ArticleNature communications2020
Single-cell RNA cap and tail sequencing (scRCAT-seq) reveals subtype-specific isoforms differing in transcript demarcation.
Article in Nature communications, 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Full-length transcriptome atlas of porcine skeletal muscle reveals isoform-resolved genetic regulatory mechanisms for muscle growth.BMC genomics · 2026Article
- Analyzing cell-type-specific isoform expression using IsoDiffR and long-read single-cell RNA sequencing.Bioinformatics (Oxford, England) · 2026Article
- Technological advances in axonal regeneration and structural plasticity: optogenetics, single-cell omics, and tissue clearing.Frontiers in cellular neuroscience · 2026Review
- Identification of a 10-species microbial signature of inflammatory bowel disease by machine learning and external validation.Cell regeneration (London, England) · 2025Article
- A comparison of integration methods for single-cell RNA sequencing data and ATAC sequencing data.Quantitative biology (Beijing, China) · 2025Review
- RNA multi-omics in single cells reveal rhythmical RNA reshaping during human and mouse oocyte maturation.BMC biology · 2025Article
- An Integrated Database for Exploring Alternative Promoters in Animals.Scientific data · 2025Article
- Predicting and comparing transcription start sites in single cell populations.PLoS computational biology · 2025Article
- Simultaneous profiling of RNA isoforms and chromatin accessibility of single cells of human retinal organoids.Nature communications · 2024Article
- Advances in single-cell long-read sequencing technologies.NAR genomics and bioinformatics · 2024Article
- CamoTSS: analysis of alternative transcription start sites for cellular phenotypes and regulatory patterns from 5' scRNA-seq data.Nature communications · 2023Article
- 'Multi-omics' data integration: applications in probiotics studies.NPJ science of food · 2023Review
- Single-Cell Molecular Barcoding to Decode Multimodal Information Defining Cell States.Molecules and cells · 2023Review
- Comprehensive mapping of alternative polyadenylation site usage and its dynamics at single-cell resolution.Proceedings of the National Academy of Sciences of the United States of America · 2022Article
- MOJITOO: a fast and universal method for integration of multimodal single-cell data.Bioinformatics (Oxford, England) · 2022Article
- Spatial epitranscriptomics reveals A-to-I editome specific to cancer stem cell microniches.Nature communications · 2022Article
- RNA polymerase II speed: a key player in controlling and adapting transcriptome composition.The EMBO journal · 2021Review
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12 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
The differences in transcription start sites (TSS) and transcription end sites (TES) among gene isoforms can affect the stability, localization, and translation efficiency of mRNA. Gene isoforms allow a single gene diverse functions across different cell types, and isoform dynamics allow different functions over time. However, methods to efficiently identify and quantify RNA isoforms genome-wide in single cells are still lacking. Here, we introduce single cell RNA Cap And Tail sequencing (scRCAT-seq), a method to demarcate the boundaries of isoforms based on short-read sequencing, with higher efficiency and lower cost than existing long-read sequencing methods. In conjunction with machine learning algorithms, scRCAT-seq demarcates RNA transcripts with unprecedented accuracy. We identified hundreds of previously uncharacterized transcripts and thousands of alternative transcripts for known genes, revealed cell-type specific isoforms for various cell types across different species, and generated a cell atlas of isoform dynamics during the development of retinal cones.
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