ArticleNucleic acids research2011
Enhancers regulate progression of development in mammalian cells.
Article in Nucleic acids research, 2011. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 7 papers.
What it found
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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.
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Who cites it
7 citing papers in PubMed, 8 citations in OpenAlex.
- Estimating the activity of transcription factors by the effect on their target genes.Bioinformatics (Oxford, England) · 2014Article
- Characterizing protein interactions employing a genome-wide siRNA cellular phenotyping screen.PLoS computational biology · 2014Article
- Childhood bone mineral content is associated with methylation status of the RXRA promoter at birth.Journal of bone and mineral research : the official journal of the American Society for Bone and Mineral Research · 2014Article
- CCAT: Combinatorial Code Analysis Tool for transcriptional regulation.Nucleic acids research · 2014Article
- Sp1 trans-activates and is required for maximal aldosterone induction of the αENaC gene in collecting duct cells.American journal of physiology. Renal physiology · 2013Article
- The genomic signature of trait-associated variants.BMC genomics · 2013Article
- Evaluation of methylation status of the eNOS promoter at birth in relation to childhood bone mineral content.Calcified tissue international · 2012Article
Corrections and comments
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Authors and funding
3 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
During development and differentiation of an organism, accurate gene regulation is central for cells to maintain and balance their differentiation processes. Transcriptional interactions between cis-acting DNA elements such as promoters and enhancers are the basis for precise and balanced transcriptional regulation. We identified modules of combinations of binding sites in proximal and distal regulatory regions upstream of all transcription start sites (TSSs) in silico and applied these modules to gene expression time-series of mouse embryonic development and differentiation of human stem cells. In addition to tissue-specific regulation controlled by combinations of transcription factors (TFs) binding at promoters, we observed that in particular the combination of TFs binding at promoters together with TFs binding at the respective enhancers regulate highly specifically temporal progression during development: whereas 40% of TFs were specific for time intervals, 79% of TF pairs and even 97% of promoter-enhancer modules showed specificity for single time intervals of the human stem cells. Predominantly SP1 and E2F contributed to temporal specificity at promoters and the forkhead (FOX) family of TFs at enhancer regions. Altogether, we characterized three classes of TFs: with binding sites being enriched at the TSS (like SP1), depleted at the TSS (like FOX), and rather uniformly distributed.
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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.