ArticleGenome research2015
Decoupling of evolutionary changes in transcription factor binding and gene expression in mammals.
Article in Genome research, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 35 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
35 citing papers in PubMed, 60 citations in OpenAlex.
- Identification and Pathway Analysis of SNP Loci Affecting Abdominal Fat Deposition in Broilers.Animals : an open access journal from MDPI · 2025Article
- Regulatory Plasticity of the Human Genome.Molecular biology and evolution · 2025Article
- Parallel Evolution at the Regulatory Base-Pair Level Contributes to Mammalian Interspecific Differences in Polygenic Traits.Molecular biology and evolution · 2024Article
- Repaglinide restrains HCC development and progression by targeting FOXO3/lumican/p53 axis.Cellular oncology (Dordrecht, Netherlands) · 2024Article
- The dynamic genetic determinants of increased transcriptional divergence in spermatids.Nature communications · 2024Article
- Decoding enhancer complexity with machine learning and high-throughput discovery.Genome biology · 2023Review
- Limited conservation in cross-species comparison of GLK transcription factor binding suggested wide-spread cistrome divergence.Nature communications · 2022Article
- Genome-wide analysis of cis-regulatory changes underlying metabolic adaptation of cavefish.Nature genetics · 2022Article
- Long-range promoter-enhancer contacts are conserved during evolution and contribute to gene expression robustness.Genome research · 2022Article
- Molecular mechanism of hyperactive tooth root formation in oculo-facio-cardio-dental syndrome.Frontiers in physiology · 2022Article
- Three topological features of regulatory networks control life-essential and specialized subsystems.Scientific reports · 2021Article
- Harnessing natural variation to identify cis regulators of sex-biased gene expression in a multi-strain mouse liver model.PLoS genetics · 2021Article
- Phylogenetic Modeling of Regulatory Element Turnover Based on Epigenomic Data.Molecular biology and evolution · 2020Article
- Independent evolution of transcript abundance and gene regulatory dynamics.Genome research · 2020Article
- Duplication and divergence of the retrovirus restriction gene Fv1 in Mus caroli allows protection from multiple retroviruses.PLoS genetics · 2020Article
- LncRNA SNHG17 aggravated prostate cancer progression through regulating its homolog SNORA71B via a positive feedback loop.Cell death & disease · 2020Article
- Clustered CTCF binding is an evolutionary mechanism to maintain topologically associating domains.Genome biology · 2020Article
- Drift and Directional Selection Are the Evolutionary Forces Driving Gene Expression Divergence in Eye and Brain Tissue ofGenetics · 2019Article
- The Role of Chromatin Accessibility in cis-Regulatory Evolution.Genome biology and evolution · 2019Article
- A quantitative framework for characterizing the evolutionary history of mammalian gene expression.Genome research · 2019Article
Corrections and comments
- Commented on by
Authors and funding
6 authors at 2 institutions in 1 country.
Funding
Abstract
To understand the evolutionary dynamics between transcription factor (TF) binding and gene expression in mammals, we compared transcriptional output and the binding intensities for three tissue-specific TFs in livers from four closely related mouse species. For each transcription factor, TF-dependent genes and the TF binding sites most likely to influence mRNA expression were identified by comparing mRNA expression levels between wild-type and TF knockout mice. Independent evolution was observed genome-wide between the rate of change in TF binding and the rate of change in mRNA expression across taxa, with the exception of a small number of TF-dependent genes. We also found that binding intensities are preferentially conserved near genes whose expression is dependent on the TF, and the conservation is shared among binding peaks in close proximity to each other near the TSS. Expression of TF-dependent genes typically showed an increased sensitivity to changes in binding levels as measured by mRNA abundance. Taken together, these results highlight a significant tolerance to evolutionary changes in TF binding intensity in mammalian transcriptional networks and suggest that some TF-dependent genes may be largely regulated by a single TF across evolution.
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.