TY  - JOUR
A1  - Schulz, Laura
A1  - Torres-Diz, Manuel
A1  - Cortes Lopez, Mariela
A1  - Hayer, Katharina E.
A1  - Asnani, Mukta
A1  - Tasian, Sarah K.
A1  - Barash, Yoseph
A1  - Sotillo, Elena
A1  - Zarnack, Katharina
A1  - König, Julian
A1  - Thomas-Tikhonenko, Andrei
T1  - Direct long-read RNA sequencing identifies a subset of questionable exitrons likely arising from reverse transcription artifacts
T2  - Genome biology
N2  - Resistance to CD19-directed immunotherapies in lymphoblastic leukemia has been attributed, among other factors, to several aberrant CD19 pre-mRNA splicing events, including recently reported excision of a cryptic intron embedded within CD19 exon 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 the CD19 exitron 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.
KW  - Long-read sequencing
KW  - Oxford Nanopore Technologies
KW  - Alternative splicing
KW  - mRNA isoforms
KW  - Exitrons
KW  - Reverse transcription
KW  - CD19
KW  - Immunotherapy
KW  - Blinatumomab
Y1  - 2021
UR  - http://publikationen.ub.uni-frankfurt.de/frontdoor/index/index/docId/62983
UR  - https://nbn-resolving.org/urn:nbn:de:hebis:30:3-629833
SN  - 1474-760X
N1  - The results published here are in part based upon data generated by the TCGA Research Network: https://www.cancer.gov/tcga.
N1  - Research in the ATT laboratory was supported by grants from the NIH (U01 CA232563), St. Baldrick’s-Stand Up to Cancer Pediatric Dream Team (SU2C-AACR-DT-27-17), the V Foundation for Cancer Research (T2018-014), and the Cookies for Kids’ Cancer (CFKC) Foundation.
N1  - Research in the KZ group and the JK laboratory was supported by grants from the German Research Foundation/Deutsche Forschungsgemeinschaft (ZA 881/2-1 and KO 4566/4-1, respectively).
VL  - 22
IS  - art. 190
SP  - 1
EP  - 12
PB  - BioMed Central
CY  - London
ER  -