Gene regulation. A paradigm for precision

Dissecting the sharp response of a canonical developmental enhancer reveals multiple sources of cooperativity

Developmental enhancers integrate graded concentrations of transcription factors (TFs) to create sharp gene expression boundaries. Here we examine the hunchback P2 (HbP2) enhancer which drives a sharp expression pattern in the Drosophila blastoderm embryo in response to the transcriptional activator Bicoid (Bcd). We systematically interrogate cis and trans factors that influence the shape and position of expression driven by HbP2, and find that the prevailing model, based on pairwise cooperative binding of Bcd to HbP2 is not adequate. We demonstrate that other proteins, such as pioneer factors, Mediator and histone modifiers influence the shape and position of the HbP2 expression pattern. Comparing our results to theory reveals how higher-order cooperativity and energy expenditure impact boundary location and sharpness. Our results emphasize that the bacterial view of transcription regulation, where pairwise interactions between regulatory proteins dominate, must be reexamined in animals, where multiple molecular mechanisms collaborate to shape the gene regulatory function.

Identification and use of the sugarcane bacilliform virus enhancer in transgenic maize

BACKGROUND

Transcriptional enhancers are able to increase transcription from heterologous promoters when placed upstream, downstream and in either orientation, relative to the promoter. Transcriptional enhancers have been used to enhance expression of specific promoters in transgenic plants and in activation tagging studies to help elucidate gene function.

RESULTS

A transcriptional enhancer from the Sugarcane Bacilliform Virus - Ireng Maleng isolate (SCBV-IM) that can cause increased transcription when integrated into the the genome near maize genes has been identified. In transgenic maize, the SCBV-IM promoter was shown to be comparable in strength to the maize ubiquitin 1 promoter in young leaf and root tissues. The promoter was dissected to identify sequences that confer high activity in transient assays. Enhancer sequences were identified and shown to increase the activity of a heterologous truncated promoter. These enhancer sequences were shown to be more active when arrayed in 4 copy arrays than in 1 or 2 copy arrays. When the enhancer array was transformed into maize plants it caused an increase in accumulation of transcripts of genes near the site of integration in the genome.

CONCLUSIONS

The SCBV-IM enhancer can activate transcription upstream or downstream of genes and in either orientation. It may be a useful tool to activate enhance from specific promoters or in activation tagging.

Chronic ethanol consumption inhibits glucokinase transcriptional activity by Atf3 and triggers metabolic syndrome in vivo

Chronic ethanol consumption induces pancreatic β-cell dysfunction through glucokinase (Gck) nitration and down-regulation, leading to impaired glucose tolerance and insulin resistance, but the underlying mechanism remains largely unknown. Here, we demonstrate that Gck gene expression and promoter activity in pancreatic β-cells were suppressed by chronic ethanol exposure in vivo and in vitro, whereas expression of activating transcription factor 3 (Atf3) and its binding to the putative Atf/Creb site (from −287 to −158 bp) on the Gck promoter were up-regulated. Furthermore, in vitro ethanol-induced Atf3 inhibited the positive effect of Pdx-1 on Gck transcriptional regulation, enhanced recruitment of Hdac1/2 and histone H3 deacetylation, and subsequently augmented the interaction of Hdac1/Pdx-1 on the Gck promoter, which were diminished by Atf3 siRNA. In vivo Atf3-silencing reversed ethanol-mediated Gck down-regulation and β-cell dysfunction, followed by the amelioration of impaired glucose tolerance and insulin resistance. Together, we identified that ethanol-induced Atf3 fosters β-cell dysfunction via Gck down-regulation and that its loss ameliorates metabolic syndrome and could be a potential therapeutic target in treating type 2 diabetes. The Atf3 gene is associated with the induction of type 2 diabetes and alcohol consumption-induced metabolic impairment and thus may be the major negative regulator for glucose homeostasis.

Plasticity in the transcriptional and epigenetic circuits regulating dendritic cell lineage specification and function

Dendritic cells (DC) are critical and functionally versatile innate immune sentinels. Here, we coarsely partition the adult DC lineage into three developmental subtypes and argue that pioneer transcription factors and chromatin remodeling are responsible for specification and plasticity between the DC subsets. Subsequently, intricate signaling-dependent transcription factor networks generate different functional states in response to pathogen stimuli within a specified DC subtype. To expand our understanding of lineage heterogeneity and functional activation states, we discuss the use of single cell genomics approaches in the context of a newly emerging systems immunology era, complementing the dichotomous definition of immune cells based solely on their surface marker expression. Rapid developments in single cell genomics are beginning to provide us with robust tools to potentially revise the working models of DC specification and the common hematopoietic tree.

Major histocompatibility complex class I core promoter elements are not essential for transcription in vivo

The role of core promoter elements in regulating transcription initiation is largely unknown for genes subject to complex regulation. Major histocompatibility complex class I genes are ubiquitously expressed and governed by tissue-specific and hormonal signals. Transcription initiates at multiple sites within the core promoter, which contains elements homologous to the canonical elements CCAAT, TATAA, Sp1 binding site (Sp1BS), and Initiator (Inr). To determine their functions, expression of class I transgenes with individually mutated elements was assessed. Surprisingly, all mutant promoters supported transcription. However, each mutated core promoter element had a distinct effect on expression: CAAT box mutations modulated constitutive expression in nonlymphoid tissues, whereas TATAA-like element mutations dysregulated transcription in lymphoid tissues. Inr mutations aberrantly elevated expression. Sp1BS element mutations resulted in variegated transgene expression. RNA polymerase II binding and histone H3K4me3 patterns correlated with transgene expression; H3K9me3 marks partially correlated. Whereas the wild-type, TATAA-like, and CAAT mutant promoters were activated by gamma interferon, the Sp1 and Inr mutants were repressed, implicating these elements in regulation of hormonal responses. These results lead to the surprising conclusion that no single element is required for promoter activity. Rather, each plays a distinct role in promoter activity, chromatin structure, tissue-specific expression, and extracellular signaling.

Cellular resolution models for even skipped regulation in the entire Drosophila embryo

Transcriptional control ensures genes are expressed in the right amounts at the correct times and locations. Understanding quantitatively how regulatory systems convert input signals to appropriate outputs remains a challenge. For the first time, we successfully model even skipped (eve) stripes 2 and 3+7 across the entire fly embryo at cellular resolution. A straightforward statistical relationship explains how transcription factor (TF) concentrations define eve's complex spatial expression, without the need for pairwise interactions or cross-regulatory dynamics. Simulating thousands of TF combinations, we recover known regulators and suggest new candidates. Finally, we accurately predict the intricate effects of perturbations including TF mutations and misexpression. Our approach imposes minimal assumptions about regulatory function; instead we infer underlying mechanisms from models that best fit the data, like the lack of TF-specific thresholds and the positional value of homotypic interactions. Our study provides a general and quantitative method for elucidating the regulation of diverse biological systems. DOI:http://dx.doi.org/10.7554/eLife.00522.001.

High-throughput chromatin immunoprecipitation for genome-wide mapping of in vivo protein-DNA interactions and epigenomic states

Dynamic protein binding to DNA elements regulates genome function and cell fate. Although methods for mapping in vivo protein-DNA interactions are becoming crucial for every aspect of genomic research, they are laborious and costly, thereby limiting progress. Here we present a protocol for mapping in vivo protein-DNA interactions using a high-throughput chromatin immunoprecipitation (HT-ChIP) approach. By using paramagnetic beads, we streamline the entire ChIP and indexed library construction process: sample transfer and loss is minimized and the need for manually labor-intensive procedures such as washes, gel extraction and DNA precipitation is eliminated. All of this allows for fully automated, cost effective and highly sensitive 96-well ChIP sequencing (ChIP-seq). Sample preparation takes 3 d from cultured cells to pooled libraries. Compared with previous methods, HT-ChIP is more suitable for large-scale in vivo studies, specifically those measuring the dynamics of a large number of different chromatin modifications/transcription factors or multiple perturbations.

A high-throughput chromatin immunoprecipitation approach reveals principles of dynamic gene regulation in mammals

Understanding the principles governing mammalian gene regulation has been hampered by the difficulty in measuring in vivo binding dynamics of large numbers of transcription factors (TF) to DNA. Here, we develop a high-throughput Chromatin ImmunoPrecipitation (HT-ChIP) method to systematically map protein-DNA interactions. HT-ChIP was applied to define the dynamics of DNA binding by 25 TFs and 4 chromatin marks at 4 time-points following pathogen stimulus of dendritic cells. Analyzing over 180,000 TF-DNA interactions we find that TFs vary substantially in their temporal binding landscapes. This data suggests a model for transcription regulation whereby TF networks are hierarchically organized into cell differentiation factors, factors that bind targets prior to stimulus to prime them for induction, and factors that regulate specific gene programs. Overlaying HT-ChIP data on gene-expression dynamics shows that many TF-DNA interactions are established prior to the stimuli, predominantly at immediate-early genes, and identified specific TF ensembles that coordinately regulate gene-induction.

Three novel downstream promoter elements regulate MHC class I promoter activity in mammalian cells

BACKGROUND

MHC CLASS I TRANSCRIPTION IS REGULATED BY TWO DISTINCT TYPES OF REGULATORY PATHWAYS: 1) tissue-specific pathways that establish constitutive levels of expression within a given tissue and 2) dynamically modulated pathways that increase or decrease expression within that tissue in response to hormonal or cytokine mediated stimuli. These sets of pathways target distinct upstream regulatory elements, have distinct basal transcription factor requirements, and utilize discrete sets of transcription start sites within an extended core promoter.

METHODOLOGY/PRINCIPAL FINDINGS

We studied regulatory elements within the MHC class I promoter by cellular transfection and in vitro transcription assays in HeLa, HeLa/CIITA, and tsBN462 of various promoter constructs. We have identified three novel MHC class I regulatory elements (GLE, DPE-L1 and DPE-L2), located downstream of the major transcription start sites, that contribute to the regulation of both constitutive and activated MHC class I expression. These elements located at the 3' end of the core promoter preferentially regulate the multiple transcription start sites clustered at the 5' end of the core promoter.

CONCLUSIONS/SIGNIFICANCE

Three novel downstream elements (GLE, DPE-L1, DPE-L2), located between +1 and +32 bp, regulate both constitutive and activated MHC class I gene expression by selectively increasing usage of transcription start sites clustered at the 5' end of the core promoter upstream of +1 bp. Results indicate that the downstream elements preferentially regulate TAF1-dependent, relative to TAF1-independent, transcription.

Thermodynamics-based models of transcriptional regulation by enhancers: the roles of synergistic activation, cooperative binding and short-range repression

Quantitative models of cis-regulatory activity have the potential to improve our mechanistic understanding of transcriptional regulation. However, the few models available today have been based on simplistic assumptions about the sequences being modeled, or heuristic approximations of the underlying regulatory mechanisms. We have developed a thermodynamics-based model to predict gene expression driven by any DNA sequence, as a function of transcription factor concentrations and their DNA-binding specificities. It uses statistical thermodynamics theory to model not only protein-DNA interaction, but also the effect of DNA-bound activators and repressors on gene expression. In addition, the model incorporates mechanistic features such as synergistic effect of multiple activators, short range repression, and cooperativity in transcription factor-DNA binding, allowing us to systematically evaluate the significance of these features in the context of available expression data. Using this model on segmentation-related enhancers in Drosophila, we find that transcriptional synergy due to simultaneous action of multiple activators helps explain the data beyond what can be explained by cooperative DNA-binding alone. We find clear support for the phenomenon of short-range repression, where repressors do not directly interact with the basal transcriptional machinery. We also find that the binding sites contributing to an enhancer's function may not be conserved during evolution, and a noticeable fraction of these undergo lineage-specific changes. Our implementation of the model, called GEMSTAT, is the first publicly available program for simultaneously modeling the regulatory activities of a given set of sequences.

The development of complex multicellular organisms requires genes to be expressed at specific stages and in specific tissues. Regulatory DNA sequences, often called cis-regulatory modules, drive the desired gene expression patterns by integrating information about the environment in the form of the activities of transcription factors. The rules by which regulatory sequences read this type of information, however, are unclear. In this work, we developed quantitative models based on physicochemical principles that directly map regulatory sequences to the expression profiles they generate. We evaluated these models on the segmentation network of the model organism Drosophila melanogaster. Our models incorporate mechanistic features that attempt to capture how activating and repressing transcription factors work in the segmentation system. By evaluating the importance of these features, we were able to gain insights on the quantitative regulatory rules. We found that two different mechanisms may contribute to cooperative gene activation and that repressors often have a short range of influence in DNA sequences. Combining the quantitative modeling with comparative sequence analysis, we also found that even functional sequences may be lost during evolution.

Histone deacetylase inhibitors: a chemical genetics approach to understanding cellular functions

There are eleven zinc dependent histone deacetylases (HDAC) in humans which have histones and many non-histone substrates. The substrates of these enzymes include proteins that have a role in regulation of gene expression, cell proliferation, cell migration, cell death, immune pathways and angiogenesis. Inhibitors of HDACs (HDACi) have been developed which alter the structure and function of these proteins, causing molecular and cellular changes that induce transformed cell death. The HDACi are being developed as anti-cancer drugs and have therapeutic potential for many non-oncologic diseases.

Conserved expression without conserved regulatory sequence: the more things change, the more they stay the same

Regulatory regions with similar transcriptional output often have little overt sequence similarity, both within and between genomes. Although cis- and trans-regulatory changes can contribute to sequence divergence without dramatically altering gene expression outputs, heterologous DNA often functions similarly in organisms that share little regulatory sequence similarities (e.g. human DNA in fish), indicating that trans-regulatory mechanisms tend to diverge more slowly and can accommodate a variety of cis-regulatory configurations. This capacity to 'tinker' with regulatory DNA probably relates to the complexity, robustness and evolvability of regulatory systems, but cause-and-effect relationships among evolutionary processes and properties of regulatory systems remain a topic of debate. The challenge of understanding the concrete mechanisms underlying cis-regulatory evolution - including the conservation of function without the conservation of sequence - relates to the challenge of understanding the function of regulatory systems in general. Currently, we are largely unable to recognize functionally similar regulatory DNA.

Evolution of cis-regulatory sequences in Drosophila

Cross-species comparison is an emerging paradigm for identifying cis-regulatory sequences and understanding their function and evolution. In this chapter, we review probabilistic models of evolution of transcription factor binding sites, which provide the theoretical basis for a number of new bioinformatics tools for comparative sequence analysis. We illustrate how important functional and evolutionary insights on binding site gain and loss can be acquired through sequence comparison. This includes the observation that binding site turnover follows a molecular clock and that its rate correlates with the strength of binding sites and the presence of other sites in the neighborhood. We also comment on emerging trends that go beyond individual binding sites to a more holistic study of regulatory evolution. We point out common technical challenges, such as reliable sequence alignment and binding site prediction, when doing comparative regulatory sequence analysis and note some potential solutions thereof.

Power-laws in interferon-B mRNA distribution in virus-infected dendritic cells

Interferon-beta (IFNB1) mRNA shows very large cell-to-cell variability in primary human dendritic cells infected by Newcastle disease virus, with copy numbers varying from a few to several thousands. Analysis of data from the direct measurement of the expression of this gene in its natural chromatin environment in primary human cells shows that the distribution of mRNA across cells follows a power law with an exponent close to -1, and thus encompasses a range of variation much more extensive than a Gaussian. We also investigate the single cell levels of IFNB1 mRNA induced by infection with Texas influenza A mutant viruses, which vary in their capacity to inhibit the signaling pathways responsible for activation of this gene. Here as well we observe power-law behavior for the distribution of IFNB1 mRNA, albeit over a truncated range of values, with exponents similar to the one for cells infected by Newcastle disease virus. We propose a model of stochastic enhanceosome and preinitiation complex formation that incorporates transcriptional pulsing. Analytical and numerical results show good agreement with the observed power laws, and thus support the existence of transcriptional pulsing of an unmodified, intact gene regulated by a natural stimulus.

A biophysical model for analysis of transcription factor interaction and binding site arrangement from genome-wide binding data

Background

How transcription factors (TFs) interact with cis-regulatory sequences and interact with each other is a fundamental, but not well understood, aspect of gene regulation.

Methodology/Principal Findings

We present a computational method to address this question, relying on the established biophysical principles. This method, STAP (sequence to affinity prediction), takes into account all combinations and configurations of strong and weak binding sites to analyze large scale transcription factor (TF)-DNA binding data to discover cooperative interactions among TFs, infer sequence rules of interaction and predict TF target genes in new conditions with no TF-DNA binding data. The distinctions between STAP and other statistical approaches for analyzing cis-regulatory sequences include the utility of physical principles and the treatment of the DNA binding data as quantitative representation of binding strengths. Applying this method to the ChIP-seq data of 12 TFs in mouse embryonic stem (ES) cells, we found that the strength of TF-DNA binding could be significantly modulated by cooperative interactions among TFs with adjacent binding sites. However, further analysis on five putatively interacting TF pairs suggests that such interactions may be relatively insensitive to the distance and orientation of binding sites. Testing a set of putative Nanog motifs, STAP showed that a novel Nanog motif could better explain the ChIP-seq data than previously published ones. We then experimentally tested and verified the new Nanog motif. A series of comparisons showed that STAP has more predictive power than several state-of-the-art methods for cis-regulatory sequence analysis. We took advantage of this power to study the evolution of TF-target relationship in Drosophila. By learning the TF-DNA interaction models from the ChIP-chip data of D. melanogaster (Mel) and applying them to the genome of D. pseudoobscura (Pse), we found that only about half of the sequences strongly bound by TFs in Mel have high binding affinities in Pse. We show that prediction of functional TF targets from ChIP-chip data can be improved by using the conservation of STAP predicted affinities as an additional filter.

Conclusions/Significance

STAP is an effective method to analyze binding site arrangements, TF cooperativity, and TF target genes from genome-wide TF-DNA binding data.

Evolution of regulatory sequences in 12 Drosophila species

Characterization of the evolutionary constraints acting on cis-regulatory sequences is crucial to comparative genomics and provides key insights on the evolution of organismal diversity. We study the relationships among orthologous cis-regulatory modules (CRMs) in 12 Drosophila species, especially with respect to the evolution of transcription factor binding sites, and report statistical evidence in favor of key evolutionary hypotheses. Binding sites are found to have position-specific substitution rates. However, the selective forces at different positions of a site do not act independently, and the evidence suggests that constraints on sites are often based on their exact binding affinities. Binding site loss is seen to conform to a molecular clock hypothesis. The rate of site loss is transcription factor–specific and depends on the strength of binding and, in some cases, the presence of other binding sites in close proximity. Our analysis is based on a novel computational method for aligning orthologous CRMs on a tree, which rigorously accounts for alignment uncertainties and exploits binding site predictions through a unified probabilistic framework. Finally, we report weak purifying selection on short deletions, providing important clues about overall spatial constraints on CRMs. Our results present a complex picture of regulatory sequence evolution, with substantial plasticity that depends on a number of factors. The insights gained in this study will help us to understand the combinatorial control of gene regulation and how it evolves. They will pave the way for theoretical models that are cognizant of the important determinants of regulatory sequence evolution and will be critical in genome-wide identification of non-coding sequences under purifying or positive selection.

The spatial–temporal expression pattern of a gene, which is crucial to its function, is controlled by cis-regulatory DNA sequences. Forming the basic units of regulatory sequences are transcription factor binding sites, often organized into larger modules that determine gene expression in response to combinatorial environmental signals. Understanding the conservation and change of regulatory sequences is critical to our knowledge of the unity as well as diversity of animal development and phenotypes. In this paper, we study the evolution of sequences involved in the regulation of body patterning in the Drosophila embryo. We find that mutations of nucleotides within a binding site are constrained by evolutionary forces to preserve the site's binding affinity to the cognate transcription factor. Functional binding sites are frequently destroyed during evolution and the rate of loss across evolutionary spans is roughly constant. We also find that the evolutionary fate of a site strongly depends on its context; a pair of interacting sites are more likely to survive mutational forces than isolated sites. Together, these findings provide new insights and pose new challenges to our understanding of cis-regulatory sequences and their evolution.

GAL4 GFP enhancer trap lines for analysis of stomatal guard cell development and gene expression

To facilitate the monitoring of guard cells during development and isolation, a population of 704 GAL4 GFP enhancer trap lines was screened and four single insert lines with guard cell GFP expression and one with developmentally-regulated guard cell GFP expression were identified. The location of the T-DNA inserts, the expression of the flanking genes, and the promoter activity of the genomic DNA upstream of the T-DNA were characterized. The results indicated that the GFP expression pattern in at least one of the lines was due to elements in the intergenic DNA immediately upstream of the T-DNA, rather than due to the activity of the promoters of genes flanking the insert, and provide evidence for the involvement of Dof elements in regulating guard cell gene expression. It is shown further that the GAL4 GFP lines can be used to track the contribution of guard cell material in vitro, and this method was used to assess the purity of guard cell samples obtained using two methods of guard cell isolation.

Integration of external signaling pathways with the core transcriptional network in embryonic stem cells

Transcription factors (TFs) and their specific interactions with targets are crucial for specifying gene-expression programs. To gain insights into the transcriptional regulatory networks in embryonic stem (ES) cells, we use chromatin immunoprecipitation coupled with ultra-high-throughput DNA sequencing (ChIP-seq) to map the locations of 13 sequence-specific TFs (Nanog, Oct4, STAT3, Smad1, Sox2, Zfx, c-Myc, n-Myc, Klf4, Esrrb, Tcfcp2l1, E2f1, and CTCF) and 2 transcription regulators (p300 and Suz12). These factors are known to play different roles in ES-cell biology as components of the LIF and BMP signaling pathways, self-renewal regulators, and key reprogramming factors. Our study provides insights into the integration of the signaling pathways into the ES-cell-specific transcription circuitries. Intriguingly, we find specific genomic regions extensively targeted by different TFs. Collectively, the comprehensive mapping of TF-binding sites identifies important features of the transcriptional regulatory networks that define ES-cell identity.

An atomic model of the interferon-beta enhanceosome

Transcriptional activation of the interferon-beta (IFN-beta) gene requires assembly of an enhanceosome containing ATF-2/c-Jun, IRF-3/IRF-7, and NFkappaB. These factors bind cooperatively to the IFN-beta enhancer and recruit coactivators and chromatin-remodeling proteins to the IFN-beta promoter. We describe here a crystal structure of the DNA-binding domains of IRF-3, IRF-7, and NFkappaB, bound to one half of the enhancer, and use a previously described structure of the remaining half to assemble a complete picture of enhanceosome architecture in the vicinity of the DNA. Association of eight proteins with the enhancer creates a continuous surface for recognizing a composite DNA-binding element. Paucity of local protein-protein contacts suggests that cooperative occupancy of the enhancer comes from both binding-induced changes in DNA conformation and interactions with additional components such as CBP. Contacts with virtually every nucleotide pair account for the evolutionary invariance of the enhancer sequence.

Mass Spectrometric Analysis of High-Mobility Group Proteins and Their Post-Translational Modifications in Normal and Cancerous Human Breast Tissues

High-mobility group (HMG) A1 proteins including HMGA1a and HMGA1b are chromosomal proteins that function in a variety of cellular processes such as cell growth, transcription regulation, neoplastic transformation, and progression. Overexpression of HMGA1 proteins has been associated with almost every type of cancer cells. Post-translational modifications (PTMs) of HMGA1 proteins in different types of human cancer cell lines have been extensively explored over the past decade. Here, we extended the identification of PTMs of HMGA1 proteins to human breast tumor tissue specimens with different carcinoma progression stages (metastatic and primary cancer) as well as the paired adjacent normal breast tissues. In this regard, we employed tandem mass spectrometry to examine the nature and sites of PTMs of HMGA1 proteins isolated from cancerous/normal human breast tissues. Novel PTMs of HMGA1a protein, that is, monomethylation at Lys30 and Lys54 as well as monophosphorylation at Ser43 and Ser48, were detected in cancer tissues. In these cancer tissues, we also found C-terminal constitutive phosphorylation in HMGA1a and HMGA1b as well as mono- and dimethylation of Arg25 in HMGA1a, which were previously found to be present in these proteins isolated from human cancer cell lines. Furthermore, a more complex spectrum of PTMs on HMGA1 proteins was correlated with a more aggressive malignancy in human breast cancer tissues.

Statistical significance of cis-regulatory modules

BACKGROUND

It is becoming increasingly important for researchers to be able to scan through large genomic regions for transcription factor binding sites or clusters of binding sites forming cis-regulatory modules. Correspondingly, there has been a push to develop algorithms for the rapid detection and assessment of cis-regulatory modules. While various algorithms for this purpose have been introduced, most are not well suited for rapid, genome scale scanning.

RESULTS

We introduce methods designed for the detection and statistical evaluation of cis-regulatory modules, modeled as either clusters of individual binding sites or as combinations of sites with constrained organization. In order to determine the statistical significance of module sites, we first need a method to determine the statistical significance of single transcription factor binding site matches. We introduce a straightforward method of estimating the statistical significance of single site matches using a database of known promoters to produce data structures that can be used to estimate p-values for binding site matches. We next introduce a technique to calculate the statistical significance of the arrangement of binding sites within a module using a max-gap model. If the module scanned for has defined organizational parameters, the probability of the module is corrected to account for organizational constraints. The statistical significance of single site matches and the architecture of sites within the module can be combined to provide an overall estimation of statistical significance of cis-regulatory module sites.

CONCLUSION

The methods introduced in this paper allow for the detection and statistical evaluation of single transcription factor binding sites and cis-regulatory modules. The features described are implemented in the Search Tool for Occurrences of Regulatory Motifs (STORM) and MODSTORM software.

Rank-statistics based enrichment-site prediction algorithm developed for chromatin immunoprecipitation on chip experiments

BACKGROUND

High density oligonucleotide tiling arrays are an effective and powerful platform for conducting unbiased genome-wide studies. The ab initio probe selection method employed in tiling arrays is unbiased, and thus ensures consistent sampling across coding and non-coding regions of the genome. Tiling arrays are increasingly used in chromatin immunoprecipitation (IP) experiments (ChIP on chip). ChIP on chip facilitates the generation of genome-wide maps of in-vivo interactions between DNA-associated proteins including transcription factors and DNA. Analysis of the hybridization of an immunoprecipitated sample to a tiling array facilitates the identification of ChIP-enriched segments of the genome. These enriched segments are putative targets of antibody assayable regulatory elements. The enrichment response is not ubiquitous across the genome. Typically 5 to 10% of tiled probes manifest some significant enrichment. Depending upon the factor being studied, this response can drop to less than 1%. The detection and assessment of significance for interactions that emanate from non-canonical and/or un-annotated regions of the genome is especially challenging. This is the motivation behind the proposed algorithm.

RESULTS

We have proposed a novel rank and replicate statistics-based methodology for identifying and ascribing statistical confidence to regions of ChIP-enrichment. The algorithm is optimized for identification of sites that manifest low levels of enrichment but are true positives, as validated by alternative biochemical experiments. Although the method is described here in the context of ChIP on chip experiments, it can be generalized to any treatment-control experimental design. The results of the algorithm show a high degree of concordance with independent biochemical validation methods. The sensitivity and specificity of the algorithm have been characterized via quantitative PCR and independent computational approaches.

CONCLUSION

The algorithm ranks all enrichment sites based on their intra-replicate ranks and inter-replicate rank consistency. Following the ranking, the method allows segmentation of sites based on a meta p-value, a composite array signal enrichment criterion, or a composite of these two measures. The sensitivities obtained subsequent to the segmentation of data using a meta p-value of 10-5, an array signal enrichment of 0.2 and a composite of these two values are 88%, 87% and 95%, respectively.

ATG deserts define a novel core promoter subclass

The MHC class I gene, PD1, has neither functional TATAA nor Initiator (Inr) elements in its core promoter and initiates transcription at multiple, dispersed sites over an extended region in vitro. Here, we define a novel core promoter feature that supports regulated transcription through selective transcription start site (TSS) usage. We demonstrate that TSS selection is actively regulated and context dependent. Basal and activated transcriptions initiate from largely nonoverlapping TSS regions. Transcripts derived from multiple TSS encode a single protein, due to the absence of any ATG triplets within approximately 430 bp upstream of the major transcription start site. Thus, the PD1 core promoter is embedded within an "ATG desert". Remarkably, extending this analysis genome-wide, we find that ATG deserts define a novel promoter subclass. They occur nonrandomly, are significantly associated with non-TATAA promoters that use multiple TSS, independent of the presence of CpG islands (CGI). We speculate that ATG deserts may provide a core promoter platform upon which complex upstream regulatory signals can be integrated, targeting multiple TSS whose products encode a single protein.

Transcriptional enhancers: Intelligent enhanceosomes or flexible billboards?

In higher eukaryotes, transcriptional enhancers play critical roles in the integration of cellular signaling information, but apart from a few well-studied model enhancers, we lack a general picture of transcriptional information processing by most enhancers. Here we discuss recent studies that have provided fresh insights on information processing that occurs on enhancers, and propose that in addition to the highly cooperative and coordinate action of "enhanceosomes", a less integrative, but more flexible form of information processing is mediated by information display or "billboard" enhancers. Application of these models has important ramifications not only for the biochemical analysis of transcription, but also for the wider fields of bioinformatics and evolutionary biology.

The role of corepressors in transcriptional regulation by nuclear hormone receptors

Nuclear receptors (also known as nuclear hormone receptors) are hormone-regulated transcription factors that control many important physiological and developmental processes in animals and humans. Defects in receptor function result in disease. The diverse biological roles of these receptors reflect their surprisingly versatile transcriptional properties, with many receptors possessing the ability to both repress and activate target gene expression. These bipolar transcriptional properties are mediated through the interactions of the receptors with two distinct classes of auxiliary proteins: corepressors and coactivators. This review focuses on how corepressors work together with nuclear receptors to repress gene transcription in the normal organism and on the aberrations in this process that lead to neoplasia and endocrine disorders. The actions of coactivators and the contributions of the same corepressors to the functions of nonreceptor transcription factors are also touched on.

The csgD promoter, a control unit for biofilm formation in Salmonella typhimurium

Expression of cellulose and curli fimbriae in Salmonella typhimurium is dependent on the transcriptional regulator CsgD. Transcription of csgD itself is influenced by a variety of regulatory stimuli. Complex nucleoprotein arrangements modulate the transcriptional activity of csgD and trigger the transition between the planktonic status and biofilm formation.

Structure, function, and regulation of budding yeast kinetochores

Kinetochores are multiprotein complexes that assemble on centromeric DNA and mediate the attachment and movement of chromosomes along the microtubules (MTs) of the mitotic spindle. This review focuses on the simplest eukaryotic centromeres and kinetochores, those found in the budding yeast Saccharomyces cerevisiae. Research on kinetochore function and chromosome segregation is focused on four questions of general significance: what specifies the location of centromeres? What are the protein components of kinetochores, and how do they assemble a MT attachment site? How do MT attachments generate force? How do cells sense the state of attachment via the spindle assembly checkpoint?

Hierarchical assembly of the budding yeast kinetochore from multiple subcomplexes

Kinetochores are multiprotein complexes that assemble on centromeric DNA and attach chromosomes to spindle microtubules. Over the past six years, the number of proteins known to localize to the Saccharomyces cerevisiae kinetochore has increased from around 10 to over 60. However, relatively little is known about the protein-protein interactions that mediate kinetochore assembly or about the overall structure of microtubule-attachment sites. Here we used biophysical techniques, affinity purification, mass spectrometry, and in vivo assays to examine the state of association of 31 centromere-binding proteins, including six proteins newly identified as kinetochore subunits. We found that yeast kinetochores resemble transcriptional enhancers in being composed of at least 17 discrete subcomplexes that assemble on DNA to form a very large structure with a mass in excess of 5 MD. Critical to kinetochore assembly are proteins that bridge subunits in direct contact with DNA and subunits bound to microtubules. We show that two newly identified kinetochore complexes, COMA (Ctf19p-Okp1p-Mcm21p-Ame1p) and MIND (Mtw1p including Nnf1p-Nsl1p-Dsn1p) function as bridges. COMA, MIND, and the previously described Ndc80 complex constitute three independent and essential platforms onto which outer kinetochore proteins assemble. In addition, we propose that the three complexes have different functions with respect to force generation and MT attachment.

Computational approaches to identify promoters and cis-regulatory elements in plant genomes

The identification of promoters and their regulatory elements is one of the major challenges in bioinformatics and integrates comparative, structural, and functional genomics. Many different approaches have been developed to detect conserved motifs in a set of genes that are either coregulated or orthologous. However, although recent approaches seem promising, in general, unambiguous identification of regulatory elements is not straightforward. The delineation of promoters is even harder, due to its complex nature, and in silico promoter prediction is still in its infancy. Here, we review the different approaches that have been developed for identifying promoters and their regulatory elements. We discuss the detection of cis-acting regulatory elements using word-counting or probabilistic methods (so-called "search by signal" methods) and the delineation of promoters by considering both sequence content and structural features ("search by content" methods). As an example of search by content, we explored in greater detail the association of promoters with CpG islands. However, due to differences in sequence content, the parameters used to detect CpG islands in humans and other vertebrates cannot be used for plants. Therefore, a preliminary attempt was made to define parameters that could possibly define CpG and CpNpG islands in Arabidopsis, by exploring the compositional landscape around the transcriptional start site. To this end, a data set of more than 5,000 gene sequences was built, including the promoter region, the 5'-untranslated region, and the first introns and coding exons. Preliminary analysis shows that promoter location based on the detection of potential CpG/CpNpG islands in the Arabidopsis genome is not straightforward. Nevertheless, because the landscape of CpG/CpNpG islands differs considerably between promoters and introns on the one side and exons (whether coding or not) on the other, more sophisticated approaches can probably be developed for the successful detection of "putative" CpG and CpNpG islands in plants.

Genes, neurons and codes: remarks on biological communication

I examine critically the application of information-theoretic ideas to biological communication during embryonic development and in the functioning central nervous system (CNS). I show that intercellular communication relies mostly on simple signals whose role is to effect a selection among predetermined cellular states. Hence, a crucial role is played by cellular memory, which stabilizes such states. Memory in cells is partly located in the nuclear DNA; no less important however is (phenotypic) memory lying in the cell's organelles and compartments. Because of combinatorial effects in gene expression patterns, cell memory is an enormously powerful mechanism, which also underlies plasticity, and thus constitutes the factor unifying genetic determination, plasticity and learning. Communication in the CNS is analyzed in some detail: here, cellular memory is embodied in anatomy (i.e., cell shape) and neurochemistry. These are the major, relatively "static" factors affecting the routing of neural impulses in the adult CNS. In addition, however, faster channeling is also required: action potentials must be directed to their targets along a few of exponentially many paths, and this dynamic routing is crucial for proper operation. I suggest that collective oscillatory modes may play a role in solving this addressing problem, in the same way that the clock signal gates the operation of man-made computers.

TFIIA abrogates the effects of inhibition by HMGB1 but not E1A during the early stages of assembly of the transcriptional preinitiation complex

Successful assembly of the transcriptional preinitiation complex (PIC) is prerequisite to transcriptional initiation. At each stage of PIC assembly, regulation may occur as repressors and activators compete with and influence the incorporation of general transcription factors (GTFs). Both TFIIA and HMGB1 bind individually to the TATA-binding protein (TBP) to increase the rate of binding and to stabilize TBP binding to the TATA element. The competitive binding between these two cofactors for TBP/TATA was examined to show that TFIIA binds preferentially to TBP and inhibits HMGB1 binding. TFIIA can also readily dissociate HMGB1 from the preestablished HMGB1/TBP/TATA complex. This suggests that TFIIA and HMGB1 may bind to the same or overlapping sites on TBP and/or compete for similar DNA sites that are 5' to the TATA element. In addition, EMSA studies show that adenovirus E1A(13S) oncoprotein is unable to disrupt either the preestablished TFIIA/TBP/TATA or TFIIA/TFIIB/TBP/TATA complexes, but does inhibit complex formation when all transcription factors were simultaneously added. The inhibitory effect of E1A(13S) on the assembly of the PIC is overcome when excess TBP is added back in the reaction, while addition of either excess TFIIA or TFIIB were ineffective. This shows that the main target for E1A(13S) is free TBP and emphasizes the primary competition between E1A and the TATA-element for unbound TBP. This may be the principal point, if not the only point, at which E1A can target TBP to exert its inhibitory effect. This work, coupled with previous findings in our laboratory, indicates that TFIIA is much more effective than TFIIB in reversing the inhibitory effect of HMGB1 binding in the early stages of PIC assembly, which is consistent with the in vitro transcription results.

Glucose regulates insulin gene transcription by hyperacetylation of histone h4

Induction of insulin gene expression in response to high blood glucose levels is essential for maintaining glucose homeostasis. Although several transcription factors including Beta-2, Ribe3b1, and Pdx-1 have been shown to play a role in glucose stimulation of insulin gene expression, the exact molecular mechanism(s) by which this regulation occurs is unknown. Previous data demonstrate that the transcription factors Beta-2/NeuroD1 and Pdx-1, which are involved in glucose-stimulated insulin gene expression, interact with the histone acetylase p300, suggesting a role for histone acetylation in glucose regulation of the insulin gene expression. We report that exposure of mouse insulinoma 6 cells to high concentrations of glucose results in hyperacetylation of histone H4 at the insulin gene promoter, which correlates with the increased level of insulin gene transcription. In addition, we demonstrate that hyperacetylation of histone H4 in response to high concentrations of glucose also occurs at the glucose transporter-2 gene promoter. Using histone deacetylase inhibitors, we show that increases in histone H4 acetylation cause stimulation of insulin gene transcription even in the absence of high concentrations of glucose. Furthermore, we show that fibroblasts, which lack insulin gene expression, also lack histone acetylation at the insulin gene promoter. In summary, our data support the idea that high concentrations of glucose stimulate insulin gene expression by causing hyperacetylation of histone H4 at the insulin gene promoter.

The circadian E-box: when perfect is not good enough

Life on earth has evolved on a photic carousel, spinning through alternating periods of light and darkness. This playful image belies the fact that only those organisms that learned how to benefit from the recurring features in their environment were allowed to ride on. This selection process has engendered many daily rhythms in our biosphere, most of which rely on the anticipatory power of an endogenously generated marker of phase: the biological clock. The basic mechanisms driving this remarkable device have been really tough to decode but are finally beginning to unravel as chronobiologists probe deeper and wider in and around the recently discovered gears of the clock. Like its chemical predecessors, biological circadian oscillators are characterized by interlaced positive and negative feedback loops, but with constants and variables carefully balanced to achieve an approximately 24h period. The loops at the heart of these biological oscillators are sustained by specific patterns of gene expression and precisely tuned posttranscriptional modifications. It follows that a molecular understanding of the biological clock hinges, in no small measure, on a better understanding of the cis-acting elements that bestow a given gene with its circadian properties. The present review summarizes what is known about these elements and what remains to be elucidated.

MMP13 promoter polymorphism is associated with atherosclerosis in the abdominal aorta of young black males

Previous studies suggested that remodeling of connective tissue is important in progression of atherosclerosis. We investigated the importance of matrix metalloproteinase 13 (MMP13), in the pathogenesis of atherosclerosis using 995 samples from the Pathobiological Determinants of Atherosclerosis in Youth collection in an association study. We identified two new MMP13 promoter polymorphisms. The genotype for one of the MMP13 polymorphisms was associated with fibrous plaque (P=0.024) in black males. Immunohistochemistry using antibodies for MMP13 showed that MMP13 is expressed in all layers of the aorta. In-vitro transfection experiments with reporter gene constructs and electrophoretic mobility-shift assays showed that the MMP13 polymorphism was a functional variant. MMP13 is therefore, a genetic risk factor for extent of fibrous plaque in the abdominal aorta in young black males. Elucidation of the currently unknown mechanism of the MMP13 polymorphism's action may provide for pharmacological intervention to reduce the severity of atherosclerotic changes in susceptible individuals.

Modifying gene expression programs by altering core promoter chromatin architecture

Transcriptional activation of the IFN-beta gene in response to virus infection requires the assembly of an enhanceosome, which instructs a recruitment program of chromatin modifiers/remodelers and general transcription factors to the promoter. This program culminates with sliding of a nucleosome blocking the core promoter to a downstream position, a prerequisite for transcriptional activation. We show that delivery of this nucleosome to the same downstream position to create an accessible IFN-beta core promoter prior to enhanceosome assembly results in major changes in the gene expression program with regard to the temporal pattern and the signal specificity of the transcriptional response. Thus, the identity of a gene expression program is achieved and maintained by the dynamic interplay between specific enhanceosomes and specific local chromatin structure.

The zinc finger/homeodomain protein deltaEF1 mediates estrogen-specific induction of the ovalbumin gene

Regulation of the ovalbumin (Ov) gene is strictly controlled by precise developmental, tissue-specific, and hormonal cues. The Ov gene is transcriptionally activated by four classes of steroid hormones: estrogens, androgens, glucocorticoids, and progestins. Although it has served as a model to study multi-hormone gene regulation for the past 30 years, the pathways that relay each hormone signal to the Ov gene are largely unclear. Extensive linker-scanner and point mutation analysis has revealed elements necessary for its induction by estrogen, androgen, progesterone, or glucocorticoid but has failed to identify any elements that are specific to the action of any one steroid hormone. These observations in conjunction with the observation that the Ov gene is indirectly regulated by steroid hormones suggest that these signals may all induce the same transcription factor. However, here we have identified two cis-acting DNA elements in the 5' flanking region of the Ov gene that are required for induction by estrogen, but not by androgen or progesterone. These elements span -152 to -146 and -810 to -806 with respect to the start point of transcription. This implies that estrogen induces the Ov gene by a separate pathway than do androgens or progestins. Gel mobility shift assays demonstrate that the estrogen-specific sequences bind the estrogen inducible transcription factor deltaEF1, suggesting that deltaEF1 plays a distinct role in mediating the estrogen signal to the Ov gene.

Analysis and function of transcriptional regulatory elements: insights from Drosophila

Analysis of gene expression is assuming an increasingly important role in elucidating the molecular basis of insect biology. Transcriptional regulation of gene expression is directed by a variety of cis-acting DNA elements that control spatial and temporal patterns of expression. This review summarizes current knowledge about properties of transcriptional regulatory elements, based largely on research in Drosophila melanogaster, and outlines ways that new technologies are providing tools to facilitate the study of transcriptional regulatory elements in other insects.