Abstract
The development of CRISPR-based barcoding methods creates an exciting opportunity to understand cellular phylogenies. We present a compact, tunable, high-capacity Cas12a barcoding system called dual acting inverted site array (DAISY). We combined high-throughput screening and machine learning to predict and optimize the 60-bp DAISY barcode sequences. After optimization, top-performing barcodes had ∼10-fold increased capacity relative to the best random-screened designs and performed reliably across diverse cell types. DAISY barcode arrays generated ∼12 bits of entropy and ∼66,000 unique barcodes. Thus, DAISY barcodes—at a fraction of the size of Cas9 barcodes—achieved high-capacity barcoding. We coupled DAISY barcoding with single-cell RNA-seq to recover lineages and gene expression profiles from ∼47,000 human melanoma cells. A single DAISY barcode recovered up to ∼700 lineages from one parental cell. This analysis revealed heritable single-cell gene expression and potential epigenetic modulation of memory gene transcription. Overall, Cas12a DAISY barcoding is an efficient tool for investigating cell-state dynamics.
Original language | English (US) |
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Pages (from-to) | 3103-3118.e8 |
Journal | Molecular Cell |
Volume | 82 |
Issue number | 16 |
DOIs | |
State | Published - Aug 18 2022 |
All Science Journal Classification (ASJC) codes
- Molecular Biology
- Cell Biology
Keywords
- CRISPR barcoding
- Cas12a
- PRC2
- high throughput screening
- lineage tracking
- machine learning
- melanoma
- online learning optimization
- single cell genomics
- transcriptional memory