ArticlePLoS computational biology2007
Frequent gain and loss of functional transcription factor binding sites.
Article in PLoS computational biology, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 103 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
103 citing papers in PubMed, 160 citations in OpenAlex.
- Inferring fungal cis-regulatory networks from genome sequences via unsupervised and interpretable representation learning.Genetics · 2026Article
- Emergence of activation or repression in transcriptional control under a fixed molecular context.Proceedings of the National Academy of Sciences of the United States of America · 2025Article
- The human intelligence evolved from proximalQuantitative biology (Beijing, China) · 2025Article
- Evidence for compensatory evolution within pleiotropic regulatory elements.Genome research · 2024Article
- Transcription factor binding sites are frequently under accelerated evolution in primates.Nature communications · 2023Article
- Article
- Article
- Phylogenetic Modeling of Regulatory Element Turnover Based on Epigenomic Data.Molecular biology and evolution · 2020Article
- Dual Eigen-modules of Cis-Element Regulation Profiles and Selection of Cognition-Language Eigen-direction along Evolution in Hominidae.Molecular biology and evolution · 2020Article
- A 14-bp stretch plays a critical role in regulating gene expression from βCurrent genetics · 2020Article
- Accelerated evolution at chaperone promoters among Antarctic notothenioid fishes.BMC evolutionary biology · 2019Article
- Promoter conservation in HDACs points to functional implications.BMC genomics · 2019Article
- The Role of Chromatin Accessibility in cis-Regulatory Evolution.Genome biology and evolution · 2019Article
- Diversification of DNA binding specificities enabled SREBP transcription regulators to expand the repertoire of cellular functions that they govern in fungi.PLoS genetics · 2018Article
- Dynamic evolution of regulatory element ensembles in primate CD4Nature ecology & evolution · 2018Article
- Cancer cell line specific co-factors modulate the FOXM1 cistrome.Oncotarget · 2017Article
- Unrealistic phylogenetic trees may improve phylogenetic footprinting.Bioinformatics (Oxford, England) · 2017Article
- Recurrent rewiring and emergence of RNA regulatory networks.Proceedings of the National Academy of Sciences of the United States of America · 2017Article
- Characterization of dFOXO binding sites upstream of the Insulin Receptor P2 promoter across the Drosophila phylogeny.PloS one · 2017Article
- Maximal Expression of the Evolutionarily Conserved Slit2 Gene Promoter Requires Sp1.Cellular and molecular neurobiology · 2016Article
43 more citing papers are in PubMed but not listed here.
Corrections and comments
- Erratum issued
Authors and funding
2 authors at 1 institution in 1 country.
Funding
Abstract
Cis-regulatory sequences are not always conserved across species. Divergence within cis-regulatory sequences may result from the evolution of species-specific patterns of gene expression or the flexible nature of the cis-regulatory code. The identification of functional divergence in cis-regulatory sequences is therefore important for both understanding the role of gene regulation in evolution and annotating regulatory elements. We have developed an evolutionary model to detect the loss of constraint on individual transcription factor binding sites (TFBSs). We find that a significant fraction of functionally constrained binding sites have been lost in a lineage-specific manner among three closely related yeast species. Binding site loss has previously been explained by turnover, where the concurrent gain and loss of a binding site maintains gene regulation. We estimate that nearly half of all loss events cannot be explained by binding site turnover. Recreating the mutations that led to binding site loss confirms that these sequence changes affect gene expression in some cases. We also estimate that there is a high rate of binding site gain, as more than half of experimentally identified S. cerevisiae binding sites are not conserved across species. The frequent gain and loss of TFBSs implies that cis-regulatory sequences are labile and, in the absence of turnover, may contribute to species-specific patterns of gene expression.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.