Genomic footprinting

2016 ◽  
Vol 13 (3) ◽  
pp. 213-221 ◽  
Author(s):  
Jeff Vierstra ◽  
John A Stamatoyannopoulos
Keyword(s):  
Genomic Footprinting

Genomic footprinting: detection of putative regulatory proteins in the promoter region of the interferon alpha-1 gene in normal human tissues

1990 ◽  
Vol 10 (6) ◽  
pp. 2554-2561
Author(s):  
M Palmieri ◽  
M G Tovey
Keyword(s):  
Promoter Region ◽  
Dimethyl Sulfate ◽  
Deletion Analysis ◽  
Regulatory Proteins ◽  
Dna Interactions ◽  
Human Spleen ◽  
Ifn Alpha ◽  
Protein Dna Interactions ◽  
Normal Human ◽  
Genomic Footprinting

Dimethyl sulfate (DMS) genomic footprinting revealed the presence of putative regulatory proteins attached to specific sequences of the promoter region of the interferon (IFN) alpha-1 gene in normal human tissue. The pattern of protein-DNA interactions observed for the human alpha-1 promoter in freshly isolated human spleen cells was identical to that seen in DNA from the B-cell line Namalwa. The protein interactions involving the human IFN alpha-1 promoter spanned a region from positions -38 to -174 relative to the cap site which encompasses that part of the IFN alpha-1 promoter previously shown by deletion analysis to confer virus inducibility on the IFN alpha-1 gene. DNase I footprinting performed on isolated nuclei revealed a pattern of protein-DNA interactions for the promoter region of the IFN alpha-1 gene similar to that obtained with DMS footprinting performed on whole cells, with the appearance or disappearance of only a few additional protected nucleotides outside the region identified by the use of DMS. These results provide the first direct evidence for the presence of proteins bound in vivo to those parts of the IFN alpha-1 promoter between positions -64 and -109 previously shown by deletion analysis to confer virus inducibility on the IFN alpha-1 gene. The pattern of protein-DNA interactions observed for the IFN alpha-1 promoter after virus induction was identical to that seen before induction, in keeping with the finding that many transcriptional activators are present in both induced and uninduced cells.

Genomic footprinting of proteins interacting with the chicken lysozome promoter

Gene ◽  
1990 ◽  
Vol 95 (2) ◽  
pp. 187-193 ◽  
Author(s):  
Albert Dölle ◽  
Wolf H. Strätling
Keyword(s):  
Genomic Footprinting

scholarly journals Genomic footprinting of the yeast zinc finger protein Rme1p and its roles in repression of the meiotic activator IME1

1998 ◽  
Vol 26 (10) ◽  
pp. 2329-2336 ◽  
Author(s):  
M. Shimizu ◽  
W. Li ◽  
P. A. Covitz ◽  
M. Hara ◽  
H. Shindo ◽  
...  
Keyword(s):  
Zinc Finger ◽  
Zinc Finger Protein ◽  
Finger Protein ◽  
Genomic Footprinting

scholarly journals MCM2–7 Proteins Are Essential Components of Prereplicative Complexes that Accumulate Cooperatively in the Nucleus during G1-phase and Are Required to Establish, But Not Maintain, the S-phase Checkpoint

2001 ◽  
Vol 12 (11) ◽  
pp. 3658-3667 ◽  
Author(s):  
Karim Labib ◽  
Stephen E. Kearsey ◽  
John F.X. Diffley
Keyword(s):  
Chromosome Replication ◽  
S Phase ◽  
G1 Phase ◽  
Checkpoint Control ◽  
Direct Role ◽  
Essential Components ◽  
Mcm Proteins ◽  
Prereplicative Complex ◽  
Genomic Footprinting ◽  
Checkpoint Signal

A prereplicative complex (pre-RC) of proteins is assembled at budding yeast origins of DNA replication during the G1-phase of the cell cycle, as shown by genomic footprinting. The proteins responsible for this prereplicative footprint have yet to be identified but are likely to be involved in the earliest stages of the initiation step of chromosome replication. Here we show that MCM2–7 proteins are essential for both the formation and maintenance of the pre-RC footprint at the origin ARS305. It is likely that pre-RCs contain heteromeric complexes of MCM2–7 proteins, since degradation of Mcm2, 3, 6, or 7 during G1-phase, after pre-RC formation, causes loss of Mcm4 from the nucleus. It has been suggested that pre-RCs on unreplicated chromatin may generate a checkpoint signal that inhibits premature mitosis during S-phase. We show that, although mitosis does indeed occur in the absence of replication if MCM proteins are degraded during G1-phase, anaphase is prevented if MCMs are degraded during S-phase. Our data indicate that pre-RCs do not play a direct role in checkpoint control during chromosome replication.

scholarly journals Genomic footprinting reveals cell type-specific DNA binding of ubiquitous factors

Cell ◽  
1987 ◽  
Vol 51 (3) ◽  
pp. 435-443 ◽  
Author(s):  
Peter B. Becker ◽  
Siegfried Ruppert ◽  
Günther Schütz
Keyword(s):  
Dna Binding ◽  
Cell Type ◽  
Cell Type Specific ◽  
Genomic Footprinting

scholarly journals Genomic footprinting of a yeast tRNA gene reveals stable complexes over the 5'-flanking region.

1989 ◽  
Vol 9 (8) ◽  
pp. 3244-3252 ◽  
Author(s):  
J M Huibregtse ◽  
D R Engelke
Keyword(s):  
Stationary Phase ◽  
Transcription Initiation ◽  
Initiation Site ◽  
Dnase I ◽  
Transcription Initiation Site ◽  
Upstream Region ◽  
Stable Complex ◽  
Coding Region ◽  
Flanking Region ◽  
Genomic Footprinting

We have shown by genomic footprinting that the 5'-flanking region of the Saccharomyces cerevisiae tRNASUP53 gene is protected from DNase I digestion. The protected region has a 5' boundary at -40 (relative to the transcription initiation site) and extends into the coding region of the gene, with a 3' boundary at approximately +15. Although the DNase I protection over this region was much greater than at the A- and B-box internal promoters, point mutations within the A or B box that reduced transcription in vitro eliminated the upstream DNase I protection. This implies that formation of a stable complex over the 5'-flanking region is dependent on interaction of the gene with transcription factor IIIC but that stability of the complex may not require continued interaction with this factor. The DNase I protection under varied growth conditions further suggested that the upstream complex is composed of two or more components. The region over the transcription initiation site (approximately +15 to -10) was less protected in stationary-phase cultures, whereas the more upstream region (approximately -10 to -40) was protected in both exponential- and stationary-phase cultures.

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