Theoretical modeling on CRISPR-coded cell lineages: efficient encoding and optimal reconstruction

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bioRxiv. 2019 Jul;. doi: 10.1101/538488

Theoretical modeling on CRISPR-coded cell lineages: efficient encoding and optimal reconstruction Espinosa Medina Lab

Sugino K, Garcia-Marques J, Espinosa-Medina I, Lee T

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Abstract

Delineating cell lineages is a prerequisite for interrogating the genesis of cell types. CRISPR/Cas9 can edit genomic sequence during development which enables to trace cell lineages. Recent studies have demonstrated the feasibility of this idea. However, the optimality of the encoding or reconstruction processes has not been adequately addressed. Here, we surveyed a multitude of reconstruction algorithms and found hierarchical clustering, with a metric based on the number of shared Cas9 edits, delivers the best reconstruction. However, the trackable depth is ultimately limited by the number of available coding units that typically decrease exponentially across cell generations. To overcome this limit, we established two strategies that better sustain the coding capacity. One involves controlling target availability via use of parallel gRNA cascades, whereas the other strategy exploits adjustable Cas9/gRNA editing rates. In summary, we provide a theoretical basis in understanding, designing, and analyzing robust CRISPR barcodes for dense reconstruction of protracted cell lineages.

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Janelia Authors

Isabel Espinosa Medina

Ken Sugino

Jorge Garcia Marques

Tzumin Lee

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Theoretical modeling on CRISPR-coded cell lineages: efficient encoding and optimal reconstruction

Abstract

Janelia Authors