• Cancer
• Cardiovascular diseases
• Extracellular matrix (ECM)
• Infectious diseases
• Inflammatory diseases
• Matrix metalloproteinase 3 (MMP-3)
• Neurodegenerative diseases

• B-cell
• ETS family
• ETS1
• Hematologic malignancies
• Leukemia
• Lymphoma
• T-cell
• Transcription factor

• Humans
• Proto-Oncogene Protein c-ets-1/metabolism
• Proto-Oncogene Protein c-ets-1/genetics
• Proto-Oncogene Mas
• Animals
• Lymphoma/genetics
• Lymphoma/metabolism
• Lymphoma/pathology
• Signal Transduction
• Gene Expression Regulation, Leukemic
• Gene Expression Regulation, Neoplastic
• Leukemia/genetics
• Leukemia/metabolism
• Leukemia/pathology

• Humans
• Core Binding Factor Alpha 2 Subunit/genetics
• Binding Sites/genetics
• Protein Binding
• Gene Expression Regulation
• DNA/chemistry

• RM1 HG011123 NHGRI NIH HHS
• R01-GM135658 NIH HHS
• NSF
• NIH

• Parkinson’s disease
• cross-linking
• organization
• self-assembly
• structure

• alpha-Synuclein
• Amyloidogenic Proteins
• Cytoskeleton
• Fluorescence

• VetenskapsrÃ¥det
• Novo Nordisk Fonden

• DNA damage
• ETS transcription factors
• PARP-1
• cancer therapy
• pharmacological inhibition

• Humans
• Leukemia
• Poly Adenosine Diphosphate Ribose
• Poly(ADP-ribose) Polymerase Inhibitors/pharmacology
• Poly(ADP-ribose) Polymerase Inhibitors/therapeutic use
• Prostatic Neoplasms
• Sarcoma, Ewing

• DNA binding protein
• DNA sequence motif
• DNA-binding domain
• ETS proto-oncogene 1 transcription factor (ETS1)
• ETS transcription factor family
• allosteric regulation
• developmental factor
• low-affinity DNA binding
• molecular dynamics
• suboptimization
• transcription enhancer
• transcription factor

• ETS-1
• reactive oxygen species
• renal injury
• vascular injury

• Ets-1
• Ku70
• PARP-1
• interaction domains

• EMT
• ETS2
• MAPK
• apoptosis
• hypopharyngeal cancer

• Competition EMSA
• Cooperative DNA binding
• Curve fitting
• Engrailed
• Extradenticle-Homothorax
• Finding dissociation constants
• Hill plots
• Modeling ligand-substrate interactions
• Quantifying cooperativity

• Allosteric Regulation/genetics
• Binding Sites
• Biophysical Phenomena
• Computational Biology
• DNA-Binding Proteins/chemistry
• DNA-Binding Proteins/genetics
• Kinetics
• Ligands
• Models, Theoretical
• Protein Binding
• Thermodynamics
• Transcription Factors/chemistry
• Transcription Factors/genetics

• R01 GM050231 NIGMS NIH HHS
• R01 GM117458 NIGMS NIH HHS

• DNA-binding protein
• DNA-protein interaction
• ETS transcription factor family
• Negative cooperativity
• PU.1
• nuclear magnetic resonance (NMR)
• protein-DNA interaction

Ets1 is an essential transcription factor (TF) for several important physiological processes, including cell proliferation and differentiation. Its recognition of the enhancer region of the TCRα gene is enhanced by the cooperative binding of the Runx1–CBFβ heterodimer, with the cancelation of phosphorylation-dependent autoinhibition. The detailed mechanism of this interesting cooperativity between Ets1 and the Runx1–CBFβ heterodimer is still largely unclear. Here, we investigated the molecular mechanisms of this cooperativity, by using molecular dynamics simulations. Consequently, we detected high flexibility of the loop region between the HI2 and H1 helices of Ets1. Upon Runx1–CBFβ heterodimer binding, this loop transiently adopts various sub-stable conformations in its interactions with the DNA. In addition, a network analysis suggested an allosteric pathway in the molecular assembly and identified some key residues that coincide with previous experimental studies. Our simulations suggest that the cooperative binding of Ets1 and the Runx1–CBFβ heterodimer alters the DNA conformation and induces sub-stable conformations of the HI2–H1 loop of Ets1. This phenomenon increases the flexibility of the regulatory module, including the HI2 helix, and destabilizes the inhibitory form of this module. Thus, we hypothesize that this effect facilitates Ets1–DNA binding and prevents the phosphorylation-dependent DNA binding autoinhibition.

• Core Binding Factor Alpha 2 Subunit/genetics
• Core Binding Factor Alpha 2 Subunit/metabolism
• Core Binding Factor beta Subunit/genetics
• Core Binding Factor beta Subunit/metabolism
• Genes, T-Cell Receptor alpha/genetics
• Humans
• Molecular Dynamics Simulation
• Nucleic Acid Conformation
• Phosphorylation
• Protein Binding
• Proto-Oncogene Protein c-ets-1/genetics
• Proto-Oncogene Protein c-ets-1/metabolism

• Japan Society for the Promotion of Science
• Japan Agency for Medical Research and Development

Transcription factors (TFs) are important regulatory proteins that govern transcriptional regulation. Today, it is known that in higher organisms different TFs have to cooperate rather than acting individually in order to control complex genetic programs. The identification of these interactions is an important challenge for understanding the molecular mechanisms of regulating biological processes. In this study, we present a new method based on pointwise mutual information, PC-TraFF, which considers the genome as a document, the sequences as sentences, and TF binding sites (TFBSs) as words to identify interacting TFs in a set of sequences.

To demonstrate the effectiveness of PC-TraFF, we performed a genome-wide analysis and a breast cancer-associated sequence set analysis for protein coding and miRNA genes. Our results show that in any of these sequence sets, PC-TraFF is able to identify important interacting TF pairs, for most of which we found support by previously published experimental results. Further, we made a pairwise comparison between PC-TraFF and three conventional methods. The outcome of this comparison study strongly suggests that all these methods focus on different important aspects of interaction between TFs and thus the pairwise overlap between any of them is only marginal.

In this study, adopting the idea from the field of linguistics in the field of bioinformatics, we develop a new information theoretic method, PC-TraFF, for the identification of potentially collaborating transcription factors based on the idiosyncrasy of their binding site distributions on the genome. The results of our study show that PC-TraFF can succesfully identify known interacting TF pairs and thus its currently biologically uncorfirmed predictions could provide new hypotheses for further experimental validation. Additionally, the comparison of the results of PC-TraFF with the results of previous methods demonstrates that different methods with their specific scopes can perfectly supplement each other. Overall, our analyses indicate that PC-TraFF is a time-efficient method where its algorithm has a tractable computational time and memory consumption.

The PC-TraFF server is freely accessible at http://pctraff.bioinf.med.uni-goettingen.de/

The online version of this article (doi:10.1186/s12859-015-0827-2) contains supplementary material, which is available to authorized users.

• Drug resistance
• EMT
• Ets1
• Triple-negative breast cancer

• DNA binding protein
• DNA-protein interaction
• ETS transcription factor family
• autoinhibition
• circular dichroism (CD)
• dimerization
• protein conformation
• protein cross-linking
• protein-nucleic acid interaction

• Apolipoprotein F
• CCAAT/enhancer binding protein
• E-twenty-six
• Lipid transfer inhibitor protein
• Promoter

Ets-2, like its closely related homologue Ets-1, is a member of the Ets family of DNA binding transcription factors. Both proteins are subject to multiple levels of regulation of their DNA binding and transactivation properties. One such regulatory mechanism is the presence of an autoinhibitory module, which in Ets-1 allosterically inhibits the DNA binding activity. This inhibition can be relieved by interaction with protein partners or cooperative binding to closely separated Ets binding sites in a palindromic arrangement. In this study we describe the 2.5 Å resolution crystal structure of a DNA complex of the Ets-2 Ets domain. The Ets domain crystallized with two distinct species in the asymmetric unit, which closely resemble the autoinhibited and DNA bound forms of Ets-1. This discovery prompted us to re-evaluate the current model for the autoinhibitory mechanism and the structural basis for cooperative DNA binding. In contrast to Ets-1, in which the autoinhibition is caused by a combination of allosteric and steric mechanisms, we were unable to find clear evidence for the allosteric mechanism in Ets-2. We also demonstrated two possibly distinct types of cooperative binding to substrates with Ets binding motifs separated by four and six base pairs and suggest possible molecular mechanisms for this behavior.

• Allosteric Regulation
• Cellular Senescence
• DNA Binding Protein
• ETS Transcription Factor Family
• Transcription Factor
• X-ray Crystallography

Gain-of-function mutant p53 is thought to induce gene expression in part by binding transcription factors bound to promoters for genes that mediate oncogenesis. We investigated the mechanism of mutant p53 binding by mapping the human genomic binding sites for p53 R273H using ChIP-Seq and showed them to localize to ETS DNA sequence motifs and locations with ETS1 and GABPA binding, both within promoters and distal to promoters. Strikingly, p53 R273H showed statistically significant and substantial binding to bidirectional promoters, which are enriched for inverted repeated ETS DNA sequence motifs. p53 R273H exhibited an exponential increase in probability of binding promoters with a higher number of ETS motifs. Both ETS1 and GABPA also showed an increase in the probability of binding to promoters with a higher number of ETS motifs. However, despite this increase in probability of binding by p53 R273H and ETS1, there was no increase in the binding signal, suggesting that the number of ETS1 and p53 R273H proteins bound per promoter is being limited. In contrast, GABPA did exhibit an increase in binding signal with higher numbers of ETS motifs per promoter. Analysis of the distance between inverted pairs of ETS motifs within promoters and binding by p53 R273H, ETS1 and GABPA, showed a novel coordination of binding for the three proteins. Both ETS1 and p53 R273H exhibited preference for binding promoters with distantly spaced ETS motifs in face-to-face and back-to-back orientations, and low binding preference to promoters with closely spaced ETS motifs. GABPA exhibited the inverse pattern of binding by preferring to bind promoters with closely spaced ETS motifs. Analysis of the helical phase between ETS motifs showed that ETS1 and p53 R273H exhibited a low preference for binding promoters with ETS motifs on the same face of the DNA helix. We propose a model for the binding of ETS1 and p53 R273H in which two inverted ETS motifs on a looped DNA helix are juxtaposed for ETS1 binding as a homodimer, with p53 R273H bound to ETS1. We propose that the formation of this DNA loop and protein-bound complex prevents additional binding of ETS1 and p53 R273H proteins to other proximal binding sites.

• Bayes Theorem
• Binding Sites/genetics
• Computer Simulation
• DNA/chemistry
• DNA/metabolism
• Kinetics
• Molecular Dynamics Simulation
• Mutation
• Nucleic Acid Conformation
• Pattern Recognition, Automated/methods
• Protein Binding
• Protein Interaction Maps
• Protein Multimerization
• Protein Structure, Secondary
• Protein Structure, Tertiary
• Proto-Oncogene Protein c-ets-1/chemistry
• Proto-Oncogene Protein c-ets-1/genetics
• Proto-Oncogene Protein c-ets-1/metabolism
• Reproducibility of Results

• U01-MH60220 NIMH NIH HHS

The Ets family of eukaryotic transcription factors is based around the conserved Ets DNA-binding domain. Although their DNA-binding selectivity is biochemically and structurally well characterized, structures of homodimeric and ternary complexes point to Ets domains functioning as versatile protein-interaction modules. In the present paper, we review the progress made over the last decade to elucidate the structural mechanisms involved in modulation of DNA binding and protein partner selection during dimerization. We see that Ets domains, although conserved around a core architecture, have evolved to utilize a variety of interaction surfaces and binding mechanisms, reflecting Ets domains as dynamic interfaces for both DNA and protein interaction. Furthermore, we discuss recent advances in drug development for inhibition of Ets factors, and the roles structural biology can play in their future.

• Ets1
• Runx1
• TCRα enhancer
• allosteric regulation
• phosphorylation

Runx1 is required for definitive hematopoiesis and is well-known for its frequent chromosomal translocations and point mutations in leukemia. Runx1 regulates a variety of genes via Ets1 activation on an Ets1•Runx1 composite DNA sequence. The structural basis of such regulation remains unresolved. To address this problem, we determined the crystal structure of the ternary complex containing Runx1_1-242 and Ets1_296-441 bound to T cell receptor alpha (TCRα) enhancer DNA. In the crystal, an Ets1-interacting domain of Runx1 is bound to the Ets1 DNA-binding domain and displaced an entire autoinhibitory module of Ets1, revealing a novel mechanism of Ets1 activation. The DNA binding and transcriptional studies with a variety of structure-guided Runx1 mutants confirmed a critical role of direct Ets1•Runx1 interaction in Ets1 activation. More importantly, the discovered mechanism provides a plausible explanation for how the Ets1•Runx1 interaction effectively activates not only a wild-type Ets1, but also a highly inhibited phosphorylated form of Ets1.

• Cancer
• ETS
• Regulation
• Target genes
• Transcription factors

Ets-1 is a transcription factor that regulates many genes involved in cancer progression and in tumour invasion. It is a poor prognostic marker for breast, lung, colorectal and ovary carcinomas. Here, we identified poly(ADP-ribose) polymerase-1 (PARP-1) as a novel interaction partner of Ets-1. We show that Ets-1 activates, by direct interaction, the catalytic activity of PARP-1 and is then poly(ADP-ribosyl)ated in a DNA-independent manner. The catalytic inhibition of PARP-1 enhanced Ets-1 transcriptional activity and caused its massive accumulation in cell nuclei. Ets-1 expression was correlated with an increase in DNA damage when PARP-1 was inhibited, leading to cancer cell death. Moreover, PARP-1 inhibitors caused only Ets-1-expressing cells to accumulate DNA damage. These results provide new insight into Ets-1 regulation in cancer cells and its link with DNA repair proteins. Furthermore, our findings suggest that PARP-1 inhibitors would be useful in a new therapeutic strategy that specifically targets Ets-1-expressing tumours.

• CIP2A
• Elk1
• Ets1
• PP2A
• biomarkers
• cancer
• p90

Tristetraprolin (TTP) is a key mediator of processes such as inflammation resolution, the inhibition of autoimmunity and in cancer. It carries out this role by the binding and degradation of mRNA transcripts, thereby decreasing their half-life. Transcripts modulated by TTP encode proteins such as cytokines, pro-inflammatory agents and immediate-early response proteins. TTP can also modulate neoplastic phenotypes in many cancers. TTP is induced and functionally regulated by a spectrum of both pro- and anti-inflammatory cytokines, mitogens and drugs in a MAPK-dependent manner. So far the contribution of p38 MAPK to the regulation of TTP expression and function has been best described.

Our results demonstrate the induction of the gene coding TTP (ZFP36) by EGF through the ERK1/2-dependent pathway and implicates the transcription factor ELK-1 in this process. We show that ELK-1 regulates ZFP36 expression by two mechanisms: by binding the ZFP36 promoter directly through ETS-binding site (+ 883 to +905 bp) and by inducing expression of EGR-1, which in turn increases ZFP36 expression through sequences located between -111 and -103 bp.

EGF activates TTP expression via ELK-1 and EGR-1 transcription factors.

Ets1 is a member of the Ets family of transcription factors. Ets1 is expressed in autoinhibited form and its DNA binding depends on partner proteins bound to adjacent sequences or the relative positioning of a second Ets-binding site (EBS). The autoinhibition of Ets1 is mediated by structural coupling of regions flanking the DNA-binding domain. The NMR structure of Ets1 revealed that the inhibitory regions comprised of helices HI1 and HI2 and H4 are packed together on the Ets domain to form an inhibitory module. The crystal structure of Ets1 unexpectedly revealed a homodimer in which homodimerisation occurs via swapping of HI1 helices. Modeling of DNA binding indicates that the Ets1 dimer can bind to two antiparallel pieces of DNA. To verify this, we crystallized and solved the structure of the complex comprised of Ets1 dimer and two pieces of DNA. DNA binding by Ets1 dimer resulted in formation of additional intermolecular protein•DNA interactions, implying that the complex formation is cooperative.

The Stromelysin-1 gene promoter contains a palindrome of two Ets-binding sites (EBS) that bind the p51 and p42 isoforms of the human Ets-1-transcription factor. A previous study established that full gene transactivation is associated with a ternary complex consisting of two p51 bound to the two EBS on the promoter. p42, only able to bind one of the two EBS, induces only very weak activity. Here, we investigate the mechanism by which the Stromelysin-1 promoter discriminates between p51 and p42. The differential stoichiometry of the two Ets-1 isoforms arises from the Stromelysin-1 EBS palindrome. The ternary complex requires the presence of two inhibitory domains flanking the DNA-binding domain and the ability to form an intramolecular autoinhibition module. Most importantly, the p51-ternary and the p42-binary complexes induce DNA curvatures with opposite orientations. These results establish that differential DNA bending, via p51 and p42 differential binding, is correlated with the Stromelysin-1 promoter activation process.

• Animals
• Cell Differentiation
• Cell Proliferation
• Epidermis/pathology
• Epithelial Cells/pathology
• Gene Expression Regulation
• Humans
• Matrix Metalloproteinase 13/genetics
• Mice
• Mice, Transgenic
• Neoplasms, Squamous Cell/etiology
• Proto-Oncogene Protein c-ets-1/genetics

• Animals
• Antibodies/immunology
• Antibodies/pharmacology
• Antigen Presentation/immunology
• Blotting, Western
• CD3 Complex/immunology
• Interferon-gamma/metabolism
• Interleukin-10/metabolism
• Interleukin-2/metabolism
• Ionomycin/pharmacology
• Kinetics
• Mice
• Mice, Inbred C57BL
• Mice, Knockout
• Ovalbumin/immunology
• Phosphorylation/drug effects
• Protein Isoforms/genetics
• Protein Isoforms/metabolism
• Proto-Oncogene Protein c-ets-1/genetics
• Proto-Oncogene Protein c-ets-1/metabolism
• Receptors, Antigen, T-Cell/genetics
• Signal Transduction/drug effects
• T-Lymphocytes, Helper-Inducer/drug effects
• T-Lymphocytes, Helper-Inducer/metabolism
• Tetradecanoylphorbol Acetate/pharmacology
• Th1 Cells/drug effects
• Th1 Cells/metabolism
• Th2 Cells/drug effects
• Th2 Cells/metabolism
• Transfection

• GM 38663 NIGMS NIH HHS
• R03 AI 067880 NIAID NIH HHS

• ets-1
• stromelysin-1 promoter
• x-ray crystallography

DUSP6 (dual-specificity phosphatase 6), also known as MKP-3 [MAPK (mitogen-activated protein kinase) phosphatase-3] specifically inactivates ERK1/2 (extracellular-signal-regulated kinase 1/2) in vitro and in vivo. DUSP6/MKP-3 is inducible by FGF (fibroblast growth factor) signalling and acts as a negative regulator of ERK activity in key and discrete signalling centres that direct outgrowth and patterning in early vertebrate embryos. However, the molecular mechanism by which FGFs induce DUSP6/MKP-3 expression and hence help to set ERK1/2 signalling levels is unknown. In the present study, we demonstrate, using pharmacological inhibitors and analysis of the murine DUSP6/MKP-3 gene promoter, that the ERK pathway is critical for FGF-induced DUSP6/MKP-3 transcription. Furthermore, we show that this response is mediated by a conserved binding site for the Ets (E twenty-six) family of transcriptional regulators and that the Ets2 protein, a known target of ERK signalling, binds to the endogenous DUSP6/MKP-3 promoter. Finally, the murine DUSP6/MKP-3 promoter coupled to EGFP (enhanced green fluorescent protein) recapitulates the specific pattern of endogenous DUSP6/MKP-3 mRNA expression in the chicken neural plate, where its activity depends on FGFR (FGF receptor) and MAPK signalling and an intact Ets-binding site. These findings identify a conserved Ets-factor-dependent mechanism by which ERK signalling activates DUSP6/MKP-3 transcription to deliver ERK1/2-specific negative-feedback control of FGF signalling.