Begell House Inc.
Critical Reviews™ in Eukaryotic Gene Expression
CRE
1045-4403
4
2-3
1994
A Compilation and Classification of DNA Binding Sites for Protein Transcription Factors from Vertebrates
117-321
10.1615/CritRevEukarGeneExpr.v4.i2-3.10
Teni
Boulikas
Institute of Molecular Medical Sciences, 460 Page Mill Road, Palo Alto, California 94306
transcription factors
protein-DNA interactions
enhancers
promoters
regulatory sequences
MARs
nucleosomes
steroid hormone receptors
Ets-1
Ap-1
HMG proteins
HNF-1
C/EBP.
The field of protein transcription regulators and their DNA sequence specificity has been the most rapidly expanding in the last few years. The concerted interplay of protein transcription factors on the regulatory regions of eukaryotic genes (promoters, enhancers, origins of replication, silencers, and matrix-attached regions) regulates transcription levels; the differential activity of genes during development and the cell cycle, between cell types, and in response to physiological stimuli results from interdigitation of regulatory circuits controlling transcription initiation, finely tuned by the relative amounts of protein factors synthesized in a cell type, their phosphorylation, isoforms within factor families, the way protein regulators are brought in contact with one another through the patchwork of their cognate sites on the regulatory regions of genes, and by regulation of their nuclear import. The varying affinity of the same factor for its cognate DNA in different promoters can also be modulated by the type of proteins it is brought into contact with, by one or more nucleotide changes in its binding sites among promoters, and by the chromatin structure.
The classification of protein transcriptional regulators attempted here according to their DNA binding specificity into those that bind AT-, GC-, GA, TG-rich and mixed motif has one obvious advantage: different protein factors that bind to the same DNA sequence will be found within the same class. In addition, this classification has allowed us to discern a class of transcriptional regulators whose binding site consists of a GA-and a CT-rich moiety; no other two pairs of dinucleotides compose a major class of factor sites. Special tribute has been paid to each individual gene that is regulated by a given transcription factor.
Control of Tumor Necrosis Factor Gene Expression
323-344
10.1615/CritRevEukarGeneExpr.v4.i2-3.20
Urs
Pauli
Institute of Veterinary Virology, University of Bern, Laenggass-Str. 122, 3012 Bern, Switzerland
regulation of transcription
promoter elements
5' and 3' flanking sequences
chromatin structure
mRNA stability
This review summarizes the known data about transcriptional control of the tumor necrosis factor genes. Mechanisms of transcriptional induction of TNF gene expression and the influences of regulatory elements in the promter and in the 3' flanking regions are discussed. Posttranscriptional events that influence regulation of TNF gene expression such as destabilization of mRNA are described. The influence of chromatin structure and possible functional implications are also reported. Although their biological effects largely overlap, it is concluded that the TNFα and TNFβ genes are differently regulated at the transcriptional level.
Expression of the BMP 2 Gene during Bone Cell Differentiation
345-355
10.1615/CritRevEukarGeneExpr.v4.i2-3.30
Nandini
Ghosh-Choudhury
University of Texas Health Science Center at San Antonio, Department of Medicine, Division of Endocrinology and Metabolism, San Antonio, TX 78284-7877
Marie A.
Harris
University of Texas Health Science Center at San Antonio, Department of Medicine, Division of Endocrinology and Metabolism, San Antonio, TX 78284-7877
Jian Q.
Feng
University of Texas Health Science Center at San Antonio, Department of Medicine, Division of Endocrinology and Metabolism, San Antonio, TX 78284-7877
Gregory R.
Mundy
Division of Endocrinology, Department of Medicine, University of Texas Health Science Center, San Antonio, TX
Stephen E.
Harris
University of Texas Health Science Center at San Antonio, Department of Medicine, Division of Endocrinology and Metabolism, San Antonio, TX 78284-7877
bone morphogenetic proteins
BMP 2 promoter
TGFβ
transgenic bone cell lines.
Bone morphogenetic protein 2 (BMP 2) and transforming growth factor β (TGFβ) are actively involved in bone formation and remodeling. TGFβ, a powerful stimulant in the early stage of bone cell growth and matrix formation, inhibits differentiation and in vitro mineralized nodule formation in primary fetal rat calvarial osteoblast system. TGFβ also negatively regulates BMP 2 expression at the transcriptional level. BMP 2 gene expression is controlled by a battery of transcriptional factors, some known and some yet to be identified. Immortalized osteoblast cell lines generated from a transgenic mouse carrying BMP 2 promoter-driven SV40 large T antigen transgene are described as powerful tools for studying regulation of BMP 2 gene expression and bone cell differentiation at the molecular level.