PIE-seq – identifying RNA-binding protein targets by dual RNA-deaminase editing and sequencing

RNA-binding proteins (RBPs) are essential for gene regulation, but it remains a challenge to identify their RNA targets across cell types. University of Chicago researchers have developed PIE-Seq to investigate Protein-RNA Interaction with dual-deaminase Editing and Sequencing by conjugating C-to-U and A-to-I base editors to RBPs. The researchers benchmark PIE-Seq and demonstrate its sensitivity in single cells, its application in the developing brain, and its scalability with 25 human RBPs. Bulk PIE-Seq identifies canonical binding features for RBPs such as PUM2 and NOVA1, and nominates additional target genes for most tested RBPs such as SRSF1 and TDP-43/TARDBP. Homologous RBPs frequently edit similar sequences and gene sets in PIE-Seq while different RBP families show distinct targets. Single-cell PIE-PUM2 uncovers comparable targets to bulk samples and applying PIE-PUM2 to the developing mouse neocortex identifies neural-progenitor- and neuron-specific target genes such as App. In summary, PIE-Seq provides an orthogonal approach and resource to uncover RBP targets in mice and human cells.

PIE-PUM2 uncovers mRNA targets in single cells

a The workflow of PIE-Seq for 10-cell and single-cell samples. b IGV browser tracks of the CDKN1B gene showing PIE-PUM2 editing sites in single-cell and ten-cell samples. C-to-U editing rates over 10% are indicated as blue (Cytosine) and red (Uracil). c Venn diagrams showing PUM2 targets identified in single-cell and ten-cell samples largely overlapped with those of bulk PIE-PUM2.