Temporally resolved transcriptional recording inE. coliDNA using a Retro-Cascorder

Sierra K. Lear, Santiago C. Lopez, Alejandro González-Delgado, Santi Bhattarai-Kline, Seth L. Shipman

Published: 2023-04-13 DOI: 10.1038/s41596-023-00819-6

gene expression

Escherichia coli

Retro-Cascorder

temporal recording

CRISPR array

AI 解读

Purification of infection-associated macropinosomes by magnetic isolation for proteomic characterization

Hi-CO: 3D genome structure analysis with nucleosome resolution

Practical and concise synthesis of nucleoside analogs

Comprehensive analysis of glycosphingolipid glycans by lectin microarrays and MALDI-TOF mass spectrometry

Human primordial germ cell-like cells specified from resetting precursors develop in human hindgut organoids

KAS-seq: genome-wide sequencing of single-stranded DNA by N3-kethoxal–assisted labeling

Detecting chromosomal interactions in Capture Hi-C data with CHiCAGO and companion tools

Capture of the newly transcribed RNA interactome using click chemistry

Design, assembly, and characterization of membrane-spanning DNA nanopores

Transcriptome-wide identification of RNA-binding protein binding sites using seCLIP-seq

查看全部

Sections

Figures

References

Biological signals occur over time in living cells. Yet most current approaches to interrogate biology, particularly gene expression, use destructive techniques that quantify signals only at a single point in time. A recent technological advance, termed t
Introduction
Materials
Procedure
Troubleshooting
Timing
Anticipated results
References
ACKNOWLEDGMENTS
ACKNOWLEDGMENTS

Yang, L. et al. Permanent genetic memory with >1-byte capacity. Nat. Methods 11, 1261–1266 (2014).
Siuti, P., Yazbek, J. & Lu, T. K. Synthetic circuits integrating logic and memory in living cells. Nat. Biotechnol. 31, 448–452 (2013).
Bonnet, J., Yin, P., Ortiz, M. E., Subsoontorn, P. & Endy, D. Amplifying genetic logic gates. Science 340, 599–603 (2013).
Farzadfard, F. & Lu, T. K. Genomically encoded analog memory with precise in vivo DNA writing in living cell populations. Science 346, 1256272 (2014).
Courbet, A., Endy, D., Renard, E., Molina, F. & Bonnet, J. Detection of pathological biomarkers in human clinical samples via amplifying genetic switches and logic gates. Sci. Transl. Med. 7, 289ra83–289ra83 (2015).
Roquet, N., Soleimany, A. P., Ferris, A. C., Aaronson, S. & Lu, T. K. Synthetic recombinase-based state machines in living cells. Science 353, aad8559 (2016).
Hsiao, V., Hori, Y., Rothermund, P. W. & Murray, M. M. A population-based temporal logic gate for timing and recording chemical events. Mol. Syst. Biol. 12, 869 (2016).
Weinberg, B. H. et al. Large-scale design of robust genetic circuits with multiple inputs and outputs for mammalian cells. Nat. Biotechnol. 35, 453–462 (2017).
Perli, S. D., Cui, C. H. & Lu, T. K. Continuous genetic recording with self-targeting CRISPR-Cas in human cells. Science 353, aag0511 (2016).
Tang, W. & Liu, D. R. Rewritable multi-event analog recording in bacterial and mammalian cells. Science 360, eaap8992 (2018).
Kempton, H. R., Love, K. S., Guo, L. Y. & Qi, L. S. Scalable biological signal recording in mammalian cells using Cas12a base editors. Nat. Chem. Biol. 1–9 (2022)
Chen, W. et al. Multiplex genomic recording of enhancer and signal transduction activity in mammalian cells. Preprint at bioRxiv https://doi.org/10.1101/2021.11.05.467434 (2021).
Loveless, T. B. et al. Molecular recording of sequential cellular events into DNA. Preprint at bioRxiv https://doi.org/10.1101/2021.11.05.467507 (2021).
Choi, J. et al. A time-resolved, multi-symbol molecular recorder via sequential genome editing. Nature 608, 98–107 (2022).
Shipman, S. L., Nivala, J., Macklis, J. D. & Church, G. M. Molecular recordings by directed CRISPR spacer acquisition. Science 353, aaf1175 (2016).
Sheth, R. U., Yim, S. S., Wu, F. L. & Wang, H. H. Multiplex recording of cellular events over time on CRISPR biological tape. Science 358, 1457–1461 (2017).
Schmidt, F., Cherepkova, M. Y. & Platt, R. J. Transcriptional recording by CRISPR spacer acquisition from RNA. Nature 562, 380–385 (2018).
Yim, S. S. et al. Robust direct digital-to-biological data storage in living cells. Nat. Chem. Biol. 17, 246–253 (2021).
Sheth, R. U. & Wang, H. H. DNA-based memory devices for recording cellular events. Nat. Rev. Genet. 19, 718–732 (2018).
Lear, S. K. & Shipman, S. L. Molecular recording: transcriptional data collection into the genome. Curr. Opin. Biotechnol. 79, 102855 (2023).
Bhattarai-Kline, S. et al. Recording gene expression order in DNA by CRISPR addition of retron barcodes. Nature https://doi.org/10.1038/s41586-022-04994-6 (2022).
Yosef, I., Goren, M. G. & Qimron, U. Proteins and DNA elements essential for the CRISPR adaptation process in Escherichia coli. Nucleic Acids Res. 40, 5569–5576 (2012).
Nuñez, J. K. et al. Cas1–Cas2 complex formation mediates spacer acquisition during CRISPR–Cas adaptive immunity. Nat. Struct. Mol. Biol. 21, 528–534 (2014).
Shipman, S. L., Nivala, J., Macklis, J. D. & Church, G. M. CRISPR–Cas encoding of a digital movie into the genomes of a population of living bacteria. Nature 547, 345–349 (2017).
Silas, S. et al. Direct CRISPR spacer acquisition from RNA by a natural reverse transcriptase–Cas1 fusion protein. Science 351, aad4234 (2016).
Tanna, T., Schmidt, F., Cherepkova, M. Y., Okoniewski, M. & Platt, R. J. Recording transcriptional histories using Record-seq. Nat. Protoc. 15, 513–539 (2020).
Schmidt, F. et al. Noninvasive assessment of gut function using transcriptional recording sentinel cells. Science 376, eabm6038 (2022).
Yehl, K. & Lu, T. Scaling computation and memory in living cells. Curr. Opin. Biomed. Eng. 4, 143–151 (2017).
Nuñez, J. K., Bai, L., Harrington, L. B., Hinder, T. L. & Doudna, J. A. CRISPR immunological memory requires a host factor for specificity. Mol. Cell 62, 824–833 (2016).
Yoganand, K. N. R., Sivathanu, R., Nimkar, S. & Anand, B. Asymmetric positioning of Cas1–2 complex and Integration Host Factor induced DNA bending guide the unidirectional homing of protospacer in CRISPR-Cas type I-E system. Nucleic Acids Res. 45, 367–381 (2017).
Sharon, E. et al. Functional genetic variants revealed by massively parallel precise genome editing. Cell 175, 544–557.e16 (2018).
Kong, X. et al. Precise genome editing without exogenous donor DNA via retron editing system in human cells. Protein Cell 12, 899–902 (2021).
Lopez, S. C., Crawford, K. D., Lear, S. K., Bhattarai-Kline, S. & Shipman, S. L. Precise genome editing across kingdoms of life using retron-derived DNA. Nat. Chem. Biol. 18, 199–206 (2022).
Zhao, B., Chen, S.-A. A., Lee, J. & Fraser, H. B. Bacterial retrons enable precise gene editing in human cells. CRISPR J. 5, 31–39 (2022).
Palka, C., Fishman, C. B., Bhattarai-Kline, S., Myers, S. A. & Shipman, S. L. Retron reverse transcriptase termination and phage defense are dependent on host RNase H1. Nucleic Acids Res. 50, 3490–3504 (2022).
Munck, C., Sheth, R. U., Freedberg, D. E. & Wang, H. H. Recording mobile DNA in the gut microbiota using an Escherichia coli CRISPR–Cas spacer acquisition platform. Nat. Commun. 11, 95 (2020).
Lee, P. Y., Costumbrado, J., Hsu, C. Y. & Kim, Y. H. Agarose gel electrophoresis for the separation of DNA fragments. J. Vis. Exp. 62, 3923 (2012).
Kluyver, T., et al. Jupyter Notebooks—a publishing format for reproducible computational workflows. In: Loizides, F. & Schmidt, B. (eds.) Positioning and Power in Academic Publishing: Players, Agents and Agendas, 87–90 (IOS Press, 2016).
Joshi, N.A. & Fass, J.N. Sickle: a sliding-window, adaptive, quality-based trimming tool for FastQ files (Version 1.33) Available at: https://github.com/najoshi/sickle. (2011).
JoVE Science Education Database. Microbiology. Serial Dilutions and Plating: Microbial Enumeration (JoVE, 2022).

Temporally resolved transcriptional recording inE. coliDNA using a Retro-Cascorder

Supplementary information

推荐阅读