ArticleRNA (New York, N.Y.)2016
RNA-seq of human reference RNA samples using a thermostable group II intron reverse transcriptase.
Article in RNA (New York, N.Y.), 2016. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 67 papers.
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Who cites it
67 citing papers in PubMed.
- Pervasive enhanced transcription in inflammatory breast cancer tumors and PBMCs impacts RNA splicing and intronic RNAs in plasma.Science advances · 2026Article
- NAP-seq for full-length noncapped RNA sequencing.Nature protocols · 2026Review
- Nano3P-seq: charting the coding and noncoding transcriptome at single-molecule resolution.Nature protocols · 2025Review
- FTO depletion does not alter mbioRxiv : the preprint server for biology · 2025Article
- Single-cell RNA-seq using UltraMarathonRT expands the known transcriptome.bioRxiv : the preprint server for biology · 2025Article
- A bacterial PrimPol-reverse transcriptase hybrid protein has a proofreading exonuclease activity that can be transferred to other reverse transcriptases.bioRxiv : the preprint server for biology · 2025Article
- SnoBIRD: a tool to identify C/D box snoRNAs and refine their annotation across all eukaryotes.Nucleic acids research · 2025Article
- Genomic and transcriptomic sequencing in prostate cancer.Current opinion in oncology · 2025Review
- SnoRNAs: The promising targets for anti-tumor therapy.Journal of pharmaceutical analysis · 2024Review
- Characterization and implementation of the MarathonRT template-switching reaction to expand the capabilities of RNA-seq.RNA (New York, N.Y.) · 2024Article
- Human cells contain myriad excised linear intron RNAs with links to gene regulation and potential utility as biomarkers.PLoS genetics · 2024Article
- NAP-seq reveals multiple classes of structured noncoding RNAs with regulatory functions.Nature communications · 2024Article
- Small RNA structural biochemistry in a post-sequencing era.Nature protocols · 2024Review
- CAG repeat expansions create splicing acceptor sites and produce aberrant repeat-containing RNAs.Molecular cell · 2024Article
- The regulatory roles of small nucleolar RNAs within their host locus.RNA biology · 2024Review
- CAG repeat expansions create splicing acceptor sites and produce aberrant repeat-containing RNAs.bioRxiv : the preprint server for biology · 2023Article
- Minimizing amplification bias during reverse transcription for in vitro selections.RNA (New York, N.Y.) · 2023Article
- Intronic small nucleolar RNAs regulate host gene splicing through base pairing with their adjacent intronic sequences.Genome biology · 2023Article
- Motif conservation, stability, and host gene expression are the main drivers of snoRNA expression across vertebrates.Genome research · 2023Article
- Detection of piRNA-54265 in human serum: evidence and significance.Cancer communications (London, England) · 2023Article
7 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
6 authors.
Funding
Abstract
Next-generation RNA sequencing (RNA-seq) has revolutionized our ability to analyze transcriptomes. Current RNA-seq methods are highly reproducible, but each has biases resulting from different modes of RNA sample preparation, reverse transcription, and adapter addition, leading to variability between methods. Moreover, the transcriptome cannot be profiled comprehensively because highly structured RNAs, such as tRNAs and snoRNAs, are refractory to conventional RNA-seq methods. Recently, we developed a new method for strand-specific RNA-seq using thermostable group II intron reverse transcriptases (TGIRTs). TGIRT enzymes have higher processivity and fidelity than conventional retroviral reverse transcriptases plus a novel template-switching activity that enables RNA-seq adapter addition during cDNA synthesis without using RNA ligase. Here, we obtained TGIRT-seq data sets for well-characterized human RNA reference samples and compared them to previous data sets obtained for these RNAs by the Illumina TruSeq v2 and v3 methods. We find that TGIRT-seq recapitulates the relative abundance of human transcripts and RNA spike-ins in ribo-depleted, fragmented RNA samples comparably to non-strand-specific TruSeq v2 and better than strand-specific TruSeq v3. Moreover, TGIRT-seq is more strand specific than TruSeq v3 and eliminates sampling biases from random hexamer priming, which are inherent to TruSeq. The TGIRT-seq data sets also show more uniform 5' to 3' gene coverage and identify more splice junctions, particularly near the 5' ends of mRNAs, than do the TruSeq data sets. Finally, TGIRT-seq enables the simultaneous profiling of mRNAs and lncRNAs in the same RNA-seq experiment as structured small ncRNAs, including tRNAs, which are essentially absent with TruSeq.
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Registered trials
Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.