ArticleGenome biology2009
Defining the chromatin signature of inducible genes in T cells.
Article in Genome biology, 2009. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 23 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
23 citing papers in PubMed.
- Article
- Deep Learning for Genomics: From Early Neural Nets to Modern Large Language Models.International journal of molecular sciences · 2023Review
- The roles of inducible chromatin and transcriptional memory in cellular defense system responses to redox-active pollutants.Free radical biology & medicine · 2021Review
- H3K27 Methylation Dynamics during CD4 T Cell Activation: Regulation of JAK/STAT and IL12RB2 Expression by JMJD3.Journal of immunology (Baltimore, Md. : 1950) · 2017Article
- Chromatin Regulation and the Histone Code in HIV Latency .The Yale journal of biology and medicine · 2017Review
- Priming of transcriptional memory responses via the chromatin accessibility landscape in T cells.Scientific reports · 2017Article
- Global intron retention mediated gene regulation during CD4+ T cell activation.Nucleic acids research · 2016Article
- Promoter H3K4 methylation dynamically reinforces activation-induced pathways in human CD4 T cells.Genes and immunity · 2016Article
- Transcriptomic analysis of mouse EL4 T cells upon T cell activation and in response to protein synthesis inhibition via cycloheximide treatment.Genomics data · 2016Article
- Focused transcription from the human CR2/CD21 core promoter is regulated by synergistic activity of TATA and Initiator elements in mature B cells.Cellular & molecular immunology · 2016Article
- Histone modifications are associated with Δ9-tetrahydrocannabinol-mediated alterations in antigen-specific T cell responses.The Journal of biological chemistry · 2014Article
- Chromatin states reveal functional associations for globally defined transcription start sites in four human cell lines.BMC genomics · 2014Article
- A chromatin modifying enzyme, SDG8, is involved in morphological, gene expression, and epigenetic responses to mechanical stimulation.Frontiers in plant science · 2014Article
- Review
- The correlation between histone modifications and gene expression.Epigenomics · 2013Article
- Review
- Modeling gene expression using chromatin features in various cellular contexts.Genome biology · 2012Article
- Revealing epigenetic patterns in gene regulation through integrative analysis of epigenetic interaction network.Molecular biology reports · 2012Article
- ATP-dependent chromatin remodeling in T cells.Biochemistry and cell biology = Biochimie et biologie cellulaire · 2012Review
- Gene induction and repression during terminal erythropoiesis are mediated by distinct epigenetic changes.Blood · 2011Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
7 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundSpecific chromatin characteristics, especially the modification status of the core histone proteins, are associated with active and inactive genes. There is growing evidence that genes that respond to environmental or developmental signals may possess distinct chromatin marks. Using a T cell model and both genome-wide and gene-focused approaches, we examined the chromatin characteristics of genes that respond to T cell activation.
resultsTo facilitate comparison of genes with similar basal expression levels, we used expression-profiling data to bin genes according to their basal expression levels. We found that inducible genes in the lower basal expression bins, especially rapidly induced primary response genes, were more likely than their non-responsive counterparts to display the histone modifications of active genes, have RNA polymerase II (Pol II) at their promoters and show evidence of ongoing basal elongation. There was little or no evidence for the presence of active chromatin marks in the absence of promoter Pol II on these inducible genes. In addition, we identified a subgroup of genes with active promoter chromatin marks and promoter Pol II but no evidence of elongation. Following T cell activation, we find little evidence for a major shift in the active chromatin signature around inducible gene promoters but many genes recruit more Pol II and show increased evidence of elongation.
conclusionsThese results suggest that the majority of inducible genes are primed for activation by having an active chromatin signature and promoter Pol II with or without ongoing elongation.
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.