Biochemistry (Mosc). 2007 Nov;72(11):1187-93.

Bioinformatical and experimental approaches to investigation of transcription factor binding sites in vertebrate genes.
Merkulova TI, Oshchepkov DY, Ignatieva EV, Ananko EA, Levitsky VG, Vasiliev GV, Klimova NV, Merkulov VM, Kolchanov NA. Source
Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, Novosibirsk, 630090, Russia. merkti@niboch.nsc.ru

Abstract
The development of computer-assisted methods for transcription factor binding sites (TFBS) recognition is necessary for study the DNA regulatory transcription code. There are a great number of experimental methods that enable TFBS identification in genome sequences. The experimental data can be used to elaborate multiple computer approaches to recognition of TFBS, each of which has its own advantages and limitations. A short review of the characteristics of computer methods of TFBS prediction based on various principles is presented. Methods used for experimental monitoring of predicted sites are analyzed. Data concerning DNA regulatory potential and its realization at the chromatin level, obtained using these methods, are discussed along with approaches to recognition of target genes of certain transcription factors in the genome sequences.

Mol Cells. 2007 Dec 31;24(3):307-15.

Inferring transcriptional interactions and regulator activities from experimental data.

Wang RS, Zhang XS, Chen L. Source
Department of Electronics, Information and Communication Engineering, Osaka Sangyo University, Osaka 574-8530, Japan.

Abstract
Gene regulation is a fundamental process in biological systems, where transcription factors (TFs) play crucial roles. Inferring transcriptional interactions between TFs and their target genes has utmost importance for understanding the complex regulatory mechanisms in cellular systems. On one hand, with the rapid progress of various high-throughput experiment techniques, more and more biological data become available, which makes it possible to quantitatively study gene regulation in a systematic manner.

On the other hand, transcription regulation is a complex biological process mediated by many events such as post-translational modifications, degradation, and competitive binding of multiple TFs. In this review, with a particular emphasis on computational methods, we report the recent advances of the research topics related to transcriptional regulatory networks, including how to infer transcriptional interactions, reveal combinatorial regulation mechanisms, and reconstruct TF activity profiles.

Biochem Soc Trans. 2008 Aug;36(Pt 4):758-65.

Computational approaches to study transcriptional regulation.

Babu MM. Source
MRC Laboratory of Molecular Biology, Cambridge, UK. madanm@mrc-lmb.cam.ac.uk

Abstract
In recent years, a number of technical and experimental advances have allowed us to obtain an unprecedented amount of information about living systems on a genomic scale. Although the complete genomes of many organisms are available due to the progress made in sequencing technology, the challenge to understand how the individual genes are regulated within the cell remains. Here, I provide an overview of current computational methods to investigate transcriptional regulation. I will first discuss how representing protein-DNA interactions as a network provides us with a conceptual framework to understand the organization of regulatory interactions in an organism. I will then describe methods to predict transcription factors and cis-regulatory elements using information such as sequence, structure and evolutionary conservation. Finally, I will discuss approaches to infer genome-scale transcriptional regulatory networks using experimentally characterized interactions from model organisms and by reverse-engineering regulatory interactions that makes use of gene expression data and genomewide location data. The methods summarized here can be exploited to discover previously uncharacterized transcriptional pathways in organisms whose genome sequence is known. In addition, such a framework and approach can be invaluable to investigate transcriptional regulation in complex microbial communities such as the human gut flora or populations of emerging pathogens. Apart from these medical applications, the concepts and methods discussed can be used to understand the combinatorial logic of transcriptional regulation and can be exploited in biotechnological applications, such as in synthetic biology experiments aimed at engineering regulatory circuits for various purposes.

Methods Mol Biol. 2006;316:291-358.

Receptor-binding sites: bioinformatic approaches.

Flower DR. Source
Edward Jenner Institute for Vaccine Research, Compton, Berkshire, UK.

Abstract
It is increasingly clear that both transient and long-lasting interactions between biomacromolecules and their molecular partners are the most fundamental of all biological mechanisms and lie at the conceptual heart of protein function. In particular, the protein-binding site is the most fascinating and important mechanistic arbiter of protein function. In this review, I examine the nature of protein-binding sites found in both ligand-binding receptors and substrate-binding enzymes. I highlight two important concepts underlying the identification and analysis of binding sites. The first is based on knowledge: when one knows the location of a binding site in one protein, one can "inherit" the site from one protein to another. The second approach involves the a priori prediction of a binding site from a sequence or a structure. The full and complete analysis of binding sites will necessarily involve the full range of informatic techniques ranging from sequence-based bioinformatic analysis through structural bioinformatics to computational chemistry and molecular physics. Integration of both diverse experimental and diverse theoretical approaches is thus a mandatory requirement in the evaluation of binding sites and the binding events that occur within them.

Novartis Found Symp. 2007;284:116-25; discussion 125-9, 158-63.

Tinkering with transcription factor proteins: the role of transcription factor adaptation in developmental evolution.
Wagner GP, Pyle AM. Source
Department of Ecology and Evolutionary Biology, Yale University, Howard Hughes Medical Institute, New Haven, CT 06520-8106, USA.

Abstract
Evolution of transcriptional regulation is often seen as being driven by the origin of transcription factor binding sites in cis-regulatory DNA. But there is strong evidence that transcriptional specificity of transcription factor proteins is determined by protein-protein interaction with other transcription factors. Here we summarize the evidence that transcription factor protein function itself is evolving and suggest that this might play an integral if not leading role in the evolution of gene regulation.

J Steroid Biochem Mol Biol. 1992 Mar;41(3-8):739-45.

Biological effects of glucocorticoid hormones on two rat colon adenocarcinoma cell lines.
Denis MG, Chadneau C, Blanchardie P, Lustenberger P. Source
Department of Medical Biochemistry, INSERM CJF 90-11, U.F.R. of Medicine, Nantes, France.

Abstract
Glucocorticoid hormones are thought to play a role in carcinogenesis as they regulate cell differentiation and proliferation. We have investigated the effect of dexamethasone on two cell lines derived from a colon carcinoma, which differ by their tumorigenicity. Dexamethasone was found to inhibit growth of both the progressive (PROb) and the regressive clone (REGb). Upon glucocorticoid treatment, PROb cells were found to secrete an additional Mr approximately 40,000 protein. The synthesis and the release in the culture medium of this protein is stimulated specifically by glucocorticoid agonists, and not by other steroid hormones. The anti-glucocorticoid RU 38486 is inefficient and suppresses the induction of this protein by dexamethasone. Induction is sensitive to actinomycin D, suggesting that regulation may be related to an alteration of the rate of mRNA synthesis. The cellular effect of glucocorticoid hormones being mediated through a specific soluble receptor, we have characterized this protein. The PROb cells contained more specific glucocorticoid-binding sites (approximately 170,000 sites per cell) than the regressive ones (REGb cells; approximately 100,000 sites per cell). In both clones, the receptor was associated with the Mr approximately 90,000 heat shock protein to yield large complexes (Stokes radius Rs approximately 7.5 nm), which were dissociated to the same extent upon heat- and salt-treatment. The steroid- and DNAbinding unit of the receptor, characterized under denaturing conditions using an antireceptor monoclonal antibody, was found to be more degraded in the PROb cell line.

Oncol Res. 2005;15(5):265-79.

A bisanthracycline (WP631) represses uPAR gene expression and cell migration of RKO colon cancer cells by interfering with transcription factorbinding to a chromatinaccessible -148/-124 promoter region.
Nair RR, Wang H, Jamaluddin MS, Fokt I, Priebe W, Boyd DD. Source

Department of Cancer Biology, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX 77030, USA.

Abstract
The urokinase receptor (uPAR), transcriptionally activated in several cancers, contributes to tumor progression by promoting cell migration and proteolysis, and repressing expression of this gene could be of therapeutic utility. Indeed, targeting regulatory element(s) in the promoter may represent an efficient means for reducing expression because only two alleles have to be neutralized. We previously identified the -148/-124 promoter region, bound with Sp1 and Sp3, as regulatory for uPAR expression in vitro. The purpose of this study was twofold: to determine (a) the accessibility of this region in its natural chromatin setting and (b) the efficacy of WP631, a bisintercalator favoring GC-rich DNA sequences, in repressing endogenous uPAR expression in RKO colon cancer cells. In these cells, DNaseI hypersensitivity, genomic footprinting, and chromatin immunoprecipitation experiments revealed that the -148/-124 uPAR promoter region was accessible in chromatin and bound with Sp1, thus validating it as a therapeutic target. WP631 treatment competed fortranscription factor binding to this regulatory region and reduced uPAR mRNA/protein. However, a chemically related compound (WP629), with low DNA binding affinity, failed to diminish uPAR protein amount. GAPDH mRNA level was only modestly affected by WP631, arguing against the possibility that this bisanthracycline universally represses expression of GC-rich promoter-driven genes. Further, uPAR function, as assessed by migration of cells across a vitronectin-coated filter, was attenuated with WP631. Thus, we have shown that the chromatinized -148/-124 regulatory region of the uPAR promoter is accessible to small molecules and that WP631, which disrupts the interaction of DNAbinding proteins with this region, diminishes uPAR expression and function.