Symbolic recording of signalling and cis-regulatory element activity to DNA

作者：Wei Chen, Junhong Choi, Xiaoyi Li, Jenny F. Nathans, Beth Martin, Wei Yang, Nobuhiko Hamazaki, Chengxiang Qiu, Jean‐Benoît Lalanne, Samuel G. Regalado, Haedong Kim, Vikram Agarwal, Eva K. Nichols, Anh Leith, Choli Lee, Jay Shendure · 发表于：Nature · 年份：2024 · DOI：10.1038/s41586-024-07706-4 · 被引用次数：56 · 研究领域：CRISPR and Genetic Engineering、RNA and protein synthesis mechanisms、RNA regulation and disease

Abstract 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 Typewriter 1 , 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...