Language
English
Publication Date
10-3-2024
Journal
Molecular Cell
DOI
10.1016/j.molcel.2024.07.008
PMID
39096899
PMCID
PMC11455606
PubMedCentral® Posted Date
10-3-2025
PubMedCentral® Full Text Version
Author MSS
Abstract
Despite the numerous sequencing methods available, the diversity in RNA size and chemical modification makes it difficult to capture all RNAs in a cell. We developed a method that combines quasi-random priming with template switching to construct sequencing libraries from RNA molecules of any length and with any type of 3' modifications, allowing for the sequencing of virtually all RNA species. Our ligation-independent detection of all types of RNA (LIDAR) is a simple, effective tool to identify and quantify all classes of coding and non-coding RNAs. With LIDAR, we comprehensively characterized the transcriptomes of mouse embryonic stem cells, neural progenitor cells, mouse tissues, and sperm. LIDAR detected a much larger variety of tRNA-derived RNAs (tDRs) compared with traditional ligation-dependent sequencing methods and uncovered tDRs with blocked 3' ends that had previously escaped detection. Therefore, LIDAR can capture all RNAs in a sample and uncover RNA species with potential regulatory functions.
Keywords
Animals, RNA, Transfer, Mice, Sequence Analysis, RNA, Male, Mouse Embryonic Stem Cells, Transcriptome, Neural Stem Cells, High-Throughput Nucleotide Sequencing, Spermatozoa
Published Open-Access
yes
Recommended Citation
Scacchetti, Alessandro; Shields, Emily J; Trigg, Natalie A; et al., "A Ligation-Independent Sequencing Method Reveals tRNA-Derived RNAs With Blocked 3′ Termini" (2024). Faculty and Staff Publications. 3876.
https://digitalcommons.library.tmc.edu/baylor_docs/3876