ArticleBMC molecular biology2007
Localization of TFIIB binding regions using serial analysis of chromatin occupancy.
Article in BMC molecular biology, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed, 14 citations in OpenAlex.
- TFIIB-Termination Factor Interaction Affects Termination of Transcription on Genome-Wide Scale.International journal of molecular sciences · 2024Article
- Protein interaction network revealed by quantitative proteomic analysis links TFIIB to multiple aspects of the transcription cycle.Biochimica et biophysica acta. Proteins and proteomics · 2024Article
- TACC3 deregulates the DNA damage response and confers sensitivity to radiation and PARP inhibition.Oncogene · 2015Article
- A new paradigm for transcription factor TFIIB functionality.Scientific reports · 2014Article
- The Arabidopsis general transcription factor TFIIB1 (AtTFIIB1) is required for pollen tube growth and endosperm development.Journal of experimental botany · 2013Article
- New insights into the role of TFIIB in transcription initiation.Transcription · 2010Article
- Gene looping is conferred by activator-dependent interaction of transcription initiation and termination machineries.The Journal of biological chemistry · 2009Article
- Genomic location analysis by ChIP-Seq.Journal of cellular biochemistry · 2009Review
- Prevalence of transcription promoters within archaeal operons and coding sequences.Molecular systems biology · 2009Article
- A genome-wide screen for beta-catenin binding sites identifies a downstream enhancer element that controls c-Myc gene expression.Molecular and cellular biology · 2008Article
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Authors and funding
4 authors at 2 institutions in 1 country.
Funding
Abstract
backgroundRNA Polymerase II (RNAP II) is recruited to core promoters by the pre-initiation complex (PIC) of general transcription factors. Within the PIC, transcription factor for RNA polymerase IIB (TFIIB) determines the start site of transcription. TFIIB binding has not been localized, genome-wide, in metazoans. Serial analysis of chromatin occupancy (SACO) is an unbiased methodology used to empirically identify transcription factor binding regions. In this report, we use TFIIB and SACO to localize TFIIB binding regions across the rat genome.
resultsA sample of the TFIIB SACO library was sequenced and 12,968 TFIIB genomic signature tags (GSTs) were assigned to the rat genome. GSTs are 20-22 base pair fragments that are derived from TFIIB bound chromatin. TFIIB localized to both non-protein coding and protein-coding loci. For 21% of the 1783 protein-coding genes in this sample of the SACO library, TFIIB binding mapped near the characterized 5' promoter that is upstream of the transcription start site (TSS). However, internal TFIIB binding positions were identified in 57% of the 1783 protein-coding genes. Internal positions are defined as those within an inclusive region greater than 2.5 kb downstream from the 5' TSS and 2.5 kb upstream from the transcription stop. We demonstrate that both TFIIB and TFIID (an additional component of PICs) bound to internal regions using chromatin immunoprecipitation (ChIP). The 5' cap of transcripts associated with internal TFIIB binding positions were identified using a cap-trapping assay. The 5' TSSs for internal transcripts were confirmed by primer extension. Additionally, an analysis of the functional annotation of mouse 3 (FANTOM3) databases indicates that internally initiated transcripts identified by TFIIB SACO in rat are conserved in mouse.
conclusionOur findings that TFIIB binding is not restricted to the 5' upstream region indicates that the propensity for PIC to contribute to transcript diversity is far greater than previously appreciated.
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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.