Direct long-read RNA sequencing identifies a subset of questionable exitrons likely arising from reverse transcription artifacts
Abstract
Resistance to CD19-directed immunotherapies in lymphoblastic leukemia has been attributed, among other factors, to several aberrantCD19pre-mRNA splicing events, including recently reported excision of a cryptic intron embedded withinCD19exon 2. While “exitrons” are known to exist in hundreds of human transcripts, we discovered, using reporter assays and direct long-read RNA sequencing (dRNA-seq), that theCD19exitron is an artifact of reverse transcription. Extending our analysis to publicly available datasets, we identified dozens of questionable exitrons, dubbed “falsitrons,” that appear only in cDNA-seq, but never in dRNA-seq. Our results highlight the importance of dRNA-seq for transcript isoform validation.
Document Details
- Document Type
- Pub Defense Publication
- Publication Date
- Jun 28, 2021
- Source ID
- 10.1186/s13059-021-02411-1
Entities
People
- Andrei Thomas-Tikhonenko
- Elena Sotillo
- Julian König
- Katharina E. Hayer
- Kathi Zarnack
- Laura Schulz
- Manuel Torres-Diz
- Mariela Cortés-lópez
- Mukta Asnani
- Sarah K. Tasian
- Yoseph Barash
Organizations
- American Association for Cancer Research
- German Research Foundation
- National Cancer Institute
- National Institute of General Medical Sciences
- United States Department of Defense
- United States National Library of Medicine
- V Foundation for Cancer Research