Change In DNA Binding Affinity Research Articles

HNF4A and HNF1A exhibit tissue specific target gene regulation in pancreatic beta cells and hepatocytes

HNF4A and HNF1A encode transcription factors that are important for the development and function of the pancreas and liver. Mutations in both genes have been directly linked to Maturity Onset Diabetes of the Young (MODY) and type 2 diabetes (T2D) risk. To better define the pleiotropic gene regulatory roles of HNF4A and HNF1A, we generated a comprehensive genome-wide map of their binding targets in pancreatic and hepatic cells using ChIP-Seq. HNF4A was found to bind and regulate known (ACY3, HAAO, HNF1A, MAP3K11) and previously unidentified (ABCD3, CDKN2AIP, USH1C, VIL1) loci in a tissue-dependent manner. Functional follow-up highlighted a potential role for HAAO and USH1C as regulators of beta cell function. Unlike the loss-of-function HNF4A/MODY1 variant I271fs, the T2D-associated HNF4A variant (rs1800961) was found to activate AKAP1, GAD2 and HOPX gene expression, potentially due to changes in DNA-binding affinity. We also found HNF1A to bind to and regulate GPR39 expression in beta cells. Overall, our studies provide a rich resource for uncovering downstream molecular targets of HNF4A and HNF1A that may contribute to beta cell or hepatic cell (dys)function, and set up a framework for gene discovery and functional validation.

Insight into the intrinsically disordered transactivation domain of NFkB as a regulator of DNA binding using UV-induced unnatural amino acid crosslinking.

Within our vast genome, specific transcription factors like NFkB manage to find target sequences amongst overwhelming nonspecific options and help elicit timely cellular responses. A transcription factor's binding affinity for specific vs. nonspecific DNA must therefore be in a delicate balance to facilitate this search. Key in vitro experiments that described these binding affinities for the dominant NFkB dimer RelA/p50 were carried out with a truncated version of RelA - excluding a large intrinsically disordered transactivation domain (TAD) that was believed to be important for transcription activation through cofactor interactions but not impactful for DNA binding. This fit with a traditional view of protein domains acting as modular units. More recently, however, we discovered a novel function of the TAD: binding experiments revealed that the TAD's presence increased RelA/p50's affinity for DNA, with the strongest increase in binding affinity observed for non-specific DNA sequences lacking kB consensus sites. Here we follow up these findings with an investigation of the TAD's mechanism of action. We present preliminary results using an unnatural amino acid crosslinker (p-benzoyl-l-phenylalanine or pBpF) in combination with mass spectrometry to probe TAD interactions that lead to the observed changes in DNA binding affinity and specificity. pBpF is incorporated into specific positions in the TAD using AMBER codon suppression, and crosslinking is initiated by UV light. Interactions are analyzed by mass spectrometry to identify key sites of contact between the TAD and the natively folded Rel-Homology Domain.

Telomere uncapping by common oxidative guanine lesions: Insights from atomistic models

Oxidative damage to DNA is widely known to contribute to aging and disease. This relationship has been extensively studied for telomeres – structures that cap chromosome ends – due to their role in cell proliferation and senescence, and exceptional susceptibility to oxidation. Indeed, the repetitive telomeric DNA sequence contains the 5′-GGG-3′ motif that has the lowest ionization potential of all trinucleotides. Accordingly, experiments consistently show that telomeric oxidative lesions are more abundant and persistent than elsewhere in the genome. This led to a hypothesis that telomeres act as sensors of prolonged oxidative stress and prevent carcinogenesis, as disruption of telomeric integrity triggers senescence or apoptosis. Here, we use atomistic alchemical Molecular Dynamics simulations to perform a combinatorial assessment of changes in DNA binding affinity of telomeric proteins induced by oxidative guanine lesions. We rank lesions by their effect on telomere integrity, as well as telomeric proteins by their sensitivity to DNA oxidation. While the binding of most proteins is abolished by DNA oxidation, HOT1 emerges as a notable exception, suggesting its potential role in sensing of oxidative damage. Through statistical analysis and free energy decomposition, we also identify common trends in structural responses of protein-DNA complexes that contribute to decreased binding affinity.

Inhibition of Human DNA Polymerases Eta and Kappa by Indole-Derived Molecules Occurs through Distinct Mechanisms.

Overexpression of human DNA polymerase kappa (hpol κ) in glioblastoma is associated with shorter survival time and resistance to the alkylating agent temozolomide (TMZ), making it an attractive target for the development of small-molecule inhibitors. We previously reported on the development and characterization of indole barbituric acid-derived (IBA) inhibitors of translesion DNA synthesis polymerases (TLS pols). We have now identified a potent and selective inhibitor of hpol κ based on the indole-aminoguanidine (IAG) chemical scaffold. The most promising IAG analogue, IAG-10, exhibited greater inhibitory action against hpol κ than any other human Y-family member, as well as pols from the A-, B-, and X-families. Inhibition of hpol κ by IAG analogues appears to proceed through a mechanism that is distinct from inhibition of hpol η based on changes in DNA binding affinity and nucleotide insertion kinetics. By way of comparison, both IAG and IBA analogues inhibited binary complex formation by hpol κ and ternary complex formation by hpol η. Decreasing the concentration of enzyme and DNA in the reaction mixture lowered the IC50 value of IAG-10 to submicromolar values, consistent with inhibition of binary complex formation for hpol κ. Chemical footprinting experiments revealed that IAG-10 binds to a cleft between the finger, little finger, and N-clasp domains on hpol κ and that this likely disrupts the interaction between the N-clasp and the TLS pol core. In cell culture, IAG-10 potentiated the antiproliferative activity and DNA damaging effects of TMZ in hpol κ-proficient cells but not in hpol κ-deficient cells, indicative of a target-dependent effect. Mutagenic replication across alkylation damage increased in hpol κ-proficient cells treated with IAG-10, while no change in mutation frequency was observed for hpol κ-deficient cells. In summary, we developed a potent and selective small-molecule inhibitor of hpol κ that takes advantage of structural features unique to this TLS enzyme to potentiate TMZ, a standard-of-care drug used in the treatment of malignant brain tumors. Furthermore, the IAG scaffold represents a new chemical space for the exploration of TLS pol inhibitors, which could prove useful as a strategy for improving patient response to genotoxic drugs.

Synthetic STARR-seq reveals how DNA shape and sequence modulate transcriptional output and noise

The binding of transcription factors to short recognition sequences plays a pivotal role in controlling the expression of genes. The sequence and shape characteristics of binding sites influence DNA binding specificity and have also been implicated in modulating the activity of transcription factors downstream of binding. To quantitatively assess the transcriptional activity of tens of thousands of designed synthetic sites in parallel, we developed a synthetic version of STARR-seq (synSTARR-seq). We used the approach to systematically analyze how variations in the recognition sequence of the glucocorticoid receptor (GR) affect transcriptional regulation. Our approach resulted in the identification of a novel highly active functional GR binding sequence and revealed that sequence variation both within and flanking GR’s core binding site can modulate GR activity without apparent changes in DNA binding affinity. Notably, we found that the sequence composition of variants with similar activity profiles was highly diverse. In contrast, groups of variants with similar activity profiles showed specific DNA shape characteristics indicating that DNA shape may be a better predictor of activity than DNA sequence. Finally, using single cell experiments with individual enhancer variants, we obtained clues indicating that the architecture of the response element can independently tune expression mean and cell-to cell variability in gene expression (noise). Together, our studies establish synSTARR as a powerful method to systematically study how DNA sequence and shape modulate transcriptional output and noise.

The Oxidation State of [4Fe4S] Clusters Modulates the DNA-Binding Affinity of DNA Repair Proteins.

A central question important to understanding DNA repair is how certain proteins are able to search for, detect, and fix DNA damage on a biologically relevant time scale. A feature of many base excision repair proteins is that they contain [4Fe4S] clusters that may aid their search for lesions. In this paper, we establish the importance of the oxidation state of the redox-active [4Fe4S] cluster in the DNA damage detection process. We utilize DNA-modified electrodes to generate repair proteins with [4Fe4S] clusters in the 2+ and 3+ states by bulk electrolysis under an O2-free atmosphere. Anaerobic microscale thermophoresis results indicate that proteins carrying [4Fe4S]3+ clusters bind to DNA 550 times more tightly than those with [4Fe4S]2+ clusters. The measured increase in DNA-binding affinity matches the calculated affinity change associated with the redox potential shift observed for [4Fe4S] cluster proteins upon binding to DNA. We further devise an electrostatic model that shows this change in DNA-binding affinity of these proteins can be fully explained by the differences in electrostatic interactions between DNA and the [4Fe4S] cluster in the reduced versus oxidized state. We then utilize atomic force microscopy (AFM) to demonstrate that the redox state of the [4Fe4S] clusters regulates the ability of two DNA repair proteins, Endonuclease III and DinG, to bind preferentially to DNA duplexes containing a single site of DNA damage (here a base mismatch) which inhibits DNA charge transport. Together, these results show that the reduction and oxidation of [4Fe4S] clusters through DNA-mediated charge transport facilitates long-range signaling between [4Fe4S] repair proteins. The redox-modulated change in DNA-binding affinity regulates the ability of [4Fe4S] repair proteins to collaborate in the lesion detection process.

Ikaros, CK2 kinase, and the road to leukemia

Ikaros encodes a zinc finger protein that is essential for hematopoiesis and that acts as a tumor suppressor in leukemia. Ikaros function depends on its ability to localize to pericentromeric-heterochromatin (PC-HC). Ikaros protein binds to the upstream regulatory elements of target genes, aids in their recruitment to PC-HC, and regulates their transcription via chromatin remodeling. We identified four novel Ikaros phosphorylation sites that are phosphorylated by CK2 kinase. Using Ikaros phosphomimetic and phosphoresistant mutants of the CK2 phosphorylation sites, we demonstrate that (1) CK2-mediated phosphorylation inhibits Ikaros' localization to PC-HC; (2) dephosphorylation of Ikaros at CK2 sites increases its binding to the promoter of the terminal deoxynucleotidetransferase (TdT) gene, leading to TdT repression during thymocyte differentiation; and (3) hyperphosphorylation of Ikaros promotes its degradation by the ubiquitin/proteasome pathway. We show that Ikaros is dephosphorylated by Protein Phosphatase 1 (PP1) via interaction at a consensus PP1-binding motif, RVXF. Point mutations that abolish Ikaros-PP1 interaction result in functional changes in DNA-binding affinity and subcellular localization, similar to those observed in hyperphosphorylated Ikaros and/or Ikaros phosphomimetic mutants. Phosphoresistant Ikaros mutations at CK2 sites restored Ikaros' DNA-binding activity and localization to PC-HC and prevented accelerated Ikaros degradation. These results demonstrate the role of CK2 kinase in lymphocyte differentiation and in regulation of Ikaros' function, and suggest that CK2 promotes leukemogenesis by inhibiting the tumor suppressor activity of Ikaros. We propose a model whereby a balance between CK2 kinase and PP1 phosphatase is essential for normal lymphocyte differentiation and for the prevention of malignant transformation.

Correlating in Vitro Measurements of Protein-DNA Binding Affinities with in Vivo Repression and Impact on the Growth Rate of the Host Organism

In order to fully decode the information of patient genomes, we must determine which protein polymorphisms alter function. One resource for addressing this question is the sequence set of naturally occurring homologs. Sequence comparisons easily identify conserved positions, which usually cannot be changed without consequence. However, the impact of changing nonconserved positions is less-easily predicted. We have devised a model system for testing computational identifications of important nonconserved positions and measuring the functional impact from amino acid substitutions at these positions. The model system is based on chimeric proteins of the LacI/GalR family; functional change can be detected as either altered in vivo repression or altered in vitro DNA binding properties. For this system to accurately model a naturally-evolving system, an observed change in repression must be large enough to impact the growth of the host organism. Here, we use a series of point mutations in an engineered LacI/GalR transcription repressor to correlate altered in vivo repression with thermodynamic measurements of DNA binding affinities and bacterial growth rates. Results will determine whether most changes in repression are due to changes in DNA-binding affinity for the in vivo operator DNA binding site, and will determine how large a change in repression is required to alter bacterial life cycles.

Glucose Mediates the Translocation of NeuroD1 by O-Linked Glycosylation

O-Linked GlcNAc modification of nuclear and cytosolic proteins has been shown to regulate the function of many cellular proteins. Increased O-linked glycosylation, observed under chronic hyperglycemia conditions, has been implicated in the pathogenesis of diabetes. However, the exact role of O-GlcNAc modification in regulating glucose homeostasis remains to be established. We report here that the subcellular localization of the pancreatic beta cell-specific transcription factor NeuroD1 is regulated by O-linked glycosylation in the mouse insulinoma cell line MIN6. Under low glucose conditions, NeuroD1 is mainly in the cytosol. However, treatment of MIN6 cells with high glucose results in O-linked GlcNAc modification of NeuroD1 and its subsequent translocation into the nucleus. Consistent with these data, treatment of MIN6 cells with O-(2-acetamido-2-deoxy-d-glucopyranosylidene)-amino N-phenylcarbamate, an inhibitor of O-GlcNAcase, causes Neuro-D1 localization to the nucleus and induction of insulin gene expression even on low glucose. Furthermore, we demonstrate that NeuroD1 interacts with the O-GlcNAc transferase, OGT only at high concentrations of glucose and depletion of OGT by using small interfering RNA oligos interferes with the nuclear localization of NeuroD1 on high glucose. On low glucose NeuroD1 interacts with the O-GlcNAcase and becomes deglycosylated, which is likely to be important for export of Neuro-D1 into cytosol in the presence of low glucose. In summary, the presented data suggest that glucose regulates the subcellular localization of NeuroD1 in pancreatic beta cells via O-linked GlcNAc modification of NeuroD1 by OGT.

The Relationship between Intranuclear Mobility of the NF-κB Subunit p65 and Its DNA Binding Affinity

It has been hypothesized that the main determinant of the intranuclear mobility of transcription factors is their ability to bind DNA. In the present study, we have extensively tested the relationship between the intranuclear mobility of the NF-kappaB subunit p65 and binding to its consensus target sequence. The affinity of p65 for this binding site is altered by mutation of specific acetylation sites, so these mutants provide a model system to study the relationship between specific DNA binding affinity and intranuclear mobility. DNA binding affinity was measured in vitro using an enzyme-linked immunosorbent assay-based method, and intranuclear mobility was measured using the fluorescence recovery after photobleaching technique on yellow fluorescent protein-tagged p65 constructs. A negative correlation was observed between DNA binding affinity and intranuclear mobility of p65 acetylation site mutants. However, moving the yellow fluorescent protein tag from the C terminus of p65 to the N terminus resulted in an increased mobility but did not significantly affect DNA binding affinity. Thus, all changes in DNA binding affinity produce alterations in mobility, but not vice versa. Finally, a positive correlation was observed between mobility and the randomness of the intranuclear distribution of p65. Our data are in line with a model in which the intranuclear mobility and distribution of a transcription factor are determined by its affinity for specific DNA sequences, which may be altered by protein-protein interactions.

Beryllofluoride Binding Mimics Phosphorylation of Aspartate in Response Regulators

Beryllofluoride Binding Mimics Phosphorylation of Aspartate in Response Regulators

Downregulation of calcineurin activity in cervical carcinoma.

BackgroundCalcineurin (CaN) is an important serine-threonine phosphatase (PP2B), which plays a crucial role in calcium-calmodulin mediated signal transduction events. Calcineurin has been implicated in pathogenesis of various diseases cardiac hypertrophy, diabetic neuropathy and Alzheimer's, however its role in neoplasia remains unclear.ResultsIn view of this we evaluated the calcineurin activity in serum and biopsy samples collected from women diagnosed with invasive squamous cell carcinoma of cervix. A significant reduction was observed in the calcineurin activity in cancer cervix patients compared to the control group. However the calcineurin activity remained unaltered in the cervical scrapes obtained from patients diagnosed with low-grade squamous intra epithelial lesions (LSIL). Interestingly the downregulation of calcineurin activity in squamous cell carcinomas was not accompanied by any significant change in DNA-binding affinity of the transcriptional factor NFAT (Nuclear Factor of Activated T-cells). All the squamous cell carcinoma samples used in the present study were positive for high-risk human papillomavirus (HPV) types.ConclusionThe present study demonstrates the downregulation of calcineurin activity in squamous cell carcinoma of cervix with high risk HPV infection. We conclude that perturbations in calcineurin-mediated pathway may be involved in development of cervical neoplasia.

The role of in vitro expression systems in the investigation of antibodies to DNA

Objectives: Antibodies to DNA are believed to be important in the developmentof tissue inflammation and clinical activity in systemic lupus erythematosus (SLE). Sequence analysis of monoclonal murine and human anti-DNA antibodies suggests that somatic mutations and basic residues are important features at the DNA-binding site. To test this hypothesis, it is possible to alter these residues by site-directed mutagenesis of cloned variable region cDNA. The mutagenized cDNA sequence is then expressed in the form of a protein molecule whose properties can be tested in assays of binding or pathogenicity. The purpose of this article is to provide a systematic review of the evidence derived by such methods in the study of anti-DNA antibodies. Methods: Various different expression systems are available. Experiments using bacterial and eukaryotic expression systems are considered in turn. The advantages and disadvantages of the systems are described and the results obtained are compared. Results and Conclusions: High yields of antibody fragments such as scFv andFab can be achieved by expression in bacteria. Such studies tend to confirm that reversion of somatic mutations or removal of basic residues at the antigen binding site reduce affinity for DNA. Tests of pathogenicity can only be performed by expressing whole antibodies in eukaryotic cells. The limited data available from expression of mutagenized cDNA in such systems argue against a simple relationship between changes in DNA binding affinity and changes in pathogenic potential. Further studies are therefore required to analyze the sequence requirements for pathogenicity.

Single-chain lambda Cro repressors confirm high intrinsic dimer-DNA affinity.

The overall affinity of the bacteriophage lambda Cro repressor for its operator DNA site is limited by dimer dissociation at submicromolar concentrations. Since Cro dimer-operator complexes form at nanomolar concentrations of Cro subunits where free dimers are rare, these dimers must bind with compensating high affinities. Previous studies of the covalent dimer Cro V55C suggest little change in DNA binding affinity even though the dimeric species is quantitatively populated; this is an apparent contradiction to the expectation of high intrinsic dimer-DNA affinity. In contrast to the disulfide linkage at the center of the dimer interface in Cro V55C, polypeptide linkers that join the two subunits allow single-chain Cro repressors to bind operator DNA with picomolar affinities. A series of five single-chain Cro repressors have been expressed from fused tandem cro genes. Each contains a peptide linker of 8-16 hydrophilic residues that connects the C-terminus of one subunit to the N-terminus of the next. All bind to operator DNA with at least 100-fold higher affinity than Cro V55C. Proteins containing the longest and shortest linkers have been purified and characterized in detail. Both exhibit similar CD spectra to wild-type Cro and enhanced thermal stability. Sedimentation equilibrium experiments show that single-chain Cro repressors do not associate at concentrations up to 30 microM. The rate of dissociation of Cro-DNA complexes is almost unchanged by covalent linkage. Biophysical characterization of Cro variants such as these, where DNA binding is uncoupled from subunit assembly, is necessary for a quantitative understanding of the structural and energetic determinants of DNA recognition in this simple model system.

CAMP-dependent Protein Kinase Is Necessary for Increased NF-E2·DNA Complex Formation during Erythroleukemia Cell Differentiation

When murine erythroleukemia (MEL) cells are induced to differentiate by hexamethylene bisacetamide (HMBA), erythroid-specific genes are transcriptionally activated; however, transcriptional activation of these genes is severely impaired in cAMP-dependent protein kinase (protein kinase A)-deficient MEL cells. The transcription factor NF-E2, composed of a 45-kDa (p45) and an 18-kDa (p18) subunit, is essential for enhancer activity of the globin locus control regions (LCRs). DNA binding of NF-E2 and alpha-globin LCR enhancer activity was significantly less in HMBA-treated protein kinase A-deficient cells compared to cells containing normal protein kinase A activity; DNA binding of several other transcription factors was the same in both cell types. In parental cells, HMBA treatment and/or prolonged activation of protein kinase A increased the amount of NF-E2.DNA complexes without change in DNA binding affinity; the expression of p45 and p18 was the same under all conditions. p45 and p18 were phosphorylated by protein kinase A in vitro, but the phosphorylation did not affect NF-E2.DNA complexes, suggesting that protein kinase A regulates NF-E2.DNA complex formation indirectly, e.g. by altering expression of a regulatory factor(s). Thus, protein kinase A appears to be necessary for increased NF-E2.DNA complex formation during differentiation of MEL cells and may influence erythroid-specific gene expression through this mechanism.

Procaine, a local anesthetic, signals through the EnvZ receptor to change the DNA binding affinity of the transcriptional activator protein OmpR

Local anesthetics are known to reduce the level of OmpF and increase the synthesis of OmpC in the outer membrane of Escherichia coli K-12. It has been shown that the anesthetics procaine and phenethyl alcohol (PEA) act at the transcriptional level for ompF and ompC and that in the case of procaine, its action is dependent on EnvZ, the membrane-bound signal transducer required for ompF and ompC expression. In an effort to further understand how anesthetics regulate ompF and ompC expression, we have analyzed the DNA binding properties of OmpR (the transcriptional activator protein for ompF and ompC genes) from cells treated with procaine or PEA. Treatment of a wild-type cell with either anesthetic converted OmpR from a low-affinity DNA binding form to a high-affinity DNA binding form. The change in DNA binding affinity was correlated with alterations in outer membrane porin profiles and could occur in the absence of protein synthesis. A strain lacking EnvZ was unable to respond to procaine to produce either the shift in the OmpR DNA binding property or cause any change in the outer membrane porin profile. PEA treatment was also dependent on EnvZ for the alteration in the OmpR DNA binding property, but it could induce ompC expression in the absence of EnvZ. Further studies suggest that the amino-terminal region of EnvZ is responsible for the procaine signalling. Our results indicate that procaine and PEA regulate ompF and ompC expression by modifying the DNA binding properties of OmpR through EnvZ signal transduction.

Unoccupied and in vitro and in vivo occupied 1,25-dihydroxyvitamin D3 intestinal receptors. Multiple biochemical forms and evidence for transformation.

The data presented herein indicate that the chick intestinal 1,25-dihydroxyvitamin D3 (1,25(OH)2D3) receptor which is localized in the chromatin fraction of a low salt homogenate (Walters, M. R., Hunziker, W., and Norman, A. W. (1980) J. Biol. Chem. 255, 6799-6805) can exist in three distinct biochemical forms. The three 1,25(OH)2D3 receptor forms depended on the absence or presence of ligand and additionally whether the ligand was acquired in vitro (4 degrees C incubation for 3-4 h) or in vivo (13 nmol of 1,25(OH)2D3 administered intramuscularly 2 h prior to sacrifice). The receptor forms were distinguished by their relative KCl extractabilities from the target tissue chromatin preparation and from a reconstituted nontarget tissue (liver) chromatin preparation, as well as their relative elution from DNA-cellulose columns when applied as a mixture. In all cases the rank order "affinity" of the receptor for chromatin or DNA was: unoccupied 1,25(OH)2D3 receptors less than in vivo occupied receptors less than in vitro occupied receptors. These changes in DNA-binding "affinity" occurred without a major change in overall surface charge of the receptor molecules as evaluated by co-elution of all three receptor forms from DEAE-Sepharose columns. Similarly, these changes in DNA-binding characteristics were not accompanied by changes in the apparent molecular weights of these receptor species (91,900 +/- 3300; 99,700 +/- 9400; 93,100 +/- 5600, respectively) as assessed by Sephacryl S-200 gel filtration chromatography in the presence of the protease inhibitor phenylmethylsulfonyl fluoride, included throughout these experiments to protect from proteolytic damage. These results represent the first demonstration of biochemical heterogeneity in the 1,25(OH)2D3 receptor system and suggest the existence of a two-step transformation process for the 1,25(OH)2D3 receptor.