RNA Polymerase III

Robert J. White

Pol III is the largest of the nuclear RNA polymerases, with an aggregate molecular weight of 600700 kD (reviewed by Thuriaux and Sentenac^1–3). This is, perhaps, surprising since pol II transcribes a much larger and more diverse set of templates, and so might have been ...

4‑1BB as a Therapeutic Target for Human Disease

Seung-Woo Lee and Michael Croft

4‑1BB (CD137) is being thought of as an attractive target for immunotherapy of many human immune diseases based on encouraging results with 4‑1BB agonistic antibody treatment in mouse models of cancer, autoimmune disease, asthma and additionally as a means to improve vaccination. In this...

A New Member of the CtBP/BARS Family from Plants: Angustifolia

Hirozaku Tsukaya

The ANGUSTIFOLIA (AN) gene in Arabidopsis thaliana (L.) Heynh. is the first \r\nhomolog of the CtBP/BARS gene family identified in plants and is responsible for the polarity-dependent control of leaf cell expansion. This review compares the sequence homology and functional similarity of the AN prote...

A Novel Test Statistic for the Identification of Local Selective Sweeps Based on Microsatellite Gene Diversity

Christian Schlotterer and Daniel Dieringer

Genome wide population surveys have recently been established as a promising approach for the identification of genomic regions subject to directional selection. Nevertheless, the analysis of multiple markers requires novel approaches for the identification of selection. In this report we introdu...

A Zinc Ribbon Motif Is Essential for the Formation of Functional Tetrameric Protein Kinase CK2

Odile Filhol, Maria Jose Benitez and Claude Cochet

Protein kinase CK2 plays an essential role in the regulation of many cellular functions. The enzyme is an heterotetrameric complex formed by the association of two catalytic alpha/alpha’ subunits with two regulatory beta subunits. High-resolution structure of the CK2beta subunit revealed the pre...

ABBREVIATIONS

Shiro Iuchi

Abbreviations for the book Zinc Finger Proteins: from Atomic Contact to Cellular Function

Amplification of hTERT, the Telomerase Reverse Transcriptase Gene in Human

Dawei Xu, Anju Zhang, Mi Hou, Magnus Björkholm and Astrid Gruber

Telomeres, the nucleoprotein structure consisting of tandemly repeated TTAGGG sequences and associated proteins, form protective caps on human linear chromosome ends, and are essential to maintenance of genomic stability and integrity.^1,2 Telomere DNA is de novo synthesized by...

Analytical Evolutionary Model for Protein Fold Occurrence in Genomes, Accounting for the Effects of Gene Duplication, Deletion, Acquisition and Selective Pressure

Michael Kamal, Nicholas M. Luscombe, Jiang Qian and Mark Gerstein*

Global surveys of protein folds in genomes measure the usage of essential molecular parts in different organisms. In a recent survey, we showed that the occurrence of protein folds in 20 completely sequence genomes follow a power-law distribution; i.e., the number of folds (F) with a given genomi...

Apoptosis by Zinc Deficiency

Kirsteen H. Maclean

Zinc is an essential trace element for all forms of life. Zinc deficiency affects many systems because of the many roles it encompasses, such as in metabolism (including the activity of more than 300 enzymes), the structure of many proteins and control of genetic expression. Homeostatic regulati...

Basonuclin: A Zinc Finger Protein of Epithelial Cells and Reproductive Germ Cells

Howard Green and Hung Tseng

Basonuclin is a C2H2 zinc finger protein first discovered in the keratinocytes of stratified squamous epithelia and in certain keratinocytes of the hair follicles. It was later detected in the reproductive germ cells of the testis and ovary and in the cells of the ocular lens epithelium. The onl...

Biological Consequences of Dosage Dependent Gene Regulation in Multicellular Eukaryotes

James A. Birchler and Donald L. Auger

Recent evidence from a variety of studies has indicated that gene regulatory mechanisms in multicellular eukaryotes operate in a dosage dependent manner. A consequence of this fact is that new mutations in regulatory loci are available for adaptive selection in the heterozygous state, which is co...

Birth and Death Models of Genome Evolution

Georgy P. Karev, Yuri I. Wolf, and Eugene V. Koonin

Gene duplication is the primary avenue of genome evolution. The gene repertoire of any species can be described as an ensemble of paralogous gene families, ranging in size from one to large numbers that amount to a substantial fraction of genes in the respective genome. Evolution of such an ensem...

C₂H₂ Zinc Fingers as DNA Binding Domains

Shiro Iuchi

A great number of C₂H₂ zinc finger proteins selectively bind to specific DNA sequences and play a critical role in controlling transcription of genes. The specific binding is achieved by zinc finger domains with ??? structure that is formed by tetrahedral binding of Zn2+ io...

Cell Cycle Reactivation in Skeletal Muscle and Other Terminally Differentiated Cells

Alessandra Sacco, Deborah Pajalunga, Lucia Latella, Francesca Siepi, Alessandro Rufini and Marco Crescenzi

This Chapter reviews, in a historical perspective, our current understanding of the cell cycle control in terminally differentiated skeletal muscle cells. Attempts at inducing reentry into the cell cycle and proliferation of terminally differentiated muscle cells are re...

Cellular Dedifferentiation During Regeneration: The Amphibian Muscle System

Elly Tanaka

Amphibian limb regeneration represents a striking system where the reversal of muscle cell differentiation occurs in response to physiological stimuli. During this process, dedifferentiation is used to form progenitor cells for tissue repair. In response to injury, m...

Chromatin Structure of Class III Genes

Robert J. White

The chromatin structure of a gene can be a major determinant of its transcrip-tional activity (reviewed in refs. 1–8). In chromatin, 146 bp of DNA is wrapped approximately twice around a nucleosome core comprising two molecules each of histones H2A, H2B, H3 and H4, arranged as tw...

Class III Genes

Robert J. White

The genes transcribed by pol III encode a variety of small RNA molecules. (Table 1) Many of these have essential functions in cellular metabolism, such as tRNA and 5S rRNA, which are required for protein synthesis, 7SL RNA, which is involved in intracellular protein transport, and the U6...

Clusters of Functionally Related Genes in Eukaryotes, Dosage Balance and Evolvability

Reiner A. Veitia

There is growing genomic evidence on clustering of functionally related genes in eukaryotes. Recent studies in yeast show a correlation between the expression patterns of adjacent and nonadjacent pairs of genes and that a significant proportion of the former are functionally related. A transcript...

Control of Imprinting at the Gnas Cluster

Jo Peters and Christine M. Williamson

Genomic imprinting is a form of epigenetic regulation in mammals whereby a small subset of genes is silenced according to parental origin. Early work had indicated regions of the genome that were likely to contain imprinted genes. Distal mouse chromosome 2 is one such region and is associated with d...

CtBP and Hematopoietic Transcriptional Regulators

Alexis Verger, Jose Perdomo and Merlin Crossley

The C-terminal binding proteins (CtBPs) are ubiquitous corepressors that recruit histone-modifying enzymes to a variety of sequence specific DNA-binding proteins and other transcriptional regulators. CtBPs appear to play an important role in mediating repression and transforming activities of a vari...

CtBP as a Redox Sensor in Transcriptional Repression

Qinghong Zhang, Clark C. Fjeld, Amanda C. Nottke and Richard H. Goodman

The corepressor CtBP (carboxyl-terminal binding protein) is involved in transcriptional pathways important for development, cell cycle regulation, and transformation. We demonstrate that CtBP binding to transcription repressors is stimulated by NAD+ and NADH, with NADH being two to three orders of m...

CtBP Corepressor Complex - A Multi-Enzyme Machinery that Coordinates Chromatin Modifications

Recent biochemical and proteomic approach has identified a CtBP super complex consisting of a host of chromatin modifying enzymes. Analysis of this complex has led to the appreciation that enzymes that mediate deacetylation and histone H3 lysine 9 methylation are present in the same biochemical comp...

CtBP Family Proteins: Unique Transcriptional Regulators in the Nucleus with Diverse Cytosolic Functions

G. Chinnadurai

CtBP family proteins are unique in animals and in plants. The invertebrates and plants contain a single CtBP family gene while vertebrates have two genes. Genetic studies in Drosophila and in mice indicate that CtBPs play pivotal roles in animal development. The vertebrate CtBPs (CtBP1 and CtBP2) ar...

CtBP Proteins in Vertebrate Development

Jeffrey D. Hildebrand

The fundamental question facing developmental biology is how the diversity of cell and tissue types that comprise a vertebrate organism can be generated from a single fertilized egg. A critical aspect of the developmental process is setting up and maintaining the differential gene expression that is...

CtBP3/BARS and Membrane Fission

Stefania Spanò, Cristina Hidalgo Carcedo and Daniela Corda

CtBP3/BARS was the third protein of the CtBP (C-terminal binding protein) family to be identified. It was initially isolated as a 50-kDa cytosolic protein during the characterisation of the molecular targets of the toxin brefeldin A (BFA). As this protein is a substrate of BFA-dependent ADP-ribosyla...