Rapidly evolving homing CRISPR barcodes

Kalhor, Reza; Mali, Prashant; Church, George M.

doi:10.1038/nmeth.4108

Cited by 197 publications

(211 citation statements)

References 33 publications

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“…Recently, high-throughput lineage-tracing methods have been developed using CRSIPR/Cas9-based multiplexing DNA barcodes synthesis [54–58]. These barcodes are stably registered in the genome and inherited during cell division and differentiation.…”

Section: Future Directionsmentioning

confidence: 99%

Challenges and emerging directions in single-cell analysis

et al. 2017

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Single-cell analysis is a rapidly evolving approach to characterize genome-scale molecular information at the individual cell level. Development of single-cell technologies and computational methods has enabled systematic investigation of cellular heterogeneity in a wide range of tissues and cell populations, yielding fresh insights into the composition, dynamics, and regulatory mechanisms of cell states in development and disease. Despite substantial advances, significant challenges remain in the analysis, integration, and interpretation of single-cell omics data. Here, we discuss the state of the field and recent advances and look to future opportunities.

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Section: Future Directionsmentioning

confidence: 99%

Challenges and emerging directions in single-cell analysis

et al. 2017

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“…By triggering expression of mSCRIBE in response to NF-κB activation, the researchers were able to record the duration of tumor necrosis factor alpha (TNF-α) exposure in vitro and lipopolysaccharide-induced inflammation in vivo [43••]. Utilizing a similar strategy, Kalhor et al traced cell lineages by barcoding cells with arrays of self-targeting sgRNAs that evolve into unique signatures that record the cumulative mutational history from prior cell generations [44]. More generally, greater understanding of programmed cellular responses to environmental cues is essential for engineering systems that interface robustly with physiological stimuli.…”

Section: Sensing Recording and Reprogramming Cellular Functionsmentioning

confidence: 99%

Mammalian synthetic biology in the age of genome editing and personalized medicine

Chen

2017

Current Opinion in Chemical Biology

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The recent expansion of molecular tool kits has propelled synthetic biology toward the design of increasingly sophisticated mammalian systems. Specifically, advances in genome editing, protein engineering, and circuitry design have enabled the programming of cells for diverse applications, including regenerative medicine and cancer immunotherapy. The ease with which molecular and cellular interactions can be harnessed promises to yield novel approaches to elucidate genetic interactions, program cellular functions, and design therapeutic interventions. Here, we review recent advancements in the development of enabling technologies and the practical applications of mammalian synthetic biology.

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“…This improvement could be implemented because these barcodes can be repeatedly targeted [25]. Additionally, Kalhor et al showed that this technique can be coupled with fluorescence in situ sequencing (FISSEQ) to preserve spatial information while achieving barcode readout.…”

Section: Self-targeting Crispr Barcodesmentioning

confidence: 99%

“…In addition, CRISPR-Cas-based recorders now enable vast numbers of barcodes to be generated over time in order to record cell lineage and important biological events. Based on the studies by Kalhor et al that quantify the information that a single CRISPR site can encode, CRISPR-based recorders can produce ~(2 5 ) n unique barcodes, where n is equal to the number of arrayed target sites [25]. Arraying ten sites together yields more than enough barcodes to label every cell in the human body (~3.7×10 13 ) [26].…”

Section: Summary and Perspectivementioning

confidence: 99%

Scaling computation and memory in living cells

Yehl

2017

Current Opinion in Biomedical Engineering

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The semiconductor revolution that began in the 20th century has transformed society. Key to this revolution has been the integrated circuit, which enabled exponential scaling of computing devices using silicon-based transistors over many decades. Analogously, decreasing costs in DNA sequencing and synthesis, along with the development of robust genetic circuits, are enabling a “biocomputing revolution”. First-generation gene circuits largely relied on assembling various transcriptional regulatory elements to execute digital and analog computing functions in living cells. Basic design rules and computational tools have since been derived so that such circuits can be scaled in order to implement complex computations. In the past five years, great strides have been made in expanding the biological programming toolkit to include recombinase- and CRISPR–based gene circuits that execute complex cellular logic and memory. Recent advances have enabled increasingly dense computing and memory circuits to function in living cells while expanding the application of these circuits from bacteria to eukaryotes, including human cells, for a wide range of uses.

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Rapidly evolving homing CRISPR barcodes

Cited by 197 publications

References 33 publications

Challenges and emerging directions in single-cell analysis

Challenges and emerging directions in single-cell analysis

Mammalian synthetic biology in the age of genome editing and personalized medicine

Scaling computation and memory in living cells

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