ArticleBMC systems biology2015
Functional redundancy of transcription factors explains why most binding targets of a transcription factor are not affected when the transcription factor is knocked out.
Article in BMC systems biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 24 papers.
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24 citing papers in PubMed, 36 citations in OpenAlex.
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- Binding profiles for 961Genome research · 2024Article
- Agonists, Antagonists and Receptors of Somatostatin: Pathophysiological and Therapeutical Implications in Neoplasias.Current issues in molecular biology · 2024Review
- Molecular and cellular dynamics of the developing human neocortex at single-cell resolution.bioRxiv : the preprint server for biology · 2024Article
- Uncovering uncharacterized binding of transcription factors from ATAC-seq footprinting data.Scientific reports · 2024Article
- Peak-agnostic high-resolution cis-regulatory circuitry mapping using single cell multiome data.Nucleic acids research · 2024Article
- Binding profiles for 954 Drosophila andbioRxiv : the preprint server for biology · 2024Article
- Deep molecular learning of transcriptional control of a synthetic CRE enhancer and its variants.iScience · 2024Article
- RNF2 regulates Wnt/ß-catenin signaling via TCF7L1 destabilization.Scientific reports · 2023Article
- Review
- FOXK2 transcription factor and its roles in tumorigenesis (Review).Oncology letters · 2022Review
- Lessons from eRNAs: understanding transcriptional regulation through the lens of nascent RNAs.Transcription · 2020Review
- Transcription factor regulatory modules provide the molecular mechanisms for functional redundancy observed among transcription factors in yeast.BMC bioinformatics · 2019Article
- Plant PHR Transcription Factors: Put on A Map.Genes · 2019Review
- A set of AP2-like genes is associated with inflorescence branching and architecture in domesticated rice.Journal of experimental botany · 2019Article
- Functional redundancy in Echinocandin B in-cluster transcription factorBiotechnology reports (Amsterdam, Netherlands) · 2018Article
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2 authors at 1 institution in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundBiologists are puzzled by the extremely low percentage (3%) of the binding targets of a yeast transcription factor (TF) affected when the TF is knocked out, a phenomenon observed by comparing the TF binding dataset and TF knockout effect dataset.
resultsThis study gives a plausible biological explanation of this counterintuitive phenomenon. Our analyses find that TFs with high functional redundancy show significantly lower percentage than do TFs with low functional redundancy. This suggests that functional redundancy may lead to one TF compensating for another, thus masking the TF knockout effect on the binding targets of the knocked-out TF. In addition, we show that seven classes of genes (lowly expressed genes, TATA box-less genes, genes containing a nucleosome-free region immediately upstream of the transcriptional start site (TSS), genes with low transcriptional plasticity, genes with a low number of bound TFs, genes with a low number of TFBSs, and genes with a short average distance of TFBSs to the TSS) are insensitive to the knockout of their promoter-binding TFs, providing clues for finding other biological explanations of the surprisingly low percentage of the binding targets of a TF affected when the TF is knocked out.
conclusionsThis study shows that one property of TFs (functional redundancy) and seven properties of genes (expression level, TATA box, nucleosome, transcriptional plasticity, the number of bound TFs, the number of TFBSs, and the average distance of TFBSs to the TSS) may be useful for explaining a counterintuitive phenomenon: most binding targets of a yeast transcription factor are not affected when the transcription factor is knocked out.
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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.