Mechanistic insights into the preference for tandem binding sites in DNA recognition by FOXM1

2021 ◽  
pp. 167426
Author(s):  
Huajun Zhang ◽  
Shuyan Dai ◽  
Xujun Liang ◽  
Jun Li ◽  
Yongheng Chen
Keyword(s):  
Binding Sites ◽  
Dna Recognition

The yeast alpha 1 and MCM1 proteins bind a single strand of their duplex DNA recognition site

1992 ◽  
Vol 12 (8) ◽  
pp. 3573-3582
Author(s):  
E J Grayhack
Keyword(s):  
Yeast Cell ◽  
Binding Sites ◽  
Dna Recognition ◽  
Binding Activity ◽  
Single Strand ◽  
Duplex Dna ◽  
Cell Type ◽  
Recognition Sequence ◽  
Binding Properties ◽  
Constitutive Factor

The yeast cell type regulator alpha 1 cooperates with a constitutive factor, MCM1 protein, to recognize the promoter and activate transcription of several alpha-specific genes. I show here that the alpha 1 and MCM1 proteins bind specifically to one of the two strands of their recognition sequence. This single-strand-binding activity shares several characteristics with the duplex-binding properties of these proteins: (i) the MCM1 protein binds alone to single-stranded and duplex sequences of both the alpha-specific (P'Q) and a-specific (P) binding sites; (ii) the alpha 1 protein requires both the MCM1 protein and the Q sequence to bind either single-stranded or duplex DNA; (iii) the alpha 1 protein stimulates binding of the MCM1 protein to both single-stranded and duplex DNAs; and (iv) the affinities of the proteins for single-stranded and duplex DNAs are comparable.

scholarly journals The yeast alpha 1 and MCM1 proteins bind a single strand of their duplex DNA recognition site.

1992 ◽  
Vol 12 (8) ◽  
pp. 3573-3582 ◽  
Author(s):  
E J Grayhack
Keyword(s):  
Yeast Cell ◽  
Binding Sites ◽  
Dna Recognition ◽  
Binding Activity ◽  
Single Strand ◽  
Duplex Dna ◽  
Cell Type ◽  
Recognition Sequence ◽  
Binding Properties ◽  
Constitutive Factor

The yeast cell type regulator alpha 1 cooperates with a constitutive factor, MCM1 protein, to recognize the promoter and activate transcription of several alpha-specific genes. I show here that the alpha 1 and MCM1 proteins bind specifically to one of the two strands of their recognition sequence. This single-strand-binding activity shares several characteristics with the duplex-binding properties of these proteins: (i) the MCM1 protein binds alone to single-stranded and duplex sequences of both the alpha-specific (P'Q) and a-specific (P) binding sites; (ii) the alpha 1 protein requires both the MCM1 protein and the Q sequence to bind either single-stranded or duplex DNA; (iii) the alpha 1 protein stimulates binding of the MCM1 protein to both single-stranded and duplex DNAs; and (iv) the affinities of the proteins for single-stranded and duplex DNAs are comparable.

TraY DNA Recognition of Its Two F Factor Binding Sites

2002 ◽  
Vol 321 (4) ◽  
pp. 563-578 ◽  
Author(s):  
Pamela L. Lum ◽  
Michael E. Rodgers ◽  
Joel F. Schildbach
Keyword(s):  
Binding Sites ◽  
Dna Recognition ◽  
Factor Binding ◽  
F Factor

scholarly journals The Rules of DNA Recognition by the Androgen Receptor

2010 ◽  
Vol 24 (5) ◽  
pp. 898-913 ◽  
Author(s):  
Sarah Denayer ◽  
Christine Helsen ◽  
Lieven Thorrez ◽  
Annemie Haelens ◽  
Frank Claessens
Keyword(s):  
Androgen Receptor ◽  
Binding Sites ◽  
Consensus Sequence ◽  
Dna Recognition ◽  
Inverted Repeats ◽  
Mineralocorticoid Receptors ◽  
Direct Repeats ◽  
Binding Motifs ◽  
Androgen Response Element ◽  
Receptor Dimer

Abstract The androgen receptor (AR) and glucocorticoid, progestagen, and mineralocorticoid receptors all recognize classical DNA response elements that are organized as inverted repeats of 5′-AGAACA-3′-like motifs with a three-nucleotide spacer. Next to such elements, the AR also recognizes a second type of androgen response element (ARE), the so-called selective AREs, which resemble more the direct repeats of the same hexamer. In this work, we show that not only the AR but also the progestagen receptor can recognize the selective AREs, whereas neither glucocorticoid nor mineralocorticoid receptor can. Recently, genomic AR-binding fragments have been postulated to contain AR-binding sites that diverge considerably from the classical ARE consensus. Extensive mutational analyses of these candidate motifs, however, reinstalls the values of the consensus sequence for the AREs as mentioned above, the importance of their dimeric nature and the presence of exactly three-nucleotide spacing. We developed a position-specific probability matrix that was used to predict with higher accuracy new AREs in different AR-binding regions. So far, all AR-binding genomic fragments that were analyzed contain AREs defined as receptor-dimer binding motifs with the ability to confer responsiveness to a reporter gene.

scholarly journals DNA recognition by splicing variants of the Wilms' tumor suppressor, WT1.

1994 ◽  
Vol 14 (6) ◽  
pp. 3800-3809 ◽  
Author(s):  
I A Drummond ◽  
H D Rupprecht ◽  
P Rohwer-Nutter ◽  
J M Lopez-Guisa ◽  
S L Madden ◽  
...  
Keyword(s):  
Growth Factor ◽  
Zinc Finger ◽  
Binding Sites ◽  
Deletion Mutant ◽  
Wilms Tumor ◽  
Zinc Fingers ◽  
Dna Recognition ◽  
Factor Ii ◽  
Splicing Variants ◽  
Recognition Elements

The Wilms' tumor suppressor, WT1, is a zinc finger transcriptional regulator which exists as multiple forms owing to alternative mRNA splicing. The most abundant splicing variants contain a nine-nucleotide insertion encoding lysine, threonine, and serine (KTS) in the H-C link region between the third and fourth WT1 zinc fingers which disrupts binding to a previously defined WT1-EGR1 binding site. We have identified WT1[+KTS] binding sites in the insulin-like growth factor II gene and show that WT1[+KTS] represses transcription from the insulin-like growth factor II P3 promoter. The highest affinity WT1[+KTS] DNA binding sites included nucleotide contacts involving all four WT1 zinc fingers. We also found that different subsets of three WT1 zinc fingers could bind to distinct DNA recognition elements. A tumor-associated, WT1 finger 3 deletion mutant was shown to bind to juxtaposed nucleotide triplets for the remaining zinc fingers 1, 2, and 4. The characterization of novel WT1 DNA recognition elements adds a new level of complexity to the potential gene regulatory activity of WT1. The results also present the possibility that altered DNA recognition by the dominant WT1 zinc finger 3 deletion mutant may contribute to tumorigenesis.

The binding of fork head proteins to DNA is partly determined by cooperation of bases

2006 ◽  
Vol 1 (4) ◽  
pp. 594-608
Author(s):  
Václav Mach
Keyword(s):  
Transcription Factors ◽  
Dna Binding ◽  
Binding Sites ◽  
In Silico ◽  
Dna Recognition ◽  
Simple Algorithm ◽  
Fork Head ◽  
Statistical Algorithm ◽  
On Line ◽  
Negative Base

AbstractOur previous study revealed that DNA recognition by the insect Fork head transcription factors depends on specific combinations of neighboring bases, a phenomenon called the base cooperation effect. This study presents a simple algorithm designed for in silico investigation of the base cooperation effect. The algorithm measures and evaluates observed and expected frequencies of various base combinations within a set of aligned binding sites. Consequently, statistically significant differences between the observed and expected frequencies are interpreted as evidence of either positive or negative base cooperation effect. Our current results suggest that the base cooperation affects DNA binding of the vertebrate members of the Fork head family, similarly to their insect homologies.The statistical algorithm used in this study is available on line (http://blast.entu.cas.cz/bias/index.htm).

scholarly journals Signatures of Protein-DNA Recognition in Free DNA Binding Sites

2009 ◽  
Vol 386 (4) ◽  
pp. 1054-1065 ◽  
Author(s):  
Jason W. Locasale ◽  
Andrew A. Napoli ◽  
Shengfeng Chen ◽  
Helen M. Berman ◽  
Catherine L. Lawson
Keyword(s):  
Dna Binding ◽  
Binding Sites ◽  
Dna Recognition ◽  
Free Dna ◽  
Dna Binding Sites
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