CtBP: A Link between Apoptosis and the Epithelial-Mesenchymal Transition

Steven M. Frisch

Adenovirus E1a proteins are potent and ubiquitously acting tumor suppressors in human tumor cells. Through interaction with CtBP (as well as other mechanisms), E1a protein sensitizes cells to several apoptotic responses including anoikis. This interaction also induces the expression of certain epith...

CtBPs as Synaptic Proteins

Susanne tom Dieck, Frank Schmitz and Johann Helmut Brandstätter

A surprising new aspect of CtBP family proteins arose from the identification of a novel CtBP protein named RIBEYE.1 RIBEYE, which consists of a unique amino-terminal A-domain and a carboxy-terminal B-domain, largely identical to CtBP2, was discovered not as a nuclear protein but as a major componen...

Curved DNA and Prokaryotic Promoters: A Mechanism for Activation of Transcription

Munehiko Asayama and Takashi Ohyama

Intrinsically curved DNA structures often occur in or around origins of DNA replication, regions that regulate transcription, and DNA recombination loci, and are found in a wide variety of cellular and viral genomes from bacteria to man. In bacterial promoters, bent DNA structures are often locat...

Curved DNA and Transcription in Eukaryotes

Takashi Ohyama

Intrinsically curved DNA structures are often found in or around transcriptional control regions of eukaryotic genes, and curved DNA may be common to all class I gene promot ers. Although not all class II gene promoters contain curved DNA structures, both TATAbox- containing and TATA-box-less pro...

Delivery of Osteogenic Regulatory Growth Factors

Delphine Logeart-Avramoglou

Growth factors play an important role in both physiological and therapeutic tissue regeneration. In this review we will focus on skeletal regeneration and give a special emphasis to the delivery of Bone Morphogenetic Proteins (BMPs). Although it is now possible to generate large amounts of recomb...

Deregulation of the HOX Gene Network and Cancer

Although the Hox genes have been identified as master regulatory genes controlling embryonic development, an alternative view on the role of the Hox gene network suggests that it regulates crucial processes at cellular level in eukaryotic organisms. Our working hypothesis considers the Hox network, ...

Detecting Hitchhiking from Patterns of DNA Polymorphism

Justin C. Fay and Chung-I Wu

The genetic basis of adaptive evolution has long escaped the grasp of evolutionary geneticists due to the difficulty of mapping an organism’s phenotype to its genotype. However, adaptive substitutions may also be identified by their effects on linked neutral variation. This has made it possible t...

Distribution and Abundance of Polymorphism in the Malaria Genome

Stephen M. Rich

Plasmodium falciparum is the most deadly of the four human malaria parasites, causing as many as 500 million malaria cases per year and more than 2 million deaths.1 Despite more than a century of biomedical research and unprecedented (indeed, unsurpassed) measures of international collaboration t...

DNA Bendability and Nucleosome Positioning in Transcriptional Regulation

Mensur Dlakic, David W. Ussery and Søren Brunak

The placement of nucleosomes along genomic DNA is determined by signals that can be specific or degenerate at the level of sequence; the latter signals are harder to find using conventional methods. In recent years, the development of sophisticated machine learning techniques that can extract sub...

DNA Methylation Reprogramming in the Germ Line

Diane J. Lees-Murdock and Column P. Walsh

In mammals, methylation occurs almost exclusively on the CpG dinucleotide in DNA and shows no preference for sequence context surrounding this target. CpGs are found on many different sequence classes and methylation of this dinucleotide is associated with repression of transcription. Reprogramming ...

DNA Primer Extension by Telomerase

Haim Manor, Yonit Haviv and Nava Baran

Telomeres are DNA-protein complexes found at the ends of linear eukaryotic chromosomes. The telomeric complexes prevent the chromosome ends from being recognized and processed as double strand breaks (for a review, see ref. 1). In most eukaryotes, the telomeric DNA consists of short repe...

DNA: Alternative Conformations and Biology

Vladimir N. Potaman and Richard R. Sinden

Local structural transitions from the common B-DNA conformation into other DNA forms can be functionally important. This chapter describes the structures of DNA forms called alternative DNA conformations that are different from the canonical B-DNA helix. Also discussed are the requirements for th...

Do DNA Triple Helices or Quadruplexes Have a Role in Transcription?

Michael W. Van Dyke

Certain DNA sequences preferentially adopt multistranded, non-B-form structures under physiological conditions. These include three-stranded DNA triplexes and four-stranded DNA quadruplexes. Several lines of evidence suggest that multiplex structures can form in vivo, either from the addition of ...

Dominance, Nonlinear Developmental Mapping and Developmental Stability

Christian Peter Klingenberg

Developmental stability is the ability of organisms to buffer against the random variation that arises spontaneously as a consequence of stochastic variation in the cellular processes that are involved in the development of morphological structures. Its converse, developmental instability, is the...

Elucidating Gene Regulatory Networks Underlying Complex Phenotypes: Genetical Genomics and Bayesian Network

Yan Cui

Microarray-based technologies have enabled comprehensive transcriptome profiling. It is becoming feasible to reconstruct gene transcriptional regulatory networks from microarray data. In this chapter, I outline a new strategy for reconstructing gene regulatory networks as part of the causal ne...

Evolution of Hox Gene Clusters

The Hox gene clusters have been one of the most prominent paradigms within Developmental Biology. This stems from the great excitement that surrounded the discovery that the genes all contained the conserved homeobox motif and that the homologous genes were operating in broadly homologous ways in th...

Evolutionary Genomics of Hox Gene Clusters

The evolution of Hox clusters in vertebrates follows different patterns than those of in-vertebrate clusters. More stringent structural constraints in vertebrates are apparent from tighter cluster organization and the systematic expulsion of repetitive material. We speculate that the tendency of ver...

Evolutionary Theories of Imprinting--Enough Already!

Tom Moore and Walter Mills

In our view, the conflict theory of imprinting explains the evolution of parental allele-specific gene expression patterns in the somatic tissues of mammals and angiosperms. Not surprisingly, given its importance in mammalian development and pathology, the evolution of imprinting continues to attrac...

Expression of Hox Genes in the Nervous System of Vertebrates

The vertebrate nervous system is a major site of Hox gene expression and function. Studies on the patterns of expression, regulation and function of the vertebrate Hox gene family have played a key role in aiding our understanding of the basic ground plan of the CNS and processes that control how un...

From Beanbag Genetics to Feedback Genetics: Bridging the Gap between Regulatory Biology and Quantitative Genetics Theory

Stig W. Omholt

This chapter addresses the abyss that currently exists between quantitative genetics theory and regulatory biology. My claim is that despite the apparent success of quantiative genetics within evolutionary biology and production biology, the conceptual and methodological foundation of the theory as ...

From Gene to Oncogenesis, the Example of Ets Transcription Factors from the PEA3 Group

Sébastien Mauen, Jean-Luc Baert and Yvan de Launoit

The PEA3 group of Ets transcription factors is composed of three highly conserved members: Erm, Er81 and Pea3. They regulate transcription of their target genes following post-translational modifications such as phosphorylation, acetylation, sumoylation and ubiquitinylation. Among their targ...

GAGA: Structural Basis for Single Cys2His2 Zinc Finger-DNA Interaction

G. Marius Clore and James G. Omichinski

The structural basis of sequence specific binding of the Cys2His2 single zinc finger DNA binding domain of the transcription factor GAGA is explored on the basis of the three-dimensional structure of a complex between the minimal DNA binding domain (DBD) of the GAGA factor (GAGA-DBD) and an oli...

Gene Regulation by HMGA and HMGB Chromosomal Proteins and Related Architectural DNA-Binding Proteins

Andrew A. Travers

The eukaryotic abundant high mobility group HMGA and HMGB proteins can act as architectural transcription factors by promoting the assembly of higher-order protein- DNA complexes which can either activate or repress gene expression. The structural organisation of both classes of protein is simila...

Gene Regulatory Networks

T. Gregory Dewey* and David J. Galas

Two gene regulatory networks inferred from different types of data are considered in this chapter. Gene expression networks are networks inferred from microarray time series data and transcription factor networks are networks obtained from a new genome-wide technique that allows an identification...

Genomic Imprinting and Human Psychology: Cognition, Behavior and Pathology

Lisa M. Goos and Gillian Ragsdale

Imprinted genes expressed in the brain are numerous and it has become clear that they play an important role in nervous system development and function. The significant influence of genomic imprinting during development sets the stage for structural and physiological variations affecting psychologic...