ArticleGenome research2007
Serum response factor binding sites differ in three human cell types.
Article in Genome research, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 50 papers.
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Who cites it
50 citing papers in PubMed, 75 citations in OpenAlex.
- Vascular injury activates the ELK1/SND1/SRF pathway to promote vascular smooth muscle cell proliferative phenotype and neointimal hyperplasia.Cellular and molecular life sciences : CMLS · 2024Article
- IVEA: an integrative variational Bayesian inference method for predicting enhancer-gene regulatory interactions.Bioinformatics advances · 2024Article
- Base-resolution UV footprinting by sequencing reveals distinctive damage signatures for DNA-binding proteins.Nature communications · 2023Article
- Hydrogel mechanics regulate fibroblast DNA methylation and chromatin condensation.Biomaterials science · 2023Article
- Serum response factor-cofactor interactions and their implications in disease.The FEBS journal · 2021Review
- TRA2A-induced upregulation of LINC00662 regulates blood-brain barrier permeability by affecting ELK4 mRNA stability in Alzheimer's microenvironment.RNA biology · 2020Article
- EGR-mediated control of STIM expression and function.Cell calcium · 2019Review
- Srf destabilizes cellular identity by suppressing cell-type-specific gene expression programs.Nature communications · 2018Article
- Syndecan-2 Attenuates Radiation-induced Pulmonary Fibrosis and Inhibits Fibroblast Activation by Regulating PI3K/Akt/ROCK Pathway via CD148.American journal of respiratory cell and molecular biology · 2018Article
- Neuroprotective effect of Ruminococcus albus on oxidatively stressed SH-SY5Y cells and animals.Scientific reports · 2017Article
- The organization and regulation of mRNA-protein complexes.Wiley interdisciplinary reviews. RNA · 2017Review
- Multi-phenotypic Role of Serum Response Factor in the Gastrointestinal System.Journal of neurogastroenterology and motility · 2016Review
- The short and long of noncoding sequences in the control of vascular cell phenotypes.Cellular and molecular life sciences : CMLS · 2015Review
- The neuronal activity-driven transcriptome.Molecular neurobiology · 2015Review
- The core and conserved role of MAL is homeostatic regulation of actin levels.Genes & development · 2014Article
- Global analyses of the effect of different cellular contexts on microRNA targeting.Molecular cell · 2014Article
- SRF phosphorylation by glycogen synthase kinase-3 promotes axon growth in hippocampal neurons.The Journal of neuroscience : the official journal of the Society for Neuroscience · 2014Article
- Identification of highly conserved putative developmental enhancers bound by SOX3 in neural progenitors using ChIP-Seq.PloS one · 2014Article
- Serum regulation of Id1 expression by a BMP pathway and BMP responsive element.Biochimica et biophysica acta · 2013Article
- Androgen-responsive serum response factor target genes regulate prostate cancer cell migration.Carcinogenesis · 2013Article
Corrections and comments
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Authors and funding
4 authors at 1 institution in 1 country.
Funding
Abstract
The serum response factor (SRF) is essential for embryonic development and maintenance of muscle cells and neurons. The mechanism by which this factor controls these divergent pathways is unclear. Here we present a genome-wide view of occupancy of SRF at its binding sites with a focus on those that vary with cell type. We used chromatin immunoprecipitation (ChIP) in combination with human promoter microarrays to identify 216 putative SRF binding sites in the human genome. We performed independent quantitative PCR validation at over half of these sites that resulted in 146 sites we assert to be true binding sites at over 90% confidence. Nearly half of the sites are bound by SRF in only one of the three cell types we tested, providing strong evidence for the diverse roles for SRF in different cell types. We also explore possible mechanisms controlling differential binding of SRF in these cell types by assaying cofactor binding, DNA methylation, histone methylation, and histone acetylation at a subset of sites bound preferentially in smooth muscle cells. Although we did not see a strong correlation between SRF binding and epigenetics modifications, at these sites, we propose that SRF cofactors may play an important role in determining cell-dependent SRF binding sites. ELK4 (previously known as SAP-1 [SRF-associated protein-1]) is ubiquitously expressed. Therefore, we expected it to occupy sites where SRF binding is common in all cell types. Indeed, 90% of SRF sites also bound by ELK4 were common to all three cell types. Together, our data provide a more complete understanding of the regulatory network controlled by SRF.
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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.