Wei Chen, Junhong Choi, Xiaoyi Li, Jenny F. Nathans, Beth Martin, Wei Yang, Nobuhiko Hamazaki, Chengxiang Qiu, Jean-Benoît Lalanne, Samuel Regalado, Haedong Kim, Vikram Agarwal, Eva Nichols, Anh Leith, Choli Lee, Jay Shendure
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引用次数: 0
摘要
测量基因表达或信号转导活性的传统方法需要在感兴趣的时间范围内破坏生物样本或对其进行实时成像。在这里,我们展示了另一种将此类生物活动稳定记录到基因组中的范例。增强子驱动的基因组记录转录活动(ENGRAM)是基于信号依赖性的质粒编辑引导核糖核酸(prime editing guide RNAs)的产生,这种引导核糖核酸介导信号特异性条形码(符号)插入基因组编码的记录单元。我们展示了这一策略如何用于多路记录数十到数百个顺式调控元件的细胞类型特异性活动,并具有高保真、高灵敏度和高重现性。利用信号转导通路响应顺式调节元件,我们还展示了 WNT、NF-κB 和 Tet-On 活性的时间和浓度依赖性基因组记录。通过将 ENGRAM 与 DNA Typewriter1 的顺序基因组编辑相结合,我们将两种正交信号通路的时间动态信息稳定地记录到基因组 DNA 上。最后,我们应用 ENGRAM 综合记录了小鼠胚胎干细胞分化为胃体(哺乳动物早期发育的体外模型)过程中近 100 个转录因子共识主题的瞬时活动。尽管这些只是概念验证实验,要完全实现这些可能性还有很多工作要做,但以符号方式记录细胞内的生物信号或状态、基因组和时间,对我们如何在生物系统中进行测量的当代范式具有广泛的补充潜力。
Symbolic recording of signalling and cis-regulatory element activity to DNA
Measurements of gene expression or signal transduction activity are conventionally performed using methods that require either the destruction or live imaging of a biological sample within the timeframe of interest. Here we demonstrate an alternative paradigm in which such biological activities are stably recorded to the genome. Enhancer-driven genomic recording of transcriptional activity in multiplex (ENGRAM) is based on the signal-dependent production of prime editing guide RNAs that mediate the insertion of signal-specific barcodes (symbols) into a genomically encoded recording unit. We show how this strategy can be used for multiplex recording of the cell-type-specific activities of dozens to hundreds of cis-regulatory elements with high fidelity, sensitivity and reproducibility. Leveraging signal transduction pathway-responsive cis-regulatory elements, we also demonstrate time- and concentration-dependent genomic recording of WNT, NF-κB and Tet-On activities. By coupling ENGRAM to sequential genome editing via DNA Typewriter1, we stably record information about the temporal dynamics of two orthogonal signalling pathways to genomic DNA. Finally we apply ENGRAM to integratively record the transient activity of nearly 100 transcription factor consensus motifs across daily windows spanning the differentiation of mouse embryonic stem cells into gastruloids, an in vitro model of early mammalian development. Although these are proof-of-concept experiments and much work remains to fully realize the possibilities, the symbolic recording of biological signals or states within cells, to the genome and over time, has broad potential to complement contemporary paradigms for how we make measurements in biological systems. Enhancer-driven genomic recording of transcriptional activity in multiplex (ENGRAM) is used for multiplex recording of the cell-type-specific activities of dozens to hundreds of cis-regulatory elements with high fidelity, sensitivity and reproducibility.
期刊介绍:
Nature is a prestigious international journal that publishes peer-reviewed research in various scientific and technological fields. The selection of articles is based on criteria such as originality, importance, interdisciplinary relevance, timeliness, accessibility, elegance, and surprising conclusions. In addition to showcasing significant scientific advances, Nature delivers rapid, authoritative, insightful news, and interpretation of current and upcoming trends impacting science, scientists, and the broader public. The journal serves a dual purpose: firstly, to promptly share noteworthy scientific advances and foster discussions among scientists, and secondly, to ensure the swift dissemination of scientific results globally, emphasizing their significance for knowledge, culture, and daily life.