ArticleRNA (New York, N.Y.)2010
Noncanonical transcript forms in yeast and their regulation during environmental stress.
Article in RNA (New York, N.Y.), 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 47 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
47 citing papers in PubMed, 77 citations in OpenAlex.
- Core gene set of the speciesbioRxiv : the preprint server for biology · 2025Article
- Chromatin Changes in Phytochrome Interacting Factor-Regulated Genes Parallel Their Rapid Transcriptional Response to Light.Frontiers in plant science · 2022Article
- Testing the Genomic Shock Hypothesis Using Transposable Element Expression in Yeast Hybrids.Frontiers in fungal biology · 2021Article
- PAS-seq 2: A fast and sensitive method for global profiling of polyadenylated RNAs.Methods in enzymology · 2021Article
- Regulation of the Ysh1 endonuclease of the mRNA cleavage/polyadenylation complex by ubiquitin-mediated degradation.RNA biology · 2020Article
- Accurate and Sensitive Quantitation of the Dynamic Heat Shock Proteome Using Tandem Mass Tags.Journal of proteome research · 2020Article
- Alternative cleavage and polyadenylation in health and disease.Nature reviews. Genetics · 2019Review
- Cellular stress alters 3'UTR landscape through alternative polyadenylation and isoform-specific degradation.Nature communications · 2018Article
- Conserved non-AUG uORFs revealed by a novel regression analysis of ribosome profiling data.Genome research · 2018Article
- Article
- Comparative analysis of alternative polyadenylation inGenome research · 2017Article
- Acidophilic green algal genome provides insights into adaptation to an acidic environment.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- mRNA detection in budding yeast with single fluorophores.Nucleic acids research · 2017Article
- Article
- Noncanonical Alternative Polyadenylation Contributes to Gene Regulation in Response to Hypoxia.The Plant cell · 2017Article
- The Antisense Transcriptome and the Human Brain.Journal of molecular neuroscience : MN · 2016Review
- PAT-seq: a method to study the integration of 3'-UTR dynamics with gene expression in the eukaryotic transcriptome.RNA (New York, N.Y.) · 2015Article
- Mapping 3' mRNA isoforms on a genomic scale.Current protocols in molecular biology · 2015Article
- Sequencing of first-strand cDNA library reveals full-length transcriptomes.Nature communications · 2015Article
- Transcriptional interference by antisense RNA is required for circadian clock function.Nature · 2014Article
Corrections and comments
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Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Surveys of transcription in many organisms have observed widespread expression of RNAs with no known function, encoded within and between canonical coding genes. The search to distinguish functional RNAs from transcriptional noise represents one of the great challenges in genomic biology. Here we report a next-generation sequencing technique designed to facilitate the inference of function of uncharacterized transcript forms by improving their coverage in sequencing libraries, in parallel with the detection of canonical mRNAs. We piloted this protocol, which is based on the capture of 3' ends of polyadenylated RNAs, in budding yeast. Analysis of transcript ends in coding regions uncovered hundreds of alternative-length coding forms, which harbored a unique sequence motif and showed signatures of regulatory function in particular gene categories; independent single-gene measurements confirmed the differential regulation of short coding forms during heat shock. In addition, our 3'-end RNA-seq method applied to wild-type strains detected putative noncoding transcripts previously reported only in RNA surveillance mutants, and many such transcripts showed differential expression in yeast cultures grown under chemical stress. Our results underscore the power of the 3'-end protocol to improve detection of noncanonical transcript forms in a sequencing experiment of standard depth, and our findings strongly suggest that many unannotated, polyadenylated RNAs may have as yet uncharacterized regulatory functions.
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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.