ArticleProceedings of the National Academy of Sciences of the United States of America2009
Ab initio construction of a eukaryotic transcriptome by massively parallel mRNA sequencing.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 134 papers.
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Who cites it
134 citing papers in PubMed.
- Beyond the ORF: Paralog-specific regulation of RPS7/eS7 mRNAs via 3'-UTRs and promoter sequences.PloS one · 2025Article
- Pleiotropic effects of PAB1 deletion: Extensive changes in the yeast proteome, transcriptome, and translatome.PLoS genetics · 2024Article
- Extended stop codon context predicts nonsense codon readthrough efficiency in human cells.Nature communications · 2024Article
- Streamlined and sensitive mono- and di-ribosome profiling in yeast and human cells.Nature methods · 2023Article
- Nucleosome retention by histone chaperones and remodelers occludes pervasive DNA-protein binding.Nucleic acids research · 2023Article
- Interaction of the La-related protein Slf1 with colliding ribosomes maintains translation of oxidative-stress responsive mRNAs.Nucleic acids research · 2023Article
- Measurement of histone replacement dynamics with genetically encoded exchange timers in yeast.Nature biotechnology · 2021Article
- Impact of uORFs in mediating regulation of translation in stress conditions.BMC molecular and cell biology · 2021Article
- The expression of Rpb10, a small subunit common to RNA polymerases, is modulated by the R3H domain-containing Rbs1 protein and the Upf1 helicase.Nucleic acids research · 2020Article
- Transcriptomic and life history responses of the mayfly Neocloeon triangulifer to chronic diel thermal challenge.Scientific reports · 2020Article
- Temperature-Dependent Alternative Splicing of Precursor mRNAs and Its Biological Significance: A Review Focused on Post-Transcriptional Regulation of a Cold Shock Protein Gene in Hibernating Mammals.International journal of molecular sciences · 2020Review
- Translation Initiation Site Profiling Reveals Widespread Synthesis of Non-AUG-Initiated Protein Isoforms in Yeast.Cell systems · 2020Article
- Article
- Differential expression of duplicated ribosomal protein genes modifies ribosome composition in response to stress.Nucleic acids research · 2020Article
- Transcriptome visualization and data availability at the Saccharomyces Genome Database.Nucleic acids research · 2020Article
- Review
- Psp2, a novel regulator of autophagy that promotes autophagy-related protein translation.Cell research · 2019Article
- RNA polymerase II (RNAP II)-associated factors are recruited to tRNA loci, revealing that RNAP II- and RNAP III-mediated transcriptions overlap in yeast.The Journal of biological chemistry · 2019Article
- Genome-Wide Discovery of DEAD-Box RNA Helicase Targets Reveals RNA Structural Remodeling in Transcription Termination.Genetics · 2019Article
- Codon stabilization coefficient as a metric to gain insights into mRNA stability and codon bias and their relationships with translation.Nucleic acids research · 2019Article
74 more citing papers are in PubMed but not listed here.
Corrections and comments
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Authors and funding
14 authors.
Funding
Abstract
Defining the transcriptome, the repertoire of transcribed regions encoded in the genome, is a challenging experimental task. Current approaches, relying on sequencing of ESTs or cDNA libraries, are expensive and labor-intensive. Here, we present a general approach for ab initio discovery of the complete transcriptome of the budding yeast, based only on the unannotated genome sequence and millions of short reads from a single massively parallel sequencing run. Using novel algorithms, we automatically construct a highly accurate transcript catalog. Our approach automatically and fully defines 86% of the genes expressed under the given conditions, and discovers 160 previously undescribed transcription units of 250 bp or longer. It correctly demarcates the 5' and 3' UTR boundaries of 86 and 77% of expressed genes, respectively. The method further identifies 83% of known splice junctions in expressed genes, and discovers 25 previously uncharacterized introns, including 2 cases of condition-dependent intron retention. Our framework is applicable to poorly understood organisms, and can lead to greater understanding of the transcribed elements in an explored genome.
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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.