Efficient genome editing in erythroid cells unveils novel MYB target genes and regulatory functions

Summary

Targeted genome editing holds great promise in biology. However, efficient genome modification, including gene knock-in (KI), remains an unattained goal in multiple cell types and loci due to poor transfection efficiencies and low target genes expression, impeding the positive selection of recombined cells. Here, we describe a genome editing approach to achieve efficient gene targeting using hard to transfect erythroid cell lines. We demonstrate robust fluorescent protein KI efficiency in low expressed transcription factor (TF) genes (e.g., Myb or Zeb1). We further show the ability to target two independent loci in individual cells, exemplified by MYB-GFP and NuMA-Cherry double KI, allowing multicolor labeling of regulatory factors at physiological endogenous levels. Our KI tagging approach allowed us to perform genome-wide TF analysis at increased signal-to-noise ratios, and highlighted previously unidentified MYB target genes and pathways. Overall, we establish a versatile CRISPR-Cas9-based platform, offering attractive opportunities for the dissection of the erythroid differentiation process.

Graphical abstract

Highlights

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  Efficient genome editing in hard-to-transfect erythroid cell lines

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  High-efficiency in-frame GFP insertion in low expressed gene loci Myb and Zeb1

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  Multi-gene targeting in individual cells: Myb-Gfp/ Numa1-Cherry double KI

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  MYB-GFP CUT&RUN analysis uncovers previously unidentified MYB target genes

Abstract

Cell biology; Genetic engineering; Molecular biology