ArticleNature protocols2014
Genome-wide identification of transcript start and end sites by transcript isoform sequencing.
Article in Nature protocols, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 42 papers.
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Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
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Who cites it
42 citing papers in PubMed.
- High-resolution profiling of bacterial transcriptomes by SEnd-seq.The Biochemical journal · 2026Review
- Direct RNA-seq provides evidence for an antiterminator function of the yeast Hrp1 protein on RNA polymerase II transcripts.RNA (New York, N.Y.) · 2026Article
- Omnivore RNA pyrophosphatase: a versatile enzyme that efficiently removes diverse protecting groups from the 5' end of RNA.Nucleic acids research · 2026Article
- Comprehensive mapping of the 5' and 3' untranslated regions ofRNA (New York, N.Y.) · 2026Article
- Intergenic accumulation of RNA polymerase II maintains the potential for swift transcriptional restart upon release from quiescence.Genome research · 2025Article
- Direct RNA-seq provides evidence for an antiterminator function of the yeast Hrp1 protein on RNA polymerase II transcripts.bioRxiv : the preprint server for biology · 2025Article
- Cellular translational enhancer elements that recruit eukaryotic initiation factor 3.RNA (New York, N.Y.) · 2025Article
- Size fractionated NET-Seq reveals a conserved architecture of transcription units around yeast genes.Yeast (Chichester, England) · 2024Article
- Article
- A vast evolutionarily transient translatome contributes to phenotype and fitness.Cell systems · 2023Article
- Genome-Wide Mapping of 5' Isoforms with 5'-Seq.Current protocols · 2023Article
- Alternative Transcription Start Site Usage and Functional Implications in Pathogenic Fungi.Journal of fungi (Basel, Switzerland) · 2022Review
- Transcriptomic diversity in human medullary thymic epithelial cells.Nature communications · 2022Article
- Long undecoded transcript isoform (LUTI) detection in meiotic budding yeast by direct RNA and transcript leader sequencing.STAR protocols · 2022Article
- Direct analysis of ribosome targeting illuminates thousand-fold regulation of translation initiation.Cell systems · 2022Article
- High-resolution analysis of cell-state transitions in yeast suggests widespread transcriptional tuning by alternative starts.Genome biology · 2021Article
- TIF-Seq2 disentangles overlapping isoforms in complex human transcriptomes.Nucleic acids research · 2020Article
- Transcript isoform sequencing reveals widespread promoter-proximal transcriptional termination in Arabidopsis.Nature communications · 2020Article
- Transcriptome visualization and data availability at the Saccharomyces Genome Database.Nucleic acids research · 2020Article
- Discovery of alternative polyadenylation dynamics from single cell types.Computational and structural biotechnology journal · 2020Review
Corrections and comments
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Authors and funding
4 authors.
Funding
Abstract
Hundreds of transcript isoforms with varying boundaries and alternative regulatory signals are transcribed from the genome, even in a genetically homogeneous population of cells. To study this transcriptional heterogeneity, we developed transcript isoform sequencing (TIF-seq), a method that allows the genome-wide profiling of full-length transcript isoforms defined by their exact 5' and 3' boundaries. TIF-seq entails the generation of full-length cDNA libraries, followed by their circularization and the sequencing of the junction fragments spanning the 5' and 3' transcript ends. By determining the respective co-occurrence of start and end sites of individual transcript molecules, TIF-seq can distinguish variations that conventional approaches for mapping single ends cannot, such as short abortive transcripts, bicistronic messages and overlapping transcripts that differ in lengths. The TIF-seq protocol we describe here can be applied to any eukaryotic organism (e.g., yeast, human), and it requires 6-10 d for generating TIF-seq libraries, 10 d for sequencing and 2-3 d for analysis.
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