scholarly journals The mouse albumin enhancer contains a negative regulatory element that interacts with a novel DNA-binding protein.

1990 ◽  
Vol 10 (8) ◽  
pp. 3896-3905 ◽  
Author(s):  
R S Herbst ◽  
E M Boczko ◽  
J E Darnell ◽  
L E Babiss
Keyword(s):  
Dna Binding ◽  
Binding Sites ◽  
Regulatory Element ◽  
Regulatory Region ◽  
Cell Types ◽  
Binding Activity ◽  
Negative Region ◽  
Albumin Gene ◽  
Dna Binding Sites ◽  
Factor C

The far-upstream mouse albumin enhancer (-10.5 to -8.43 kilobases) has both positive and negative regulatory domains which contribute to the rate and tissue specificity of albumin gene transcription. (R. S. Herbst, N. Friedman, J. E. Darnell, Jr., and L. E. Babiss, Proc. Natl. Acad. Sci. USA 86:1553-1557). In this work, the negative regulatory region has been functionally localized to sequences -8.7 to -8.43 kilobases upstream of the albumin gene cap site. In the absence of the albumin-modulating region (in which there are binding sites for the transcription factor C/EBP), the negative region can suppress a neighboring positive-acting element, thereby interfering with albumin enhancer function. The negative region is also capable of negating the positive action of the heterologous transthyretin enhancer in an orientation-independent fashion. Within this negative-acting region we can detect two DNA-binding sites, both of which are recognized by a protein present in all cell types tested. This DNA-binding activity is not competed for by any of a series of known DNA-binding sites, and hence this new protein is a candidate for a role in suppressing the albumin gene in nonhepatic cells.

The mouse albumin enhancer contains a negative regulatory element that interacts with a novel DNA-binding protein

1990 ◽  
Vol 10 (8) ◽  
pp. 3896-3905
Author(s):  
R S Herbst ◽  
E M Boczko ◽  
J E Darnell ◽  
L E Babiss
Keyword(s):  
Dna Binding ◽  
Binding Sites ◽  
Regulatory Element ◽  
Regulatory Region ◽  
Cell Types ◽  
Binding Activity ◽  
Negative Region ◽  
Albumin Gene ◽  
Dna Binding Sites ◽  
Factor C

The far-upstream mouse albumin enhancer (-10.5 to -8.43 kilobases) has both positive and negative regulatory domains which contribute to the rate and tissue specificity of albumin gene transcription. (R. S. Herbst, N. Friedman, J. E. Darnell, Jr., and L. E. Babiss, Proc. Natl. Acad. Sci. USA 86:1553-1557). In this work, the negative regulatory region has been functionally localized to sequences -8.7 to -8.43 kilobases upstream of the albumin gene cap site. In the absence of the albumin-modulating region (in which there are binding sites for the transcription factor C/EBP), the negative region can suppress a neighboring positive-acting element, thereby interfering with albumin enhancer function. The negative region is also capable of negating the positive action of the heterologous transthyretin enhancer in an orientation-independent fashion. Within this negative-acting region we can detect two DNA-binding sites, both of which are recognized by a protein present in all cell types tested. This DNA-binding activity is not competed for by any of a series of known DNA-binding sites, and hence this new protein is a candidate for a role in suppressing the albumin gene in nonhepatic cells.

scholarly journals On the mechanistic nature of epistasis in a canonical cis-regulatory element

eLife ◽  
2017 ◽  
Vol 6 ◽  
Author(s):  
Mato Lagator ◽  
Tiago Paixão ◽  
Nicholas H Barton ◽  
Jonathan P Bollback ◽  
Călin C Guet
Keyword(s):  
Dna Binding ◽  
First Principles ◽  
Binding Sites ◽  
Molecular Mechanisms ◽  
Regulatory Element ◽  
Comprehensive Theory ◽  
Dna Binding Sites ◽  
Regulatory Mutations ◽  
Predictive Theory ◽  
Environmental Dependence

Understanding the relation between genotype and phenotype remains a major challenge. The difficulty of predicting individual mutation effects, and particularly the interactions between them, has prevented the development of a comprehensive theory that links genotypic changes to their phenotypic effects. We show that a general thermodynamic framework for gene regulation, based on a biophysical understanding of protein-DNA binding, accurately predicts the sign of epistasis in a canonical cis-regulatory element consisting of overlapping RNA polymerase and repressor binding sites. Sign and magnitude of individual mutation effects are sufficient to predict the sign of epistasis and its environmental dependence. Thus, the thermodynamic model offers the correct null prediction for epistasis between mutations across DNA-binding sites. Our results indicate that a predictive theory for the effects of cis-regulatory mutations is possible from first principles, as long as the essential molecular mechanisms and the constraints these impose on a biological system are accounted for.

scholarly journals A Retroviral Promoter and a Cellular Enhancer Define a Bipartite Element Which Controls env ERVWE1 Placental Expression

2004 ◽  
Vol 78 (22) ◽  
pp. 12157-12168 ◽  
Author(s):  
Sarah Prudhomme ◽  
Guy Oriol ◽  
François Mallet
Keyword(s):  
Binding Sites ◽  
Regulatory Element ◽  
Regulatory Region ◽  
Cell Types ◽  
Regulatory Elements ◽  
Site Directed Mutagenesis ◽  
Basic Activity ◽  
Flanking Sequences ◽  
High Level ◽  
Functional Analyses

ABSTRACT The HERV-W family contains hundreds of loci diversely expressed in several physiological and pathological contexts. A unique locus termed ERVWE1 encodes an envelope glycoprotein (syncytin) involved in hominoid placental physiology. Here we show that syncytin expression is regulated by a bipartite element consisting of a cyclic AMP (cAMP)-inducible long terminal repeat (LTR) retroviral promoter adjacent to a cellular enhancer conferring a high level of expression and placental tropism. Deletion mutant analysis showed that the ERVWE1 5′ LTR contains binding sites essential for basal placental activity in the region from positions +1 to +125. The region from positions +125 to +310 represents a cAMP-responsive core HERV-W promoter active in all cell types. Site-directed mutagenesis analysis highlighted the complexity of U3 regulation. ERVWE1 placenta-specific positive (e.g., T240) and negative (e.g., G71) regulatory sites were identified, as were essential sites required for basic activity (e.g., A247). The flanking sequences of the ERVWE1 provirus contain several putative regulatory elements. The upstream HERV-H and HERV-P LTRs were found to be inactive. Conversely, the 436-bp region located between the HERV-P LTR and ERVWE1 was shown to be an upstream regulatory element (URE) which is significantly active in placenta cells. This URE acts as a tissue-specific enhancer. Genetic and functional analyses of hominoid UREs revealed large differences between UREs of members of the Hominidae and the Hylobatidae. These data allowed the identification of a positive regulatory region from positions −436 to −128, a mammalian apparent LTR retrotransposon negative regulatory region from positions −128 to −67, and a trophoblast-specific enhancer (TSE) from positions −67 to −35. Putative AP-2, Sp-1, and GCMa binding sites are essential constituents of the 33-bp TSE.

scholarly journals Molecular architecture of the DNA-binding sites of the P-loop ATPases MipZ and ParA from Caulobacter crescentus

2020 ◽  
Vol 48 (9) ◽  
pp. 4769-4779 ◽  
Author(s):  
Laura Corrales-Guerrero ◽  
Binbin He ◽  
Yacine Refes ◽  
Gaël Panis ◽  
Gert Bange ◽  
...  
Keyword(s):  
Dna Binding ◽  
Binding Sites ◽  
Caulobacter Crescentus ◽  
Bioinformatic Analysis ◽  
Binding Activity ◽  
Molecular Architecture ◽  
Exchange Mass Spectrometry ◽  
Dna Binding Activity ◽  
Spatiotemporal Regulation ◽  
Dna Binding Sites

Abstract The spatiotemporal regulation of chromosome segregation and cell division in Caulobacter crescentus is mediated by two different P-loop ATPases, ParA and MipZ. Both of these proteins form dynamic concentration gradients that control the positioning of regulatory targets within the cell. Their proper localization depends on their nucleotide-dependent cycling between a monomeric and a dimeric state and on the ability of the dimeric species to associate with the nucleoid. In this study, we use a combination of genetic screening, biochemical analysis and hydrogen/deuterium exchange mass spectrometry to comprehensively map the residues mediating the interactions of MipZ and ParA with DNA. We show that MipZ has non-specific DNA-binding activity that relies on an array of positively charged and hydrophobic residues lining both sides of the dimer interface. Extending our analysis to ParA, we find that the MipZ and ParA DNA-binding sites differ markedly in composition, although their relative positions on the dimer surface and their mode of DNA binding are conserved. In line with previous experimental work, bioinformatic analysis suggests that the same principles may apply to other members of the P-loop ATPase family. P-loop ATPases thus share common mechanistic features, although their functions have diverged considerably during the course of evolution.

scholarly journals Analysis of two distinct single-stranded DNA binding sites on the recA nucleoprotein filament.

1993 ◽  
Vol 268 (30) ◽  
pp. 22525-22530
Author(s):  
A Zlotnick ◽  
R.S. Mitchell ◽  
R.K. Steed ◽  
S.L. Brenner
Keyword(s):  
Dna Binding ◽  
Binding Sites ◽  
Single Stranded Dna ◽  
Dna Binding Sites

Identification of single-stranded-DNA-binding proteins that interact with muscle gene elements

1991 ◽  
Vol 11 (4) ◽  
pp. 1944-1953
Author(s):  
I M Santoro ◽  
T M Yi ◽  
K Walsh
Keyword(s):  
Dna Binding ◽  
Binding Proteins ◽  
Regulatory Element ◽  
Dna Binding Proteins ◽  
Binding Activity ◽  
Sequence Motif ◽  
Mobility Shift ◽  
Specific Sequence ◽  
Single Stranded Dna ◽  
Muscle Gene

A sequence-specific DNA-binding protein from skeletal-muscle extracts that binds to probes of three muscle gene DNA elements is identified. This protein, referred to as muscle factor 3, forms the predominant nucleoprotein complex with the MCAT gene sequence motif in an electrophoretic mobility shift assay. This protein also binds to the skeletal actin muscle regulatory element, which contains the conserved CArG motif, and to a creatine kinase enhancer probe, which contains the E-box motif, a MyoD-binding site. Muscle factor 3 has a potent sequence-specific, single-stranded-DNA-binding activity. The specificity of this interaction was demonstrated by sequence-specific competition and by mutations that diminished or eliminated detectable complex formation. MyoD, a myogenic determination factor that is distinct from muscle factor 3, also bound to single-stranded-DNA probes in a sequence-specific manner, but other transcription factors did not. Multiple copies of the MCAT motif activated the expression of a heterologous promoter, and a mutation that eliminated expression was correlated with diminished factor binding. Muscle factor 3 and MyoD may be members of a class of DNA-binding proteins that modulate gene expression by their abilities to recognize DNA with unusual secondary structure in addition to specific sequence.

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