ArticleGenome research2009
A canonical promoter organization of the transcription machinery and its regulators in the Saccharomyces genome.
Article in Genome research, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 124 papers.
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Who cites it
124 citing papers in PubMed.
- Predicting dynamic expression patterns in budding yeast with a fungal DNA language model.Research square · 2025Article
- Predicting dynamic expression patterns in budding yeast with a fungal DNA language model.bioRxiv : the preprint server for biology · 2025Article
- Histone acetylation readers Bdf1 and Yaf9 direct SWR1 remodeler to +1 nucleosome.Science advances · 2025Article
- Yeast heterochromatin stably silences only weak regulatory elements by altering burst duration.Cell reports · 2024Article
- The Mediator kinase module enhances polymerase activity to regulate transcriptional memory after heat stress in Arabidopsis.The EMBO journal · 2024Article
- Yeast Heterochromatin Only Stably Silences Weak Regulatory Elements by Altering Burst Duration.bioRxiv : the preprint server for biology · 2023Article
- SIR telomere silencing depends on nuclear envelope lipids and modulates sensitivity to a lysolipid.The Journal of cell biology · 2023Article
- Structure and functional determinants of Rad6-Bre1 subunits in the histone H2B ubiquitin-conjugating complex.Nucleic acids research · 2023Article
- Nucleosome Remodeling at the YeastInternational journal of molecular sciences · 2023Article
- Article
- The chromatin remodeler Ino80 mediates RNAPII pausing site determination.Genome biology · 2021Article
- Additional Layer of Regulation via Convergent Gene Orientation in Yeasts.Molecular biology and evolution · 2020Article
- Parallel Concerted Evolution of Ribosomal Protein Genes in Fungi and Its Adaptive Significance.Molecular biology and evolution · 2020Article
- Chromatin-sensitive cryptic promoters putatively drive expression of alternative protein isoforms in yeast.Genome research · 2019Article
- NF-Y controls fidelity of transcription initiation at gene promoters through maintenance of the nucleosome-depleted region.Nature communications · 2019Article
- Transcription-dependent spreading of the Dal80 yeast GATA factor across the body of highly expressed genes.PLoS genetics · 2019Article
- Developmental transitions in Arabidopsis are regulated by antisense RNAs resulting from bidirectionally transcribed genes.RNA biology · 2017Article
- Abf1 and other general regulatory factors control ribosome biogenesis gene expression in budding yeast.Nucleic acids research · 2017Article
- Tail and Kinase Modules Differently Regulate Core Mediator Recruitment and Function In Vivo.Molecular cell · 2016Article
- Sequence-directed nucleosome-depletion is sufficient to activate transcription from a yeast core promoter in vivo.Biochemical and biophysical research communications · 2016Article
64 more citing papers are in PubMed but not listed here.
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2 authors.
Funding
Abstract
The predominant organizational theme by which the transcription machinery and chromatin regulators are positioned within promoter regions or throughout genes in a genome is largely unknown. We mapped the genomic location of diverse representative components of the gene regulatory machinery in Saccharomyces cerevisiae to an experimental resolution of <40 bp. Sequence-specific gene regulators, chromatin regulators, mediator, and RNA polymerase (Pol) II were found primarily near the downstream border from the "-1" nucleosome, which abuts against the approximately 140-bp nucleosome-free promoter region (NFR). General transcription factors TFIIA, -B, -D, -E, -F, -H were located near the downstream edge from the NFR. The -1 nucleosome dissociated upon Pol II recruitment, but not upon recruitment of only TBP and TFIIB. The position of many sequence-specific regulators in promoter regions correlated with the position of specific remodeling complexes, potentially reflecting functional interactions. Taken together the findings suggest that the combined action of activators and chromatin remodeling complexes remove the -1 nucleosome after the preinitiation complex (PIC) has partially assembled, but before or concomitant with Pol II recruitment. We find PIC assembly, which includes Pol II recruitment, to be a significant rate-limiting step during transcription, but that additional gene-specific rate-limiting steps associated with Pol II occur after recruitment.
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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.