ArticleProceedings of the National Academy of Sciences of the United States of America2006
A high-resolution map of transcription in the yeast genome.
Article in Proceedings of the National Academy of Sciences of the United States of America, 2006. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 382 papers, 1 of them a synthesis that pooled it.
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Who cites it
382 citing papers in PubMed, 1 synthesis or guideline pooled it, 700 citations in OpenAlex.
- GBAF, a small BAF sub-complex with big implications: a systematic review.Epigenetics & chromatin · 2020Pooled it
- Light-based footprinting of a eukaryotic genome.Science advances · 2026Article
- Life beyond 6000 genes: from sequence to synthesis in a post-genomics era.FEMS yeast research · 2026Review
- The hidden power of antisense long non-coding RNAs: a dive into a novel regulatory layer mediated by double-stranded RNA formation.RNA biology · 2025Review
- The patterns of alternative TSS usage explain the highly heterogeneous landscape of 5'UTR lengths in eukaryotes.NAR genomics and bioinformatics · 2025Article
- The multiple layers of RNA response in double-strand break repair.Experimental & molecular medicine · 2025Review
- Identification and Functions of lncRNAs in Fungi.Non-coding RNA · 2025Review
- The Direct and Individual Transcriptional Function of the Human Homodimeric and Heterodimeric Basic Helix-Loop-Helix Transcription Factors E47 and Scleraxis.FASEB journal : official publication of the Federation of American Societies for Experimental Biology · 2025Article
- Comparative Analysis of Transcriptome Data of Wings from Different Developmental Stages of theInternational journal of molecular sciences · 2025Article
- RNA Structure: Past, Future, and Gene Therapy Applications.International journal of molecular sciences · 2024Review
- Osmotic disruption of chromatin induces Topoisomerase 2 activity at sites of transcriptional stress.Nature communications · 2024Article
- RNA-mediated double-strand break repair by end-joining mechanisms.Nature communications · 2024Article
- Article
- Review
- RNA Pol II Assembly Affects ncRNA Expression.International journal of molecular sciences · 2023Article
- Review
- 3'-End Processing of Eukaryotic mRNA: Machinery, Regulation, and Impact on Gene Expression.Annual review of biochemistry · 2023Review
- Functional analysis of a random-sequence chromosome reveals a high level and the molecular nature of transcriptional noise in yeast cells.Molecular cell · 2023Article
- The Functional Meaning of 5'UTR in Protein-Coding Genes.International journal of molecular sciences · 2023Review
- Distinct chromosomal "niches" in the genome ofNAR genomics and bioinformatics · 2022Article
322 more citing papers are in PubMed but not listed here.
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
9 authors at 3 institutions in 3 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
There is abundant transcription from eukaryotic genomes unaccounted for by protein coding genes. A high-resolution genome-wide survey of transcription in a well annotated genome will help relate transcriptional complexity to function. By quantifying RNA expression on both strands of the complete genome of Saccharomyces cerevisiae using a high-density oligonucleotide tiling array, this study identifies the boundary, structure, and level of coding and noncoding transcripts. A total of 85% of the genome is expressed in rich media. Apart from expected transcripts, we found operon-like transcripts, transcripts from neighboring genes not separated by intergenic regions, and genes with complex transcriptional architecture where different parts of the same gene are expressed at different levels. We mapped the positions of 3' and 5' UTRs of coding genes and identified hundreds of RNA transcripts distinct from annotated genes. These nonannotated transcripts, on average, have lower sequence conservation and lower rates of deletion phenotype than protein coding genes. Many other transcripts overlap known genes in antisense orientation, and for these pairs global correlations were discovered: UTR lengths correlated with gene function, localization, and requirements for regulation; antisense transcripts overlapped 3' UTRs more than 5' UTRs; UTRs with overlapping antisense tended to be longer; and the presence of antisense associated with gene function. These findings may suggest a regulatory role of antisense transcription in S. cerevisiae. Moreover, the data show that even this well studied genome has transcriptional complexity far beyond current annotation.
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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.