Wide-Scale Analysis of Human Functional Transcription Factor Binding Reveals a Strong Bias towards the Transcription Start Site

We introduce a novel method to screen the promoters of a set of genes with shared biological function, against a precompiled library of motifs, and find those motifs which are statistically over-represented in the gene set. The gene sets were obtained from the functional Gene Ontology (GO) classification; for each set and motif we optimized the sequence similarity score threshold, independently for every location window (measured with respect to the TSS), taking into account the location dependent nucleotide heterogeneity along the promoters of the target genes. We performed a high throughput analysis, searching the promoters (from 200bp downstream to 1000bp upstream the TSS), of more than 8000 human and 23,000 mouse genes, for 134 functional Gene Ontology classes and for 412 known DNA motifs. When combined with binding site and location conservation between human and mouse, the method identifies with high probability functional binding sites that regulate groups of biologically related genes. We found many location-sensitive functional binding events and showed that they clustered close to the TSS. Our method and findings were put to several experimental tests. By allowing a "flexible" threshold and combining our functional class and location specific search method with conservation between human and mouse, we are able to identify reliably functional TF binding sites. This is an essential step towards constructing regulatory networks and elucidating the design principles that govern transcriptional regulation of expression. The promoter region proximal to the TSS appears to be of central importance for regulation of transcription in human and mouse, just as it is in bacteria and yeast.Comment: 31 pages, including Supplementary Information and figure

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

Failure of functional imaging with gallium-68-DOTA-D-Phe1-Tyr3-octreotide positron emission tomography to localize the site of ectopic adrenocorticotropic hormone secretion: a case report

<p>Abstract</p> <p>Introduction</p> <p>The diagnostic efficacy of biochemical and imaging modalities for investigating the causes of Cushing's syndrome are limited. We report a case demonstrating the limitations of these modalities, especially the inability of functional imaging to help localize the site of ectopic adrenocorticotropic hormone secretion.</p> <p>Case presentation</p> <p>A 37-year-old Arabian woman presented with 12 months of progressive Cushing's syndrome-like symptoms. Biochemical evaluation confirmed adrenocorticotropic hormone -dependent Cushing's syndrome. However, the anatomical site of her excess adrenocorticotropic hormone secretion was not clearly delineated by further investigations. Magnetic resonance imaging of our patient's pituitary gland failed to demonstrate the presence of an adenoma. Spiral computed tomography of her chest only revealed the presence of a non-specific 7 mm lesion in her left inferobasal lung segment. Functional imaging, including a positron emission tomography scan using 18-fluorodeoxyglucose and gallium-68-DOTA-D-Phe1-Tyr3-octreotide, also failed to show increased metabolic activity in the lung lesion or in her pituitary gland. Our patient was commenced on medical treatment with ketoconazole and metyrapone to control the clinical features associated with her excess cortisol secretion. Despite initial normalization of her urinary free cortisol excretion rate, levels began to rise eight months after commencement of medical treatment. Repeated imaging of her pituitary gland, chest and pelvis again failed to clearly localize a source of her excess adrenocorticotropic hormone secretion. The bronchial nodule was stable in size on serial imaging and repeatedly reported as having a nonspecific appearance of a small granuloma or lymph node. We re-explored the treatment options and endorsed our patient's favored choice of resection of the bronchial nodule, especially given that her symptoms of cortisol excess were difficult to control and refractory. Subsequently, our patient had the bronchial nodule resected. The histological appearance of the lesion was consistent with that of a carcinoid tumor and immunohistochemical analysis revealed that the tumor stained strongly positive for adrenocorticotropic hormone. Furthermore, removal of the lung lesion resulted in a normalization of our patient's 24-hour urinary free cortisol excretion rate and resolution of her symptoms and signs of hypercortisolemia.</p> <p>Conclusion</p> <p>This case report demonstrates the complexities and challenges in diagnosing the causes of adrenocorticotropic hormone -dependent Cushing's syndrome. Functional imaging may not always localize the site of ectopic adrenocorticotropic hormone secretion.</p

Four priority areas to advance invasion science in the face of rapid environmental change

Unprecedented rates of introduction and spread of non-native species pose burgeoning challenges to biodiversity, natural resource management, regional economies, and human health. Current biosecurity efforts are failing to keep pace with globalization, revealing critical gaps in our understanding and response to invasions. Here, we identify four priority areas to advance invasion science in the face of rapid global environmental change. First, invasion science should strive to develop a more comprehensive framework for predicting how the behavior, abundance, and interspecific interactions of non-native species vary in relation to conditions in receiving environments and how these factors govern the ecological impacts of invasion. A second priority is to understand the potential synergistic effects of multiple co-occurring stressors— particularly involving climate change—on the establishment and impact of non-native species. Climate adaptation and mitigation strategies will need to consider the possible consequences of promoting non-native species, and appropriate management responses to non-native species will need to be developed. The third priority is to address the taxonomic impediment. The ability to detect and evaluate invasion risks is compromised by a growing deficit in taxonomic expertise, which cannot be adequately compensated by new molecular technologies alone. Management of biosecurity risks will become increasingly challenging unless academia, industry, and governments train and employ new personnel in taxonomy and systematics. Fourth, we recommend that internationally cooperative biosecurity strategies consider the bridgehead effects of global dispersal networks, in which organisms tend to invade new regions from locations where they have already established. Cooperation among countries to eradicate or control species established in bridgehead regions should yield greater benefit than independent attempts by individual countries to exclude these species from arriving and establishing

The ability of thiourea to scavenge hydrogen peroxide and hydroxyl radicals during the intra-coronal bleaching of bloodstained root-filled teeth

The document attached has been archived with permission from the Australian Dental Association. An external link to the publisher’s copy is included.Background: Hydrogen peroxide, an agent used in the intra-coronal bleaching of root-filled teeth for over a century, has been shown to diffuse from the pulp chamber to the outer root surface. Furthermore, it has been demonstrated that destructive hydroxyl radicals, the by-products of the bleaching process, have been detected on the external root surface. The control of such diffusion may be of importance in minimizing the risk of invasive cervical resorption (ICR) which has been linked to intra-coronal bleaching of discoloured root-filled teeth using hydrogen peroxide. The aims of the present in vitro study are to quantify the diffusion of hydrogen peroxide and hydroxyl radicals to the outer root surface following intra-coronal bleaching, and to evaluate the ability of thiourea incorporated into the bleaching protocol to scavenge residual hydrogen peroxide and hydroxyl radicals. Methods: Thirty-five single rooted premolar teeth with intact cementum at the cemento-enamel junction were used in this project. Thirty teeth were stained with red blood cells and root-filled with gutta-percha and AH26. The five unstained teeth were root-filled and constituted a negative control (Group 1). The stained teeth were divided equally into the following experimental groups and subjected to various intra-coronal bleaching regimes: Group 2 – ‘walking bleach’ with 20μl 30 per cent w/w hydrogen peroxide; Group 3 – 20μl 30 per cent w/w hydrogen peroxide and thermocatalytically activated; Group 4 – 20μl acidified thiourea; Group 5 – 20μl acidified thiourea and 20μl 30 per cent w/w hydrogen peroxide; Group 6 – 20μl acidified thiourea and 20μl one per cent sodium hypochlorite; Group 7 – 20μl acidified thiourea, 20μl one per cent sodium hypochlorite and 20μl 30 per cent w/w hydrogen peroxide. The reaction products of the bleaching process were quantified at the outer root surface using high performance liquid chromatography and electrochemical detection (HPLC-ECD).Results: Results showed that hydrogen peroxide used alone in Groups 2 and 3 was able to be detected at the outer root surface in 100 per cent of the samples, and that the presence of the hydroxyl radical generated in both groups was detected in equal amounts (P<0.05). When thiourea was incorporated into the bleaching protocols in Groups 5–7, it was shown to scavenge both hydrogen peroxide and hydroxyl radicals to a significant degree (P<0.05). Conclusions: Acidulated thiourea is an effective scavenger of residual hydrogen peroxide and hydroxyl radicals generated during the intra-coronal bleaching of bloodstained root-filled teeth.DS Farmer, P Burcham, PD Mari

A global characterization of the translational and transcriptional programs induced by methionine restriction through ribosome profiling and RNA-seq

Background: Among twenty amino acids, methionine has a special role as it is coded by the translation initiation codon and methionyl-tRNAi (Met-tRNAi) is required for the assembly of the translation initiation complex. Thus methionine may play a special role in global gene regulation. Methionine has also been known to play important roles in cell growth, development, cancer, and aging. In this work, we characterize the translational and transcriptional programs induced by methionine restriction (MetR) and investigate the potential mechanisms through which methionine regulates gene expression, using the budding yeast S. cerevisiae as the model organism. Results: Using ribosomal profiling and RNA-seq, we observed a broad spectrum of gene expression changes in response to MetR and identified hundreds of genes whose transcript level and/or translational efficiency changed significantly. These genes show clear functional themes, suggesting that cell slows down its growth and cell cycle progression and increases its stress resistance and maintenance in response to MetR. Interestingly, under MetR cell also decreases glycolysis and increases respiration, and increased respiration was linked to lifespan extension caused by caloric restriction. Analysis of genes whose translational efficiency changed significantly under MetR revealed different modes of translational regulation: 1) Ribosome loading patterns in the 5&apos;UTR and coding regions of genes with increased translational efficiency suggested mechanisms both similar and different from that for the translational regulation of Gcn4 under general amino acid starvation condition; 2) Genes with decreased translational efficiency showed strong enrichment of lysine, glutamine, and glutamate codons, supporting the model that methionine can regulate translation by controlling tRNA thiolation. Conclusions: MetR induced a broad spectrum of gene expression changes at both the transcriptional and translational levels, with clear functional themes indicative of the physiological state of the cell under MetR. Different modes of translational regulation were induced by MetR, including the regulation of the ribosome loading at 5&apos;UTR and regulation by tRNA thiolation. Since MetR extends the lifespan of many species, the list of genes we identified in this study can be good candidates for studying the mechanisms of lifespan extension.National Institutes of Health [AG043080]SCI(E)ARTICLE1

GRISOTTO: A greedy approach to improve combinatorial algorithms for motif discovery with prior knowledge

<p>Abstract</p> <p>Background</p> <p>Position-specific priors (PSP) have been used with success to boost EM and Gibbs sampler-based motif discovery algorithms. PSP information has been computed from different sources, including orthologous conservation, DNA duplex stability, and nucleosome positioning. The use of prior information has not yet been used in the context of combinatorial algorithms. Moreover, priors have been used only independently, and the gain of combining priors from different sources has not yet been studied.</p> <p>Results</p> <p>We extend RISOTTO, a combinatorial algorithm for motif discovery, by post-processing its output with a greedy procedure that uses prior information. PSP's from different sources are combined into a scoring criterion that guides the greedy search procedure. The resulting method, called GRISOTTO, was evaluated over 156 yeast TF ChIP-chip sequence-sets commonly used to benchmark prior-based motif discovery algorithms. Results show that GRISOTTO is at least as accurate as other twelve state-of-the-art approaches for the same task, even without combining priors. Furthermore, by considering combined priors, GRISOTTO is considerably more accurate than the state-of-the-art approaches for the same task. We also show that PSP's improve GRISOTTO ability to retrieve motifs from mouse ChiP-seq data, indicating that the proposed algorithm can be applied to data from a different technology and for a higher eukaryote.</p> <p>Conclusions</p> <p>The conclusions of this work are twofold. First, post-processing the output of combinatorial algorithms by incorporating prior information leads to a very efficient and effective motif discovery method. Second, combining priors from different sources is even more beneficial than considering them separately.</p

Four priority areas to advance invasion science in the face of rapid environmental change

Unprecedented rates of introduction and spread of non-native species pose burgeoning challenges to biodiversity, natural resource management, regional economies, and human health. Current biosecurity efforts are failing to keep pace with globalization, revealing critical gaps in our understanding and response to invasions. Here, we identify four priority areas to advance invasion science in the face of rapid global environmental change. First, invasion science should strive to develop a more comprehensive framework for predicting how the behavior, abundance, and interspecific interactions of non-native species vary in relation to conditions in receiving environments and how these factors govern the ecological impacts of invasion. A second priority is to understand the potential synergistic effects of multiple co-occurring stressors— particularly involving climate change—on the establishment and impact of non-native species. Climate adaptation and mitigation strategies will need to consider the possible consequences of promoting non-native species, and appropriate management responses to non-native species will need to be developed. The third priority is to address the taxonomic impediment. The ability to detect and evaluate invasion risks is compromised by a growing deficit in taxonomic expertise, which cannot be adequately compensated by new molecular technologies alone. Management of biosecurity risks will become increasingly challenging unless academia, industry, and governments train and employ new personnel in taxonomy and systematics. Fourth, we recommend that internationally cooperative biosecurity strategies consider the bridgehead effects of global dispersal networks, in which organisms tend to invade new regions from locations where they have already established. Cooperation among countries to eradicate or control species established in bridgehead regions should yield greater benefit than independent attempts by individual countries to exclude these species from arriving and establishing

Diabetes-related molecular signatures in infrared spectra of human saliva

WOS: 000290261500001PubMed ID: 20630088Background: There is an ongoing need for improvements in non-invasive, point-of-care tools for the diagnosis and prognosis of diabetes mellitus. Ideally, such technologies would allow for community screening. Methods: In this study, we employed infrared spectroscopy as a novel diagnostic tool in the prediction of diabetic status by analyzing the molecular and sub-molecular spectral signatures of saliva collected from subjects with diabetes (n = 39) and healthy controls (n = 22). Results: Spectral analysis revealed differences in several major metabolic components - lipid, proteins, glucose, thiocyanate and carboxylate - that clearly demarcate healthy and diseased saliva. The overall accuracy for the diagnosis of diabetes based on infrared spectroscopy was 100% on the training set and 88.2% on the validation set. Therefore, we have established that infrared spectroscopy can be used to generate complex biochemical profiles in saliva and identify several potential diabetes-associated spectral features. Conclusions: Infrared spectroscopy may represent an appropriate tool with which to identify novel diseases mechanisms, risk factors for diabetic complications and markers of therapeutic efficacy. Further study into the potential utility of infrared spectroscopy as diagnostic and prognostic tool for diabetes is warranted

Learning a Prior on Regulatory Potential from eQTL Data

Genome-wide RNA expression data provide a detailed view of an organism's biological state; hence, a dataset measuring expression variation between genetically diverse individuals (eQTL data) may provide important insights into the genetics of complex traits. However, with data from a relatively small number of individuals, it is difficult to distinguish true causal polymorphisms from the large number of possibilities. The problem is particularly challenging in populations with significant linkage disequilibrium, where traits are often linked to large chromosomal regions containing many genes. Here, we present a novel method, Lirnet, that automatically learns a regulatory potential for each sequence polymorphism, estimating how likely it is to have a significant effect on gene expression. This regulatory potential is defined in terms of “regulatory features”—including the function of the gene and the conservation, type, and position of genetic polymorphisms—that are available for any organism. The extent to which the different features influence the regulatory potential is learned automatically, making Lirnet readily applicable to different datasets, organisms, and feature sets. We apply Lirnet both to the human HapMap eQTL dataset and to a yeast eQTL dataset and provide statistical and biological results demonstrating that Lirnet produces significantly better regulatory programs than other recent approaches. We demonstrate in the yeast data that Lirnet can correctly suggest a specific causal sequence variation within a large, linked chromosomal region. In one example, Lirnet uncovered a novel, experimentally validated connection between Puf3—a sequence-specific RNA binding protein—and P-bodies—cytoplasmic structures that regulate translation and RNA stability—as well as the particular causative polymorphism, a SNP in Mkt1, that induces the variation in the pathway