In Vivo Footprinting of a Muscle Specific Enhancer by Ligation Mediated PCR

Science ◽  
1990 ◽  
pp. 802-802
Author(s):  
P. R. Mueller ◽  
B. Wold
Keyword(s):  
In Vivo Footprinting

In Vivo Footprinting of the Interaction of Proteins with DNA and RNA

1997 ◽  
pp. 73-109 ◽  
Author(s):  
Thierry Grange ◽  
Gildas Rigaud ◽  
Edouard Bertrand ◽  
Micheline Fromont-Racine ◽  
Maria Lluisa Espinás ◽  
...  
Keyword(s):  
Dna And Rna ◽  
In Vivo Footprinting

Cytokine-induced changes in chromatin structure and in vivo footprints in the inducible NOS promoter

2001 ◽  
Vol 280 (3) ◽  
pp. L390-L399 ◽  
Author(s):  
Jane K. Mellott ◽  
Harry S. Nick ◽  
Michael F. Waters ◽  
Timothy R. Billiar ◽  
David A. Geller ◽  
...  
Keyword(s):  
Epithelial Cells ◽  
Protein Interactions ◽  
Molecular Mechanisms ◽  
Cell Types ◽  
Specific Pattern ◽  
Mrna Levels ◽  
Inos Gene ◽  
In Vivo Footprinting ◽  
Induced Changes

Transcription of the human inducible nitric oxide synthase ( iNOS) gene is regulated by inflammatory cytokines in a tissue-specific manner. To determine whether differences in cytokine-induced mRNA levels between pulmonary epithelial cells (A549) and hepatic biliary epithelial cells (AKN-1) result from different protein or DNA regulatory mechanisms, we identified cytokine-induced changes in DNase I-hypersensitive (HS) sites in 13 kb of the iNOS 5′-flanking region. Data showed both constitutive and inducible HS sites in an overlapping yet cell type-specific pattern. Using in vivo footprinting and ligation-mediated PCR to detect potential DNA or protein interactions, we examined one promoter region near −5 kb containing both constitutive and cytokine-induced HS sites. In both cell types, three in vivo footprints were present in both control and cytokine-treated cells, and each mapped within a constitutive HS site. The remaining footprint appeared only in response to cytokine treatment and mapped to an inducible HS site. These studies, performed on chromatin in situ, identify a portion of the molecular mechanisms regulating transcription of the human iNOS gene in both lung- and liver-derived epithelial cells.

Genomic sequencing and in vivo footprinting

1989 ◽  
Vol 176 (2) ◽  
pp. 201-208 ◽  
Author(s):  
H.P. Saluz ◽  
J.P. Jost
Keyword(s):  
Genomic Sequencing ◽  
In Vivo Footprinting

scholarly journals In vivo footprinting and high-resolution methylation analysis of the mouse hypoxanthine phosphoribosyltransferase gene 5' region on the active and inactive X chromosomes.

1996 ◽  
Vol 16 (11) ◽  
pp. 6190-6199 ◽  
Author(s):  
M D Litt ◽  
I K Hornstra ◽  
T P Yang
Keyword(s):  
High Resolution ◽  
X Chromosome ◽  
X Chromosome Inactivation ◽  
Chromosome Inactivation ◽  
Genomic Sequencing ◽  
Hypoxanthine Phosphoribosyltransferase ◽  
Hprt Gene ◽  
Methylation Analysis ◽  
In Vivo Footprinting

To investigate potential mechanisms regulating the hypoxanthine phosphoribosyltransferase (HPRT) gene by X-chromosome inactivation, we performed in vivo footprinting and high-resolution DNA methylation analysis on the 5' region of the active and inactive mouse HPRT alleles and compared these results with those from the human HPRT gene. We found multiple footprinted sites on the active mouse HPRT allele and no footprints on the inactive allele. Comparison of the footprint patterns of the mouse and human HPRT genes demonstrated that the in vivo binding of regulatory proteins between these species is generally conserved but not identical. Detailed nucleotide sequence comparison of footprinted regions in the mouse and human genes revealed a novel 9-bp sequence associated with transcription factor binding near the transcription sites of both genes, suggesting the identification of a new conserved initiator element. Ligation-mediated PCR genomic sequencing showed that all CpG dinucleotides examined on the active allele are unmethylated, while the majority of CpGs on the inactive allele are methylated and interspersed with a few hypomethylated sites. This pattern of methylation on the inactive mouse allele is notably different from the unusual methylation pattern of the inactive human gene, which exhibited strong hypomethylation specifically at GC boxes. These studies, in conjunction with other genomic sequencing studies of X-linked genes, demonstrate that (i) the active alleles are essentially unmethylated, (ii) the inactive alleles are hypermethylated, and (iii) the high-resolution methylation patterns of the hypermethylated inactive alleles are not strictly conserved. There is no obvious correlation between the pattern of methylated sites on the inactive alleles and the pattern of binding sites for transcription factors on the active alleles. These results are discussed in relationship to potential mechanisms of transcriptional regulation by X-chromosome inactivation.

In vivo footprinting studies suggest a role for chromatin in transcription of the human 7SK gene

Gene ◽  
2000 ◽  
Vol 247 (1-2) ◽  
pp. 33-44 ◽  
Author(s):  
Diana C Boyd ◽  
Ingo H Greger ◽  
Shona Murphy
Keyword(s):  
In Vivo Footprinting

scholarly journals Activation of Escherichia coli rRNA Transcription by FIS during a Growth Cycle

1998 ◽  
Vol 180 (6) ◽  
pp. 1525-1532 ◽  
Author(s):  
J. Alex Appleman ◽  
Wilma Ross ◽  
Julia Salomon ◽  
Richard L. Gourse
Keyword(s):  
Escherichia Coli ◽  
Site Occupancy ◽  
Growth Conditions ◽  
Growth Cycle ◽  
Rrna Synthesis ◽  
Rrna Transcription ◽  
Low Culture ◽  
State Growth ◽  
In Vivo Footprinting

ABSTRACT rRNA transcription in Escherichia coli is activated by the FIS protein, which binds upstream of rrnp 1promoters and interacts directly with RNA polymerase. Analysis of the contribution of FIS to rrn transcription under changing physiological conditions is complicated by several factors: the wide variation in cellular FIS concentrations with growth conditions, the contributions of several other regulatory systems to rRNA synthesis, and the pleiotropy of fis mutations. In this report, we show by in vivo footprinting and Western blot analysis that occupancy of the rrnBp 1 FIS sites correlates with cellular levels of FIS. We find, using two methods of measurement (pulse induction of a FIS-activated hybrid promoter and primer extension from an unstable transcript made fromrrnBp 1), that the extent of transcription activation by FIS parallels the degree of FIS site occupancy and therefore cellular FIS levels. FIS activates transcription throughout exponential growth at low culture density, butrrnp 1 transcription increases independently of FIS immediately following upshift, before FIS accumulates. These results support the model that FIS is one of a set of overlapping signals that together contribute to transcription fromrrnp 1 promoters during steady-state growth.

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