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조회903

Memorial Sloan Kettering Cancer Center

Nature, Jul 17 2024, | https://doi.org/10.1038/s41586-024-07706-4 Symbolic recording of signalling and cis-regulatory element activity to DNA

Wei Chen^1,2,11, Junhong Choi^1,3,4,5,11, Xiaoyi Li^1,5, Jenny F. Nathans^1,5,6, Beth Martin^1,5, Wei Yang^1,5, Nobuhiko Hamazaki^1,5,7,8,9, Chengxiang Qiu^1,5, Jean-Benoît Lalanne¹, Samuel Regalado^1,5, Haedong Kim^1,5, Vikram Agarwal¹, Eva Nichols¹, Anh Leith¹, Choli Lee^1,5 & Jay Shendure^1,3,5,9,10

¹Department of Genome Sciences, University of Washington, Seattle, WA, USA.

²Molecular Engineering and Sciences Institute, University of Washington, Seattle, WA, USA.

³Howard Hughes Medical Institute, Seattle, WA, USA.

⁴Developmental Biology Program, Memorial Sloan Kettering Cancer Center, New York, NY, USA.

⁵Seattle Hub for Synthetic Biology, Seattle, WA, USA.

⁶Medical Scientist Training Program, University of Washington, Seattle, WA, USA.

⁷Department of Obstetrics & Gynecology, University of Washington, Seattle, WA, USA.

⁸Institute for Stem Cell & Regenerative Medicine, University of Washington, Seattle, WA, USA.

⁹Brotman Baty Institute for Precision Medicine, University of Washington, Seattle, WA, USA.

¹⁰Allen Discovery Center for Cell Lineage Tracing, Seattle, WA, USA.

¹¹These authors contributed equally: Wei Chen, Junhong Choi.

Corresponding authors

Correspondence to Wei Chen or Jay Shendure.

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 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.

논문정보

형식Research article
게재일2024년 07월 (BRIC 등록일 2024-07-19)
연구진국외 연구진
분야 생명과학 > 분자생물학

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