The Ah Receptor Recognizes DNA Binding Sites for the B Cell Transcription Factor, BSAP: A Possible Mechanism for Dioxin-Mediated Alteration of CD19 Gene Expression in Human B Lymphocytes

1995 ◽  
Vol 212 (1) ◽  
pp. 27-34 ◽  
Author(s):  
S.A. Masten ◽  
K.T. Shiverick
Keyword(s):  
Gene Expression ◽  
Transcription Factor ◽  
Dna Binding ◽  
B Cell ◽  
B Lymphocytes ◽  
Binding Sites ◽  
Ah Receptor ◽  
Dna Binding Sites

ERP, a new member of the ets transcription factor/oncoprotein family: cloning, characterization, and differential expression during B-lymphocyte development

1994 ◽  
Vol 14 (5) ◽  
pp. 3292-3309
Author(s):  
M Lopez ◽  
P Oettgen ◽  
Y Akbarali ◽  
U Dendorfer ◽  
T A Libermann
Keyword(s):  
Transcription Factor ◽  
Dna Binding ◽  
Gene Family ◽  
B Cell ◽  
Binding Sites ◽  
B Lymphocyte ◽  
Striking Similarity ◽  
Lymphocyte Development ◽  
B Lymphocyte Development ◽  
Ets Transcription Factor

The ets gene family encodes a group of proteins which function as transcription factors under physiological conditions and, if aberrantly expressed, can cause cellular transformation. We have recently identified two regulatory elements in the murine immunoglobulin heavy-chain (IgH) enhancer, pi and microB, which exhibit striking similarity to binding sites for ets-related proteins. To identify ets-related transcriptional regulators expressed in pre-B lymphocytes that may interact with either the pi or the microB site, we have used a PCR approach with degenerate oligonucleotides encoding conserved sequences in all members of the ets family. We have cloned the gene for a new ets-related transcription factor, ERP (ets-related protein), from the murine pre-B cell line BASC 6C2 and from mouse lung tissue. The ERP protein contains a region of high homology with the ETS DNA-binding domain common to all members of the ets transcription factor/oncoprotein family. Three additional smaller regions show homology to the ELK-1 and SAP-1 genes, a subgroup of the ets gene family that interacts with the serum response factor. Full-length ERP expresses only negligible DNA-binding activity by itself. Removal of the carboxy terminus enables ERP to interact with a variety of ets-binding sites including the E74 site, the IgH enhancer pi site, and the lck promoter ets site, suggesting a carboxy-terminal negative regulatory domain. At least three ERP-related transcripts are expressed in a variety of tissues. However, within the B-cell lineage, ERP is highly expressed primarily at early stages of B-lymphocyte development, and expression declines drastically upon B-cell maturation, correlating with the enhancer activity of the IgH pi site. These data suggest that ERP might play a role in B-cell development and in IgH gene regulation.

scholarly journals Accurate and sensitive quantification of protein-DNA binding affinity

2018 ◽  
Vol 115 (16) ◽  
pp. E3692-E3701 ◽  
Author(s):  
Chaitanya Rastogi ◽  
H. Tomas Rube ◽  
Judith F. Kribelbauer ◽  
Justin Crocker ◽  
Ryan E. Loker ◽  
...  
Keyword(s):  
Gene Expression ◽  
Dna Binding ◽  
Binding Sites ◽  
Biophysical Model ◽  
Regulatory Sequences ◽  
Binding Modes ◽  
Perfect Agreement ◽  
Dna Binding Sites

Transcription factors (TFs) control gene expression by binding to genomic DNA in a sequence-specific manner. Mutations in TF binding sites are increasingly found to be associated with human disease, yet we currently lack robust methods to predict these sites. Here, we developed a versatile maximum likelihood framework named No Read Left Behind (NRLB) that infers a biophysical model of protein-DNA recognition across the full affinity range from a library of in vitro selected DNA binding sites. NRLB predicts human Max homodimer binding in near-perfect agreement with existing low-throughput measurements. It can capture the specificity of the p53 tetramer and distinguish multiple binding modes within a single sample. Additionally, we confirm that newly identified low-affinity enhancer binding sites are functional in vivo, and that their contribution to gene expression matches their predicted affinity. Our results establish a powerful paradigm for identifying protein binding sites and interpreting gene regulatory sequences in eukaryotic genomes.

scholarly journals Intermolecular epistasis shaped the function and evolution of an ancient transcription factor and its DNA binding sites

eLife ◽  
2015 ◽  
Vol 4 ◽  
Author(s):  
Dave W Anderson ◽  
Alesia N McKeown ◽  
Joseph W Thornton
Keyword(s):  
Transcription Factor ◽  
Dna Binding ◽  
Binding Sites ◽  
Steroid Hormone Receptor ◽  
Biological Processes ◽  
Epistatic Interactions ◽  
Dna Binding Sites ◽  
Evolutionary Paths ◽  
Historical Transition ◽  
Transcription Factor Proteins

Complexes of specifically interacting molecules, such as transcription factor proteins (TFs) and the DNA response elements (REs) they recognize, control most biological processes, but little is known concerning the functional and evolutionary effects of epistatic interactions across molecular interfaces. We experimentally characterized all combinations of genotypes in the joint protein-DNA sequence space defined by an historical transition in TF-RE specificity that occurred some 500 million years ago in the DNA-binding domain of an ancient steroid hormone receptor. We found that rampant epistasis within and between the two molecules was essential to specific TF-RE recognition and to the evolution of a novel TF-RE complex with unique derived specificity. Permissive and restrictive epistatic mutations across the TF-RE interface opened and closed potential evolutionary paths accessible by the other, making the evolution of each molecule contingent on its partner's history and allowing a molecular complex with novel specificity to evolve.

scholarly journals The CREB Site in the Proximal Enhancer Is Critical for Cooperative Interaction with the Other Transcription Factor Binding Sites To Enhance Transcription of the Major Intermediate-Early Genes in Human Cytomegalovirus-Infected Cells

2009 ◽  
Vol 83 (17) ◽  
pp. 8893-8904 ◽  
Author(s):  
Philip Lashmit ◽  
Shuhui Wang ◽  
Hongmei Li ◽  
Hiroki Isomura ◽  
Mark F. Stinski
Keyword(s):  
Transcription Factor ◽  
Dna Binding ◽  
Human Cytomegalovirus ◽  
Binding Sites ◽  
Human Fibroblast ◽  
The Other ◽  
Cooperative Interaction ◽  
Independent Effect ◽  
Viral Gene ◽  
Dna Binding Sites

ABSTRACT One of the two SP1 sites in the proximal enhancer of the human cytomegalovirus (HCMV) major immediate-early (MIE) promoter is essential for transcription in human fibroblast cells (H. Isomura, M. F. Stinski, A. Kudoh, T. Daikoku, N. Shirata, and T. Tsurumi, J. Virol. 79:9597-9607, 2005). Upstream of the two SP1 sites to −223 relative to the +1 transcription start site, there are an additional five DNA binding sites for eukaryotic transcription factors. We determined the effects of the various transcription factor DNA binding sites on viral MIE RNA transcription, viral gene expression, viral DNA synthesis, or infectious virus production. We prepared recombinant HCMV bacterial artificial chromosome (BAC) DNAs with either one site missing or one site present upstream of the two SP1 sites. Infectious recombinant HCMV BAC DNAs were transfected into various cell types to avoid the effect of the virion-associated transactivators. Regardless of the cell type, which included human fibroblast, endothelial, and epithelial cells, the CREB site had the most significant and independent effect on the MIE promoter. The other sites had a minor independent effect. However, the combination of the different transcription factor DNA binding sites was significantly stronger than multiple duplications of the CREB site. These findings indicate that the CREB site in the presence of the other sites has a major role for the replication of HCMV.

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