能力.
- 基于CRISPR的基因扰动是功能基因组学研究的强大工具.
研究的目的:
- 引入CRISPR和转录组学测试用于转化酶可访问的染色体 (CAT-ATAC),一种用于同时测量转录组,染色体可访问性和CRISPR指导RNA (gRNA) 身份的新型测试.
- 为了证明CAT-ATAC在基因和药物干扰下构建基因调节网络的实用性.
- 通过使用CAT-ATAC识别涉及药物耐药性的新基因和途径.
主要方法:
- 将CRISPR指导RNA (gRNA) 捕获集成到10×基因组学多基因组试验中.
- 在诱导多能干细胞 (iPSC) 和癌症细胞系中输送lentiviral gRNA.
- 应用CAT-ATAC来绘制与达沙替尼抗性相关的基因调节网络.
主要成果:
- 实现了高捕获率 (高达77%) 的lentiviral gRNAs使用阵列和聚合交付.
- 在经历药物和遗传干扰的细胞中成功构建基因调节网络 (GRNs).
- 确定了一种与达沙替尼抗性相关的GRN,涉及HIC2和ZFPM2,并验证了ZFPM2在抗性中的作用.
结论:
- 在单个细胞中,CAT-ATAC可实现高含量,多维的基因型-表型映射.
- 该试验有助于发现基因和细胞相互作用和功能.
- CAT-ATAC是一个强大的工具,用于剖析复杂的生物过程,如耐药性.
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