ArticleBMC genomics2022
A versatile 5' RACE-Seq methodology for the accurate identification of the 5' termini of mRNAs.
Article in BMC genomics, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 20 papers, 1 of them a synthesis that pooled it.
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Who cites it
20 citing papers in PubMed, 1 synthesis or guideline pooled it, 24 citations in OpenAlex.
- Next-Generation and Single-Cell Sequencing Approaches to Study Atherosclerosis and Vascular Inflammation Pathophysiology: A Systematic Review.Frontiers in cardiovascular medicine · 2022Pooled it
- High-resolution profiling of bacterial transcriptomes by SEnd-seq.The Biochemical journal · 2026Review
- Enhanced recovery of terminal sequences of viral RNAs via fine-tuning of the high-throughput sequencing library preparation and evidence of a non-templated nucleotide addition at the 3' end of the minus strand in members of the genusThe Journal of general virology · 2026Article
- A miR172e/Plants (Basel, Switzerland) · 2026Article
- Genetic characterization of two novel picornaviruses from birds, white-tailed eagle (Haliaeetus albicilla) and pied avocet (Recurvirostra avosetta) in Hungary.Scientific reports · 2026Article
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- T-cell receptor therapy in ovarian cancer: concepts and challenges.Journal of ovarian research · 2025Review
- Cryptic intronic transcriptional initiation generates efficient endogenous mRNA templates for C9orf72-associated RAN translation.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- Beyond the Cut: Long-read sequencing reveals complex genomic and transcriptomic changes in AAV-CRISPR therapy for Duchenne Muscular Dystrophy.bioRxiv : the preprint server for biology · 2025Article
- Transposable elements as genome regulators in normal and malignant haematopoiesis.Blood cancer journal · 2025Review
- Detection of mRNA Transcript Variants.Genes · 2025Review
- 5'-UTR G-Quadruplex-Mediated Translation Regulation in Eukaryotes: Current Understanding and Methodological Challenges.International journal of molecular sciences · 2025Review
- Precision and efficacy of RNA-guided DNA integration in high-expressing muscle loci.Molecular therapy. Nucleic acids · 2024Article
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- A reliable and quick method for screening alternative splicing variants for low-abundance genes.PloS one · 2024Article
- First detection and complete genome sequence of a new potexvirus naturally infecting Adenium obesum.Archives of virology · 2023Article
- T-Cell Receptor Repertoire Sequencing in the Era of Cancer Immunotherapy.Clinical cancer research : an official journal of the American Association for Cancer Research · 2023Article
- Article
- Ryegrass mottle virus complete genome determination and development of infectious cDNA by combining two methods- 3' RACE and RNA-Seq.PloS one · 2023Article
- T-Cell Receptor Repertoire Sequencing and Its Applications: Focus on Infectious Diseases and Cancer.International journal of molecular sciences · 2022Review
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundTechnological advancements in the era of massive parallel sequencing have enabled the functional dissection of the human transcriptome. However, 5' ends of mRNAs are significantly underrepresented in these datasets, hindering the efficient analysis of the complex human transcriptome. The implementation of the template-switching mechanism at the reverse transcription stage along with 5' rapid amplification of cDNA ends (RACE) constitutes the most prominent and efficient strategy to specify the actual 5' ends of cDNAs. In the current study, we developed a 5' RACE-seq method by coupling a custom template-switching and 5' RACE assay with targeted nanopore sequencing, to accurately unveil 5' termini of mRNA targets.
resultsThe optimization of the described 5' RACE-seq method was accomplished using the human BCL2L12 as control gene. We unveiled that the selection of hybrid DNA/RNA template-switching oligonucleotides as well as the complete separation of the cDNA extension incubation from the template-switching process, significantly increase the overall efficiency of the downstream 5' RACE. Collectively, our results support the existence of two distinct 5' termini for BCL2L12, being in complete accordance with the results derived from both direct RNA and PCR-cDNA sequencing approaches from Oxford Nanopore Technologies. As proof of concept, we implemented the described 5' RACE-seq methodology to investigate the 5' UTRs of several kallikrein-related peptidases (KLKs) gene family members. Our results confirmed the existence of multiple annotated 5' UTRs of the human KLK gene family members, but also identified novel, previously uncharacterized ones.
conclusionsIn this work we present an in-house developed 5' RACE-seq method, based on the template-switching mechanism and targeted nanopore sequencing. This approach enables the broad and in-depth study of 5' UTRs of any mRNA of interest, by offering a tremendous sequencing depth, while significantly reducing the cost-per reaction compared to commercially available kits.
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