Consensus DNA Motif Research Articles

Determining DNA-Protein Binding Affinities and Specificities from Crude Lysates Using a Combined SILAC/TMT Labeling Strategy.

In recent years, quantitative mass spectrometry-based interaction proteomics technology has proven very useful in identifying specific DNA-protein interactions using single pull-downs from crude lysates. Here, we applied a SILAC/TMT-based higher-order multiplexing approach to develop an interaction proteomics workflow called Protein-nucleic acid Affinity and Specificity quantification by MAss spectrometry in Nuclear extracts or PASMAN. In PASMAN, DNA pull-downs using a concentration range of specific and control DNA baits are performed in SILAC-labeled nuclear extracts. MS1-based quantification to determine specific DNA-protein interactions is then combined with sequential TMT-based quantification of fragmented SILAC peptides, allowing the generation of Hill-like curves and determination of apparent binding affinities. We benchmarked PASMAN using the SP/KLF motif and further applied it to gain insights into two CGCG-containing consensus DNA motifs. These motifs are recognized by two BEN domain-containing proteins, BANP and BEND3, which we find to interact with these motifs with distinct affinities. Finally, we profiled the BEND3 proximal proteome, revealing the NuRD complex as the major BEND3 proximal protein complex in vivo. In summary, PASMAN represents, to our knowledge, the first higher-order multiplexing-based interaction proteomics method that can be used to decipher specific DNA-protein interactions and their apparent affinities in various biological and pathological contexts.

Epigenetic Fine Mapping and Functional Dissection of Inherited Non-Coding Variation Impacting the Pharmacogenomics of Acute Lymphoblastic Leukemia Treatment

Acute lymphoblastic leukemia (ALL) is the most prevalent childhood cancer. Despite cure rates exceeding 90%, relapsed ALL is the 5th most common pediatric cancer. Although chemotherapeutic drug resistance remains the primary cause of treatment failure and relapse, it remains unclear to what extent non-coding inherited DNA sequence variants impact gene regulatory programs that contribute to differences in chemotherapeutic drug resistance and clinical outcome in childhood ALL. To address this knowledge gap we performed epigenetic fine mapping on inherited non-coding DNA sequence variants associated with ex vivo resistance to six antileukemic agents (dexamethasone, prednisolone, l-asparaginase, vincristine, 6-mercaptopurine and 6-thioguanine) in primary ALL cells from pediatric patients and inherited non-coding DNA sequence variants associated with clinical outcome (persistence of minimal residual disease and relapse) in pediatric patient cohorts using chromatin accessibility data from over 130 primary ALL cells, ALL cell lines and ALL xenografts. This analysis fine mapped over 1700 variants (sentinel variants and variants in high linkage disequilibrium; r2>0.8) to cis-regulatory elements in the ALL genome. To comprehensively dissect the functional effects of these fine mapped variants on gene regulatory activity we performed massively parallel reporter assays (MPRAs) in 10 human ALL cell lines of both B- and T-cell lineages. MPRAs utilized 23 DNA barcodes per variant allele and tested variants at bidirectional promoters using both sequence orientations. In total, 98,168 oligonucleotides each containing 175-bp of genomic sequence centered on each variant allele and a unique 10-bp barcode sequence were evaluated for gene regulatory activity. MPRA identified 558 variants with significant and concordant allele-specific activities in three or more ALL cell lines. Expression quantitative trait loci (eQTL) mapping and HiChIP three-dimensional promoter loop profiling identified candidate target genes for a subset of functional variants. We additionally evaluated the functional effects of top ranked variants using luciferase reporter assays and CRISPR/Cas9 genome editing. These variants were associated with the expression of B3GNT5, CACUL1, HERC1, KDM4C and VRK3. Notably, two of these functional variants (rs10411204 and rs1247117) impacted transcription factor (TF) consensus DNA motifs for AP-1 family TFs and PU.1. Collectively, these data suggest that many inherited non-coding variants associated with pharmacogenomic traits in childhood ALL have significant gene regulatory effects. Importantly, the identification of chemotherapeutic drug resistance-associated molecular pathways perturbed by inherited non-coding variants can improve our ability to circumvent drug resistance with novel therapeutic approaches.

CsLOB1 regulates susceptibility to citrus canker through promoting cell proliferation in citrus.

Citrus sinensis lateral organ boundary 1 (CsLOB1) was previously identified as a critical disease susceptibility gene for citrus bacterial canker, which is caused by Xanthomonas citri subsp. citri (Xcc). However, the molecular mechanisms of CsLOB1 in citrus response to Xcc are still elusive. Here, we constructed transgenic plants overexpressing and RNAi-silencing of CsLOB1 using the canker-disease susceptible 'wanjincheng' orange (C. sinensis Osbeck) as explants. CsLOB1-overexpressing plants exhibited dwarf phenotypes with smaller and thicker leaf, increased branches and adventitious buds clustered on stems. These phenotypes were followed by a process of pustule- and canker-like development that exhibited enhanced cell proliferation. Pectin depolymerization and expansin accumulation were enhanced by CsLOB1 overexpression, while cellulose and hemicellulose synthesis were increased by CsLOB1 silence. Whilst overexpression of CsLOB1 increased susceptibility, RNAi-silencing of CsLOB1 enhanced resistance to canker disease without impairing pathogen entry. Transcriptome analysis revealed that CsLOB1 positively regulated cell wall degradation and modification processes, cytokinin metabolism, and cell division. Additionally, 565 CsLOB1-targeted genes were identified in chromatin immunoprecipitation-sequencing (ChIP-seq) experiments. Motif discovery analysis revealed that the most highly overrepresented binding sites had a conserved 6-bp 'GCGGCG' consensus DNA motif. RNA-seq and ChIP-seq data suggested that CsLOB1 directly activates the expression of four genes involved in cell wall remodeling, and three genes that participate in cytokinin and brassinosteroid hormone pathways. Our findings indicate that CsLOB1 promotes cell proliferation by mechanisms depending on cell wall remodeling and phytohormone signaling, which may be critical to citrus canker development and bacterial growth in citrus.

Mechanism of forkhead transcription factors binding to a novel palindromic DNA site.

Forkhead transcription factors bind a canonical consensus DNA motif, RYAAAYA (R = A/G, Y = C/T), as a monomer. However, the molecular mechanisms by which forkhead transcription factors bind DNA as a dimer are not well understood. In this study, we show that FOXO1 recognizes a palindromic DNA element DIV2, and mediates transcriptional regulation. The crystal structure of FOXO1/DIV2 reveals that the FOXO1 DNA binding domain (DBD) binds the DIV2 site as a homodimer. The wing1 region of FOXO1 mediates the dimerization, which enhances FOXO1 DNA binding affinity and complex stability. Further biochemical assays show that FOXO3, FOXM1 and FOXI1 also bind the DIV2 site as homodimer, while FOXC2 can only bind this site as a monomer. Our structural, biochemical and bioinformatics analyses not only provide a novel mechanism by which FOXO1 binds DNA as a homodimer, but also shed light on the target selection of forkhead transcription factors.

Characterization of the interaction interface and conformational dynamics of human TGIF1 homeodomain upon the binding of consensus DNA

The TG interacting factor-1 homeodomain (TGIF1-HD) binds with the consensus DNA motif 5′-TGTCA-3′ in gene promoters through its three-amino acid loop extension (TALE) type homeodomain, and then recruits co-regulators to regulate gene expression. Although the solution NMR structure of human TGIF1-HD has been reported previously, little is known about its DNA binding mechanism. NMR titrations have been extensively used to study mechanisms of ligand binding to target proteins; however, an intermediate exchange occurred predominantly between TGIF1-HD in the free and bound states when titrated with the consensus DNA, which resulted in poor-quality NMR spectra and precluded further exploration of its interaction interface and conformational dynamics. Here, the helix α3 of TGIF1-HD was speculated as the specific DNA binding interface by hydrogen–deuterium exchange mass spectrometry (HDX-MS) experiments, and subsequently confirmed by chemical exchange saturation transfer (CEST) spectroscopy. In addition, simultaneous conformational changes in other regions, including α1 and α2, were induced by DNA binding, explaining the observation of chemical shift perturbations from extensive residues besides those located in α3. Further, low-populated DNA-bound TGIF1-HD undergoing a slow exchange at a rate of 130.2 ± 3.6 s−1 was derived from the analysis of the CEST data, and two residues, R220 and R221, located in the middle of α3 were identified to be crucial for DNA binding. Our study provides structural and dynamic insights into the mechanisms of TGIF1-HD recognition of extensive promoter DNA.

Presence of a consensus DNA motif at nearby DNA sequence of the mutation susceptible CG nucleotides

Complexity in tissues affected by cancer arises from somatic mutations and epigenetic modifications in the genome. The mutation susceptible hotspots present within the genome indicate a non-random nature and/or a position specific selection of mutation. An association exists between the occurrence of mutations and epigenetic DNA methylation. This study is primarily aimed at determining mutation status, and identifying a signature for predicting mutation prone zones of tumor suppressor (TS) genes. Nearby sequences from the top five positions having a higher mutation frequency in each gene of 42 TS genes were selected from a cosmic database and were considered as mutation prone zones. The conserved motifs present in the mutation prone DNA fragments were identified. Molecular docking studies were done to determine putative interactions between the identified conserved motifs and enzyme methyltransferase DNMT1. Collective analysis of 42 TS genes found GC as the most commonly replaced and AT as the most commonly formed residues after mutation. Analysis of the top 5 mutated positions of each gene (210 DNA segments for 42 TS genes) identified that CG nucleotides of the amino acid codons (e.g., Arginine) are most susceptible to mutation, and found a consensus DNA “T/AGC/GAGGA/TG” sequence present in these mutation prone DNA segments. Similar to TS genes, analysis of 54 oncogenes not only found CG nucleotides of the amino acid Arg as the most susceptible to mutation, but also identified the presence of similar consensus DNA motifs in the mutation prone DNA fragments (270 DNA segments for 54 oncogenes) of oncogenes. Docking studies depicted that, upon binding of DNMT1 methylates to this consensus DNA motif (C residues of CpG islands), mutation was likely to occur. Thus, this study proposes that DNMT1 mediated methylation in chromosomal DNA may decrease if a foreign DNA segment containing this consensus sequence along with CG nucleotides is exogenously introduced to dividing cancer cells.

CiMYB17, a stress-induced chicory R2R3-MYB transcription factor, activates promoters of genes involved in fructan synthesis and degradation.

In Cichorium intybus, inulin metabolism is mediated by fructan-active enzymes (FAZYs): sucrose:sucrose 1-fructosyltransferase (1-SST), fructan:fructan 1-fructosyltransferase (1-FFT), and fructan 1-exohydrolases 1, 2a and 2b (1-FEH1, -2a and -2b), respectively. While these enzymes have been rigorously characterized, the transcriptional network orchestrating their development- and stress-related expression has remained largely unknown. Here, the possible role of R2R3-MYB transcription factors in FAZY regulation was explored via bioinformatic identification of R2R3-MYBs (using an RNA sequencing (RNAseq) database), studies of co-expression of these factors with target genes, invivo transient transactivation assays of FAZY target promoters (dual luciferase assay), and a yeast one-hybrid assay investigating the specificity of the binding of these factors to cis-elements. The chicory MYB transcription factor CiMYB17 specifically activated promoters of 1-SST and 1-FFT by binding to the consensus DNA-motif DTTHGGT. Unexpectedly, CiMYB17 also activated promoters of fructan exohydrolase genes. The stimulatory effect on promoter activities of sucrose transporter and cell wall invertase genes points to a general role in regulating the source-sink relationship. Co-induction of CiMYB17 with 1-SST and 1-FFT (and, less consistently, with 1-FEH1/2) in nitrogen-starved or abscisic acid (ABA)-treated chicory seedlings and in salt-stressed chicory hairy roots supports a role in stress-induced fructan metabolism, including de novo fructan synthesis and trimming of pre-existing fructans, whereas the reduced expression of CiMYB17 in developing taproots excludes a role in fructan accumulation under normal growth conditions.

Abstract B15: Targeting PBX1 signaling to sensitize carboplatin cytotoxicity in ovarian cancer

Abstract Introduction: Resistance to chemotherapy represents a major obstacle to achieving long-term remission in ovarian cancer patients. Thereby, there is an unmet need to understand the pathogenesis of chemoresistance and to develop effective strategy to overcome drug resistance. To better understand the molecular etiology of drug resistance, we previously studied ovarian high-grade serous carcinoma (HGSC) to identify the genes and pathways they controlled in the development of chemoresistance. Toward this goal, we have demonstrated Notch3 pathway as one of the molecular contributors to carboplatin resistance in ovarian cancer cells. We further identified that PBX1, a TALE homeodomain transcription factor and proto-oncogene, mediates the functions of Notch3 signaling. This finding together with the fact that PBX1 is involved in several tumor-promoting functions raises the possibility that PBX1 may play an important role in chemoresistance. Thus, in this study, we aim to determine the roles of PBX1 in the development of carboplatin resistance in ovarian HGSC. Experimental procedures: Western blot and immunohistochemistry were performed to determine the expression levels of PBX1 in primary and recurrent/chemoresistant ovarian HGSC tissues and cell lines. To assess the functional roles of PBX1, PBX1 siRNA or cDNA was transfected into ovarian cancer cell lines. Stem cell-like characteristics were measured using an ALDH1 staining kit and flow cytometry to identify verapamil-sensitive side populations. A small molecule inhibitor targeting the binding between PBX1 and DNA was employed in mouse ovarian cancer xenograft models. Results: Immunohistochemistry demonstrated that PBX1 protein was upregulated in recurrent post-chemotherapy HGSCs as compared to the matched primary tumors. Western blot analysis showed that carboplatin-resistant (CR) ovarian cancer cell lines expressed higher protein levels of PBX1 than both parental cells and paclitaxel resistant cells. Gene knockdown of PBX1 using siRNA significantly suppressed growth in CR cell lines, indicating the dependence of CR cells on PBX1 expression. Since ALDH1, a stem cell marker, was also upregulated in CR cells as compared to the parental cells, we determined whether ectopic expression of PBX1 in PBX1-low ovarian cancer cells enhanced stem-cell phenotypes. Indeed, the fraction of verapamil-sensitive side population and the number of ALDH1 positive cells both increased in ovarian cells transfected with the PBX1-expressing plasmids, as were the stem cell associated markers including ABCB1 and GPR160. Moreover, we designed a novel small molecule inhibitor that disrupted the Pbx1/DNA complex and this PBX1 inhibitor potently interrupted the binding of PBX1 to the consensus DNA motif responsible for PBX1 binding. We observed an anti-proliferative effect of this inhibitor in CR ovarian cancer lines and an anti-tumorigenic effect in ovarian cancer mouse xenografts. Conclusion: This study demonstrates that PBX1 is a marker for recurrent post-chemotherapy HGSCs. Inactivating PBX1 using gene silencing and small molecule inhibitors enhances cytotoxicity of CR-resistant ovarian cancer cells. The above findings should have significant implications in cancer biology, and promise a novel strategy to combat ovarian cancer patients suffering from chemoresistance. Citation Format: Jin G. Jung, Joon T. Park, Alexader Stoeck, Tasmeen Hussain, Ren-Chin Wu, Ie-Ming Shih, Tian-Li Wang. Targeting PBX1 signaling to sensitize carboplatin cytotoxicity in ovarian cancer. [abstract]. In: Proceedings of the AACR Precision Medicine Series: Drug Sensitivity and Resistance: Improving Cancer Therapy; Jun 18-21, 2014; Orlando, FL. Philadelphia (PA): AACR; Clin Cancer Res 2015;21(4 Suppl): Abstract nr B15.

A quantitative proteomics tool to identify DNA-protein interactions in primary cells or blood.

Interactions between transcription factors and genomic DNA, and in particular their impact on disease and cell fate, have been extensively studied on a global level using techniques based on next-generation sequencing. These approaches, however, do not allow an unbiased study of protein complexes that bind to certain DNA sequences. DNA pulldowns from crude lysates combined with quantitative mass spectrometry were recently introduced to close this gap. Established protocols, however, are restricted to cell lines because they are based on metabolic labeling or require large amounts of material. We introduce a high-throughput-compatible DNA pulldown that combines on-bead digestion with direct dimethyl labeling or label-free protein quantification. We demonstrate that our method can efficiently identify transcription factors binding to their consensus DNA motifs in extracts from primary foreskin fibroblasts and peripheral blood mononuclear cells (PBMCs) freshly isolated from human donors. Nuclear proteomes with absolute quantification of nearly 7000 proteins in K562 cells and PBMCs clearly link differential interactions to differences in protein abundance, hence stressing the importance of selecting relevant cell extracts for any interaction in question. As shown for rs6904029, a SNP highly associated with chronic lymphocytic leukemia, our approach can provide invaluable functional data, for example, through integration with GWAS.

A new inflammatory role for p53 in human macrophages

A new inflammatory role for p53 in human macrophages

PGC7 suppresses TET3 for protecting DNA methylation

Ten-eleven translocation (TET) family enzymes convert 5-methylcytosine to 5-hydroxylmethylcytosine. However, the molecular mechanism that regulates this biological process is not clear. Here, we show the evidence that PGC7 (also known as Dppa3 or Stella) interacts with TET2 and TET3 both in vitro and in vivo to suppress the enzymatic activity of TET2 and TET3. Moreover, lacking PGC7 induces the loss of DNA methylation at imprinting loci. Genome-wide analysis of PGC7 reveals a consensus DNA motif that is recognized by PGC7. The CpG islands surrounding the PGC7-binding motifs are hypermethylated. Taken together, our study demonstrates a molecular mechanism by which PGC7 protects DNA methylation from TET family enzyme-dependent oxidation.

A Novel Branched Chain Amino Acids Responsive Transcriptional Regulator, BCARR, Negatively Acts on the Proteolytic System in Lactobacillus helveticus

Transcriptional negative regulation of the proteolytic system of Lactobacillus helveticus CM4 in response to amino acids seems to be very important for the control of antihypertensive peptide production; however, it remains poorly understood. A 26-kDa protein with N-terminal cystathionine β-synthase domains (CBS domain protein), which seems to be involved in the regulatory system, was purified by using a DNA-sepharose bound 300-bp DNA fragment corresponding to the upstream regions of the six proteolytic genes that are down-regulated by amino acids. The CBS domain protein bound to a DNA fragment corresponding to the region upstream of the pepV gene in response to branched chain amino acids (BCAAs). The expression of the pepV gene in Escherichia coli grown in BCAA-enriched medium was repressed when the CBS domain protein was co-expressed. These results reveal that the CBS domain protein acts as a novel type of BCAA-responsive transcriptional regulator (BCARR) in L. helveticus. From comparative analysis of the promoter regions of the six proteolysis genes, a palindromic AT-rich motif, 5′-AAAAANNCTWTTATT-3′, was predicted as the consensus DNA motif for the BCARR protein binding. Footprint analysis using the pepV promotor region and gel shift analyses with the corresponding short DNA fragments strongly suggested that the BCARR protein binds adjacent to the pepV promoter region and affects the transcription level of the pepV gene in the presence of BCAAs. Homology search analysis of the C-terminal region of the BCARR protein suggested the existence of a unique βαββαβ fold structure that has been reported in a variety of ACT (aspartate kinase-chorismate mutase-tyrA) domain proteins for sensing amino acids. These results also suggest that the sensing of BCAAs by the ACT domain might promote the binding of the BCARR to DNA sequences upstream of proteolysis genes, which affects the gene expression of the proteolytic system in L. helveticus.

STAT5b in LGL leukemia - a novel therapeutic target?

<i>STAT5b</i> in LGL leukemia - a novel therapeutic target?

SOX2 Co-Occupies Distal Enhancer Elements with Distinct POU Factors in ESCs and NPCs to Specify Cell State

SOX2 is a master regulator of both pluripotent embryonic stem cells (ESCs) and multipotent neural progenitor cells (NPCs); however, we currently lack a detailed understanding of how SOX2 controls these distinct stem cell populations. Here we show by genome-wide analysis that, while SOX2 bound to a distinct set of gene promoters in ESCs and NPCs, the majority of regions coincided with unique distal enhancer elements, important cis-acting regulators of tissue-specific gene expression programs. Notably, SOX2 bound the same consensus DNA motif in both cell types, suggesting that additional factors contribute to target specificity. We found that, similar to its association with OCT4 (Pou5f1) in ESCs, the related POU family member BRN2 (Pou3f2) co-occupied a large set of putative distal enhancers with SOX2 in NPCs. Forced expression of BRN2 in ESCs led to functional recruitment of SOX2 to a subset of NPC-specific targets and to precocious differentiation toward a neural-like state. Further analysis of the bound sequences revealed differences in the distances of SOX and POU peaks in the two cell types and identified motifs for additional transcription factors. Together, these data suggest that SOX2 controls a larger network of genes than previously anticipated through binding of distal enhancers and that transitions in POU partner factors may control tissue-specific transcriptional programs. Our findings have important implications for understanding lineage specification and somatic cell reprogramming, where SOX2, OCT4, and BRN2 have been shown to be key factors.

SPATA18, a Spermatogenesis-Associated Gene, Is a Novel Transcriptional Target of p53 and p63

The transcription factor p53 functions not only to suppress tumorigenesis but also to maintain normal development and homeostasis. Although p53 was implicated in different aspects of fertility, including spermatogenesis and implantation, the mechanism underlying p53 involvement in spermatogenesis is poorly resolved. In this study we describe the identification of a spermatogenesis-associated gene, SPATA18, as a novel p53 transcriptional target and show that SPATA18 transcription is induced by p53 in a variety of cell types of both human and mouse origin. p53 binds a consensus DNA motif that resides within the first intron of SPATA18. We describe the spatiotemporal expression patterns of SPATA18 in mouse seminiferous tubules and suggest that SPATA18 transcription is regulated in vivo by p53. We also demonstrate the induction of SPATA18 by p63 and suggest that p63 can compensate for the loss of p53 activity in vivo. Our data not only enrich the known collection of p53 targets but may also provide insights on spermatogenesis defects that are associated with p53 deficiency.

Leucine-Responsive Regulatory Protein (Lrp) Acts as a Virulence Repressor inSalmonella entericaSerovar Typhimurium

Leucine-responsive regulatory protein (Lrp) is a global gene regulator that influences expression of a large number of genes including virulence-related genes in Escherichia coli and Salmonella. No systematic studies examining the regulation of virulence genes by Lrp have been reported in Salmonella. We report here that constitutive expression of Lrp [lrp(Con)] dramatically attenuates Salmonella virulence while an lrp deletion (Deltalrp) mutation enhances virulence. The lrp(Con) mutant caused pleiotropic effects that include defects in invasion, cytotoxicity, and colonization, whereas the Deltalrp mutant was more proficient at these activities than the wild-type strain. We present evidence that Lrp represses transcription of key virulence regulator genes--hilA, invF, and ssrA--in Salmonella pathogenicity island 1 (SPI-1) and 2 (SPI-2), by binding directly to their promoter regions, P(hilA), P(invF), and P(ssrA). In addition, Western blot analysis showed that the expression of the SPI-1 effector SipA was reduced in the lrp(Con) mutant and enhanced in the Deltalrp mutant. Computational analysis revealed putative Lrp-binding consensus DNA motifs located in P(hilA), P(invF), and P(ssrA). These results suggest that Lrp binds to the consensus motifs and modulates expression of the linked genes. The presence of leucine enhanced Lrp binding to P(invF) in vitro and the addition of leucine to growth medium decreased the level of invF transcription. However, leucine had no effect on expression of hilA and ssrA or on cellular levels of Lrp. In addition, Lrp appears to be an antivirulence gene, since the deletion mutant showed enhanced cell invasion, cytotoxicity, and hypervirulence in BALB/c mice.

LATERAL ORGAN BOUNDARIES defines a new family of DNA-binding transcription factors and can interact with specific bHLH proteins

Conserved in a variety of evolutionarily divergent plant species, LOB DOMAIN (LBD) genes define a large, plant-specific family of largely unknown function. LBD genes have been implicated in a variety of developmental processes in plants, although to date, relatively few members have been assigned functions. LBD proteins have previously been predicted to be transcription factors, however supporting evidence has only been circumstantial. To address the biochemical function of LBD proteins, we identified a 6-bp consensus motif recognized by a wide cross-section of LBD proteins, and showed that LATERAL ORGAN BOUNDARIES (LOB), the founding member of the family, is a transcriptional activator in yeast. Thus, the LBD genes encode a novel class of DNA-binding transcription factors. Post-translational regulation of transcription factors is often crucial for control of gene expression. In our study, we demonstrate that members of the basic helix–loop–helix (bHLH) family of transcription factors are capable of interacting with LOB. The expression patterns of bHLH048 and LOB overlap at lateral organ boundaries. Interestingly, the interaction of bHLH048 with LOB results in reduced affinity of LOB for the consensus DNA motif. Thus, our studies suggest that bHLH048 post-translationally regulates the function of LOB at lateral organ boundaries.

Modeling gene expression control using Omes Law

Mol Syst Biol. 2: 2006.0013 The binding of transcription factors (TFs) to specific sites in the genome is a crucial step in the molecular process controlling gene expression. The in vitro sequence specificity of these regulatory proteins can generally be well represented by consensus DNA motifs or slightly more sophisticated sequence profiles called position‐specific scoring matrices. These are widely used to scan genome sequences in order to find novel transcriptional target genes. Unfortunately, usually only a small fraction of the ‘hits’ thus obtained are functional in vivo , where local chromatin structure and TF–TF interactions come into play. Taking into account the context provided by the surrounding noncoding DNA is therefore essential. In a recent study currently published in Molecular Systems Biology, Nguyen and D'haeseleer (2006) present a promising strategy for determining which context features are most important for a given TF binding motif. Their approach belongs to a growing class of methods that fit simple mathematical models of transcription regulation to DNA microarray data to map gene regulation networks. Many of the molecular players that govern gene expression are known, but our knowledge about their interactions with the DNA and with each other is very incomplete. Information about the gene regulatory network is only implicitly represented in the large volume of functional genomics data now available to us. The strengths of the ‘arrows’ between TFs and their target genes and the condition‐specific activities of the regulatory ‘nodes’ need to be inferred by computational means. A detailed mathematical model that accurately describes the molecular …

A 5′-distal enhanceosome in the PDGF-A gene is activated in choriocarcinoma cells via ligand-independent binding of vitamin D receptor and constitutive jun kinase signaling

Overexpression of platelet-derived growth factor A-chain (PDGF-A) is clearly linked to autocrine and paracrine stimulation of malignant growth in many human cancers. We have shown previously that PDGF-A overexpression in choriocarcinoma, hepatoma and lung carcinoma cell lines is driven by the activity of a 66 bp enhancer element (ACE66) located approximately 7 kb upstream of the PDGF-A transcription start site. In this study, the ACE66 element is shown to be activated in JEG-3 choriocarcinoma cells through synergistic interactions between consensus DNA motifs for binding of vitamin D receptor, AP1 and ELK1. Binding of the vitamin D/retinoid-X receptor (VDR/RXRalpha) heterodimer to the ACE66 element was reconstituted in vitro with recombinant VDR/RXRalpha and with JEG-3 nuclear extract, and was verified in living JEG-3 cells by chromatin immunoprecipitation analysis. Transcriptional activity of the ACE66 element, as well as occupancy of the element by VDR/RXRalpha, was shown to be independent of stimulation with the hormonal VDR ligand, 1,25-dihydroxyvitamin D3. The jun kinase pathway of mitogen-activated protein kinase (MAPK) signaling was shown to activate the ACE66 enhancer, most likely through activation of factors binding to the AP1 element. These results identify a novel mechanism of transcriptional enhancement involving ligand-independent activity of the VDR/RXR heterodimer and MAPK signaling pathways that appears to play an important role in the overexpression of PDGF in many different settings of human malignancy.

Sequence-specific High Mobility Group Box Factors Recognize 10–12-Base Pair Minor Groove Motifs

Sequence-specific High Mobility Group Box Factors Recognize 10–12-Base Pair Minor Groove Motifs