ArticleGenome biology2007
A TATA binding protein regulatory network that governs transcription complex assembly.
Article in Genome biology, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 27 papers.
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Who cites it
27 citing papers in PubMed.
- An integrated SAGA and TFIID PIC assembly pathway selective for poised and induced promoters.Genes & development · 2022Article
- Molecular determinants underlying functional innovations of TBP and their impact on transcription initiation.Nature communications · 2020Article
- Conformational changes and catalytic inefficiency associated with Mot1-mediated TBP-DNA dissociation.Nucleic acids research · 2019Article
- P-TEFb Regulates Transcriptional Activation in Non-coding RNA Genes.Frontiers in genetics · 2019Article
- Affinity and competition for TBP are molecular determinants of gene expression noise.Nature communications · 2016Article
- The conformational state of the nucleosome entry-exit site modulates TATA box-specific TBP binding.Nucleic acids research · 2014Article
- Mot1 redistributes TBP from TATA-containing to TATA-less promoters.Molecular and cellular biology · 2013Article
- One small step for Mot1; one giant leap for other Swi2/Snf2 enzymes?Biochimica et biophysica acta · 2011Review
- Genome-wide transcriptional dependence on conserved regions of Mot1.Molecular and cellular biology · 2011Article
- The mRNA cap-binding complex stimulates the formation of pre-initiation complex at the promoter via its interaction with Mot1p in vivo.Nucleic acids research · 2011Article
- Understanding protein evolutionary rate by integrating gene co-expression with protein interactions.BMC systems biology · 2010Article
- Histone H2B ubiquitination and beyond: Regulation of nucleosome stability, chromatin dynamics and the trans-histone H3 methylation.Epigenetics · 2010Review
- Direct transactivator-transcription factor IID (TFIID) contacts drive yeast ribosomal protein gene transcription.The Journal of biological chemistry · 2010Article
- Genome-wide localization analysis of a complete set of Tafs reveals a specific effect of the taf1 mutation on Taf2 occupancy and provides indirect evidence for different TFIID conformations at different promoters.Nucleic acids research · 2010Article
- GCN5 is a positive regulator of origins of DNA replication in Saccharomyces cerevisiae.PloS one · 2010Article
- Basal core promoters control the equilibrium between negative cofactor 2 and preinitiation complexes in human cells.Genome biology · 2010Article
- Distinct promoter dynamics of the basal transcription factor TBP across the yeast genome.Nature structural & molecular biology · 2009Article
- Regulon-specific control of transcription elongation across the yeast genome.PLoS genetics · 2009Article
- The basal initiation machinery: beyond the general transcription factors.Current opinion in cell biology · 2009Review
- Core and periphery structures in protein interaction networks.BMC bioinformatics · 2009Article
Corrections and comments
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Authors and funding
2 authors.
Funding
Abstract
backgroundEukaryotic genes are controlled by proteins that assemble stepwise into a transcription complex. How the individual biochemically defined assembly steps are coordinated and applied throughout a genome is largely unknown. Here, we model and experimentally test a portion of the assembly process involving the regulation of the TATA binding protein (TBP) throughout the yeast genome.
resultsBiochemical knowledge was used to formulate a series of coupled TBP regulatory reactions involving TFIID, SAGA, NC2, Mot1, and promoter DNA. The reactions were then linked to basic segments of the transcription cycle and modeled computationally. A single framework was employed, allowing the contribution of specific steps to vary from gene to gene. Promoter binding and transcriptional output were measured genome-wide using ChIP-chip and expression microarray assays. Mutagenesis was used to test the framework by shutting down specific parts of the network.
conclusionThe model accounts for the regulation of TBP at most transcriptionally active promoters and provides a conceptual tool for interpreting genome-wide data sets. The findings further demonstrate the interconnections of TBP regulation on a genome-wide scale.
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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.