ArticleNucleic acids research2018
SEASTAR: systematic evaluation of alternative transcription start sites in RNA.
Article in Nucleic acids research, 2018. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 21 papers.
What it found
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The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
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
21 citing papers in PubMed, 28 citations in OpenAlex.
- Transcript diversity reflects deleterious RNA processing errors shaped by population size in metazoans.PLoS biology · 2026Article
- Opportunities for RNA sequencing in physiology: from big data to understanding homeostasis and heterogeneity.Function (Oxford, England) · 2026Review
- KIAA1522 isoform switching regulates LTR-RTs activity in distinct pluripotency states of hESCs.Science China. Life sciences · 2025Article
- Quantification of single cell-type-specific alternative transcript initiation.bioRxiv : the preprint server for 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
- Challenges in identifying mRNA transcript starts and ends from long-read sequencing data.Genome research · 2024Review
- Pan-cancer transcriptome analysis reveals widespread regulation through alternative tandem transcription initiation.Science advances · 2024Article
- LncSEA 2.0: an updated platform for long non-coding RNA related sets and enrichment analysis.Nucleic acids research · 2024Article
- Current technical advancements in plant epitranscriptomic studies.The plant genome · 2023Review
- Alternative Transcripts Diversify Genome Function for Phenome Relevance to Health and Diseases.Genes · 2023Review
- Large-scale manipulation of promoter DNA methylation reveals context-specific transcriptional responses and stability.Genome biology · 2022Article
- Widespread occurrence of hybrid internal-terminal exons in human transcriptomes.Science advances · 2022Article
- Article
- Single-cell RNA cap and tail sequencing (scRCAT-seq) reveals subtype-specific isoforms differing in transcript demarcation.Nature communications · 2020Article
- A rapid and simple quantitative method for specific detection of smaller coterminal RNA by PCR (DeSCo-PCR): application to the detection of viral subgenomic RNAs.RNA (New York, N.Y.) · 2020Article
- An integrated multi-omics approach identifies the landscape of interferon-α-mediated responses of human pancreatic beta cells.Nature communications · 2020Article
- tappAS: a comprehensive computational framework for the analysis of the functional impact of differential splicing.Genome biology · 2020Article
- Discrete functional and mechanistic roles of chromodomain Y-like 2 (CDYL2) transcript variants in breast cancer growth and metastasis.Theranostics · 2020Article
- Gene Regulatory Network Perturbation by Genetic and Epigenetic Variation.Trends in biochemical sciences · 2018Review
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
4 authors at 3 institutions in 2 countries.
Funding
Abstract
Alternative first exons diversify the transcriptomes of eukaryotes by producing variants of the 5' Untranslated Regions (5'UTRs) and N-terminal coding sequences. Accurate transcriptome-wide detection of alternative first exons typically requires specialized experimental approaches that are designed to identify the 5' ends of transcripts. We developed a computational pipeline SEASTAR that identifies first exons from RNA-seq data alone then quantifies and compares alternative first exon usage across multiple biological conditions. The exons inferred by SEASTAR coincide with transcription start sites identified directly by CAGE experiments and bear epigenetic hallmarks of active promoters. To determine if differential usage of alternative first exons can yield insights into the mechanism controlling gene expression, we applied SEASTAR to an RNA-seq dataset that tracked the reprogramming of mouse fibroblasts into induced pluripotent stem cells. We observed dynamic temporal changes in the usage of alternative first exons, along with correlated changes in transcription factor expression. Using a combined sequence motif and gene set enrichment analysis we identified N-Myc as a regulator of alternative first exon usage in the pluripotent state. Our results demonstrate that SEASTAR can leverage the available RNA-seq data to gain insights into the control of gene expression and alternative transcript variation in eukaryotic transcriptomes.
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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.