En masse evaluation of RNA guides (EMERGe) for ADARs

Abstract

Adenosine Deaminases Acting on RNA (ADARs) convert adenosine to inosine in duplex RNA, and through the delivery of guide RNAs, can be directed to edit specific adenosine sites. As ADARs are endogenously expressed in humans, their editing capacities hold therapeutic potential and allow us to target disease-relevant sequences in RNA through the rationale design of guide RNAs. However, current design principles are not suitable for difficult-to-edit target sites, posing challenges to unlocking the full therapeutic potential of this approach. This chapter discusses how we circumvent this barrier through an in vitro screening method, En Masse Evaluation of RNA Guides (EMERGe), which enables comprehensive screening of ADAR substrate libraries and facilitates the identification of editing-enabling guide strands for specific adenosines. From library generation and screening to next generation sequencing (NGS) data analysis to verification experiments, we describe how a sequence of interest can be identified through this high-throughput screening method. Furthermore, we discuss downstream applications of selected guide sequences, challenges in maximizing library coverage, and potential to couple the screen with machine learning or deep learning models.

Keywords: ADAR; High-throughput screening; Next-generation sequencing; RNA-editing.

Fig. 1

An overview of the EMERGe workflow. The ssDNA starting material is synthesized chemically via the phosphoramidite method to include T7 promoter, target adenosine, hairpin linker, and randomized N10 library. After amplification via PCR the now dsDNA is transcribed with T7 RNA polymerase to form the EMERGe RNA hairpin. The hairpin is subjected to deamination by ADAR then reverse transcribed to enable NGS readout of N10 sequences and their associated levels of adenosine deamination. These data are processed and tabulated to discern library sequences that support high levels of deamination. Created with Biorender.com.

Fig. 2

(A) Example 96 nucleotide EMERGe library design. Highlighted in green are regions used in data processing script and highlighted in purple is the library region. (B) Mock results after running processing code and further data processing. The top N10 sequences with the respective GAG and GGG reads of the target A is ranked based on percent editing.

Fig. 3

Example of a heat map generated from a single nucleotide variant analysis of a guide RNA. 5’ to 3’ target sequence with the target A in red and 3’ to 5’ candidate guide shown above heat map. Created with Biorender.com.

Fig. 4

In vitro co-transcriptional 3’ cleavage with HDV sequence and T7 RNA Polymerase for gRNA synthesis. Created with Biorender.com.

Fig. 5

Workflow for guide RNA verification experiments. Target and gRNA generated through in vitro transcription and hybridized. Duplex RNA is react with ADAR, product is then subjected through RT-PCR, followed by Sanger sequencing.