ArticleGenome biology2024
Detecting haplotype-specific transcript variation in long reads with FLAIR2.
Article in Genome biology, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- RNA sequencing significantly improves HYDIN diagnosis and defines the effects of common deletions in primary ciliary dyskinesia.European journal of human genetics : EJHG · 2026Article
- Review
- SNP calling, haplotype phasing and allele-specific analysis with long RNA-seq reads.Nature methods · 2026Article
- HPRC2: A human pangenome reference with near-complete coverage of common genetic variation.bioRxiv : the preprint server for biology · 2026Article
- LongPolyASE: an end-to-end framework for allele-specific gene and isoform analysis in polyploids using long-read RNA-seq.Plant methods · 2026Article
- A new integrated genetic and transcriptomic approach for investigating DUX4 and DUX4C.Journal of human genetics · 2026Article
- Transcriptome Profiling of Leaves and Roots from Rooibos (Plants (Basel, Switzerland) · 2026Article
- An rRNA-depleted full-length transcriptome strategy using nanopore sequencing for identification of novel lncRNA isoforms.Communications biology · 2026Article
- RNA-binding proteins and ribonucleoproteins as determinants of immunity.Nature reviews. Immunology · 2026Review
- TUSCO: benchmarking transcriptome reconstruction with endogenous single-isoform controls.Nature communications · 2026Article
- IFDlong: a model-based isoform and fusion detector for accurate annotation and quantification of long-read RNA-seq data.Genome biology · 2026Article
- Sample-specific haplotype-resolved protein isoform characterization via long-read RNA-seq-based proteogenomics.bioRxiv : the preprint server for biology · 2026Article
- Dynamic modulation of N6-methyladenosine by ionizing radiation in human cells.Biochemistry and biophysics reports · 2026Article
- Review
- Beyond counting: how single-cell long-read sequencing turns transcriptome complexity into precision targets.Frontiers in oncology · 2026Review
- Long-Read Sequencing Reveals RNA Splicing Complexity in Human Diseases.Computational and structural biotechnology journal · 2026Review
- Benchmarking methods for genome annotation using nanopore direct RNA in a non-model crop plant.Bioinformatics advances · 2026Article
- To be or not to be a protein coding mutation, that's the question!NAR genomics and bioinformatics · 2025Review
- Assembly of a high-quality Polypterus senegalus diploid genome.Genes & genomics · 2025Article
- ASET: an end-to-end pipeline for quantification and visualization of allele specific expression.BMC bioinformatics · 2025Article
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6 authors.
Funding
Abstract
backgroundRNA-seq has brought forth significant discoveries regarding aberrations in RNA processing, implicating these RNA variants in a variety of diseases. Aberrant splicing and single nucleotide variants (SNVs) in RNA have been demonstrated to alter transcript stability, localization, and function. In particular, the upregulation of ADAR, an enzyme that mediates adenosine-to-inosine editing, has been previously linked to an increase in the invasiveness of lung adenocarcinoma cells and associated with splicing regulation. Despite the functional importance of studying splicing and SNVs, the use of short-read RNA-seq has limited the community's ability to interrogate both forms of RNA variation simultaneously.
resultsWe employ long-read sequencing technology to obtain full-length transcript sequences, elucidating cis-effects of variants on splicing changes at a single molecule level. We develop a computational workflow that augments FLAIR, a tool that calls isoform models expressed in long-read data, to integrate RNA variant calls with the associated isoforms that bear them. We generate nanopore data with high sequence accuracy from H1975 lung adenocarcinoma cells with and without knockdown of ADAR. We apply our workflow to identify key inosine isoform associations to help clarify the prominence of ADAR in tumorigenesis.
conclusionsUltimately, we find that a long-read approach provides valuable insight toward characterizing the relationship between RNA variants and splicing patterns.
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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.