Biomolecular Systems Engineering - NCCR MSE

Biomolecular Systems Engineering

Transcriptional recording by CRISPR spacer acquisition from RNA. (a) Expression of CRISPR proteins RT–Cas1 and Cas2 leads to the acquisition of intracellular RNAs, providing a molecular memory of transcriptional events stored within DNA. b, Comparison of RNA-seq and Record–seq. RNA-seq captures the transcriptome of a population of cells at a single point in time, providing a transient snapshot of cellular events. By contrast, Record–seq permanently stores information about prior transcriptional events in a CRISPR array, providing a molecular record that can be used to reconstruct transcriptional events that occurred over time. [Adapted from Schmidt et al., Nature, 2018]
Transcriptional recording by CRISPR spacer acquisition from RNA. (a) Expression of CRISPR proteins RT–Cas1 and Cas2 leads to the acquisition of intracellular RNAs, providing a molecular memory of transcriptional events stored within DNA. b, Comparison of RNA-seq and Record–seq. RNA-seq captures the transcriptome of a population of cells at a single point in time, providing a transient snapshot of cellular events. By contrast, Record–seq permanently stores information about prior transcriptional events in a CRISPR array, providing a molecular record that can be used to reconstruct transcriptional events that occurred over time. [Adapted from Schmidt et al., Nature, 2018]

We engineer synthetic cellular memory platforms that enable the reconstruction of cellular histories and can be applied as living diagnostics.

A fundamental challenge in biology is to understand how cells function and integrate complex molecular information to perform different behaviors. For example, the differentiation of a stem cell into two daughter cells with distinct identities or the transformation of a normal cell into a cancer cell. This challenge has motivated the creation of numerous technologies facilitating detailed intracellular observations at the level of DNA, RNA, protein, and metabolites. Despite the power of these approaches, they generally require destructive methods and therefore observations are limited to a few snapshots in time or select asynchronous cellular processes. One provocative solution to this is to introduce DNA writing and molecular recording platforms within cells that enable the encoding, storage, and retrieval of molecular information.

Towards the goal of continuously recording molecular events within cells, my laboratory is developing and applying Record-seq, a ‘transcriptional recording’ platform that employs CRISPR spacer acquisition from RNA to capture and convert intracellular RNAs into DNA, permanently storing transcriptional information in the DNA of living cells. The newly acquired sequences serve as transcriptional records, which are retrievable via deep sequencing and can be leverage to reconstruct cellular histories. This technology provides an entirely new mode of interrogating dynamic biological and physiological processes and opens up numerous avenues for future work in engineering cellular systems.

Publications

F. Schmidt, M. Y. Cherepkova, R. Platt “Transcriptional recording by CRISPR spacer acquisition from RNA“ Nature 2018. [DOI]
G. Wang, R. D. Chow, L. Ye, C. D. Guzman, X. Dai, M. B. Dong, F. Zhang, P. A. Sharp, R. Platt, S. Chen “Mapping a functional cancer genome atlas of tumor suppressors in mouse liver using AAV-CRISPR–mediated direct in vivo screening“ Sci. Adv. 2018. [DOI]
R. D. Chow, C. D. Guzman, G. Wang, F. Schmidt, M. W. Youngblood, L. Ye, Y. Errami, M. B. Dong, M. A. Martinez, F. Zhang, P. Renauer, K. Bilguvar, M. Gunel, P. A. Sharp, R. Platt, S. Chen “AAV-mediated direct in vivo CRISPR screen identifies functional suppressors in glioblastoma“ Nat. Neurosci. 2017. [DOI]
F. Schmidt, R. Platt “Applications of CRISPR-Cas for synthetic biology and genetic recording“ Curr. Opin. Syst. Biol. 2017, 5:9-15. [DOI]
R. Platt, Y. Zhou, I. M. Slaymaker, A. S. Shetty, N. R. Weisbach, J. Kim, J. Sharma, M. Desai, S. Sood, H. R. Kempton, G. R. Crabtree, G. Feng, F. Zhang “Chd8 Mutation Leads to Autistic-like Behaviors and Impaired Striatal Circuits“ Cell Rep. 2017, 19:335-50. [DOI]