Widespread interaction between ADAR1 and transcriptional byproducts

Abstract

Background: ADAR1, an adenosine-to-inosine (A-to-I) RNA editing enzyme, has an emerging role in cancer immunotherapy. ADAR1 presumably works by suppressing cellular innate immunity response to endogenously generated double-stranded RNAs through RNA editing. However, RNA species that are directly regulated by ADAR1 mediated RNA editing processes remain poorly defined. Results:In this study, we used a novel bioinformatics approach to track ADAR1-RNA interactions. By integrating DNA-seq, RNA-seq, and ADAR1 RNA immunoprecipitation sequencing (fRIP-seq) data of K562 cell line, we provided the first in-situ landscape profiling of ADAR1 RNA binding and editing activities. With long RNA fragments captured by ADAR1 immunoprecipitation, we were able to identify exon junctions and genomic boundaries used by ADAR1-associated RNAs and thus we could possibly trace pre-RNA processing steps that had been acting on them. Our methodology allowed us to establish the knowledge of transcriptome-wide scenario of ADAR1 activities. Intriguingly, we found that ADAR1 had a tendency to interact with transcriptional byproducts originated from obscure regions such as introns and intergenic regions. Conclusions:Our observation might shed light on the dual role of ADAR1 proteins not only in diversifying the transcriptome, but also in reigning RNA debris from obscure regions. Moreover, as the functional potential of seemly transcriptional byproducts is just beginning to emerge, this study would bridge ADAR1 with other fields of RNA biology.

Repurposing RNA sequencing for discovery of RNA modifications in clinical cohorts

“…A further layer of more aggressive filters was also introduced to further ensure the precision of our calls and to generate a cleaner list of sites (table S1). Specifically, sites were discarded if (i) >80% of the supporting reads are spanning an unannotated splicing junction, (ii) they are in or next to a homopolymer ≥6 nucleotides, (iii) almost all mismatches on the supporting reads disappear if substituted with an indel, or (iv) mismatches are from the last 20 bp of the supporting reads as was previously applied (63).…”