scholarly journals Natural selection driven by DNA binding proteins shapes genome-wide motif statistics

2016 ◽  
Author(s):  
Long Qian ◽  
Edo Kussell
Keyword(s):  
Transcription Factors ◽  
Dna Binding ◽  
Binding Proteins ◽  
Dna Binding Proteins ◽  
Large Collection ◽  
Functional Sites ◽  
Genome Wide ◽  
A Genome ◽  
Global Selection

AbstractEctopic DNA binding by transcription factors and other DNA binding proteins can be detrimental to cellular functions and ultimately to organismal fitness. The frequency of protein-DNA binding at non-functional sites depends on the global composition of a genome with respect to all possible short motifs, or k-mer words. To determine whether weak yet ubiquitous protein-DNA interactions could exert significant evolutionary pressures on genomes, we correlate in vitro measurements of binding strengths on all 8-mer words from a large collection of transcription factors, in several different species, against their relative genomic frequencies. Our analysis reveals a clear signal of purifying selection to reduce the large number of weak binding sites genome-wide. This evolutionary process, which we call global selection, has a detectable hallmark in that similar words experience similar evolutionary pressure, a consequence of the biophysics of protein-DNA binding. By analyzing a large collection of genomes, we show that global selection exists in all domains of life, and operates through tiny selective steps, maintaining genomic binding landscapes over long evolutionary timescales.

scholarly journals Multiple sequence-specific transcription factors modulate cytomegalovirus enhancer activity in vitro.

1988 ◽  
Vol 8 (4) ◽  
pp. 1809-1811 ◽  
Author(s):  
P Ghazal ◽  
H Lubon ◽  
L Hennighausen
Keyword(s):  
Transcription Factors ◽  
Dna Binding ◽  
Human Cytomegalovirus ◽  
Binding Proteins ◽  
Dna Binding Proteins ◽  
Competition Assay ◽  
Multiple Sequence ◽  
Enhancer Activity ◽  
Enhancer Sequences

The possibility of DNA-binding proteins interacting in vitro with the polymerase II transcriptional machinery was explored by using a competition assay with individual target sequences for enhancer-binding factors. Transcription factors binding to at least five specific enhancer sequences mediate the activity of the human cytomegalovirus immediate-early 1 gene in vitro. Furthermore, our data suggest that individual DNA-bound enhancer factors can interact with the promoter transcription complex.

scholarly journals Multiple sequence-specific transcription factors modulate cytomegalovirus enhancer activity in vitro

1988 ◽  
Vol 8 (4) ◽  
pp. 1809-1811
Author(s):  
P Ghazal ◽  
H Lubon ◽  
L Hennighausen
Keyword(s):  
Transcription Factors ◽  
Dna Binding ◽  
Human Cytomegalovirus ◽  
Binding Proteins ◽  
Dna Binding Proteins ◽  
Competition Assay ◽  
Multiple Sequence ◽  
Enhancer Activity ◽  
Enhancer Sequences

The possibility of DNA-binding proteins interacting in vitro with the polymerase II transcriptional machinery was explored by using a competition assay with individual target sequences for enhancer-binding factors. Transcription factors binding to at least five specific enhancer sequences mediate the activity of the human cytomegalovirus immediate-early 1 gene in vitro. Furthermore, our data suggest that individual DNA-bound enhancer factors can interact with the promoter transcription complex.

scholarly journals Photoaffinity labeling of transcription factors by DNA-templated crosslinking

2015 ◽  
Vol 6 (1) ◽  
pp. 745-751 ◽  
Author(s):  
Ying Liu ◽  
Wenlu Zheng ◽  
Wan Zhang ◽  
Nan Chen ◽  
Yang Liu ◽  
...  
Keyword(s):  
Transcription Factors ◽  
Dna Binding ◽  
Binding Site ◽  
Binding Proteins ◽  
Photoaffinity Labeling ◽  
Dna Binding Proteins ◽  
Probe System ◽  
Dual Probe

A dual-probe system can specifically capture DNA-binding proteins with an unmodified binding site.

scholarly journals Regulation of Transcription by Hypoxia Requires a Multiprotein Complex That Includes Hypoxia-Inducible Factor 1, an Adjacent Transcription Factor, and p300/CREB Binding Protein

1998 ◽  
Vol 18 (7) ◽  
pp. 4089-4096 ◽  
Author(s):  
Benjamin L. Ebert ◽  
H. Franklin Bunn
Keyword(s):  
Transcription Factor ◽  
Transcription Factors ◽  
Dna Binding ◽  
Binding Proteins ◽  
Binding Protein ◽  
Hypoxia Inducible Factor ◽  
Dna Binding Proteins ◽  
Creb Binding Protein ◽  
Multiprotein Complex ◽  
Hypoxia Inducible Factor 1

ABSTRACT Molecular adaptation to hypoxia depends on the binding of hypoxia-inducible factor 1 (HIF-1) to cognate response elements in oxygen-regulated genes. In addition, adjacent sequences are required for hypoxia-inducible transcription. To investigate the mechanism of interaction between these cis-acting sequences, the multiprotein complex binding to the lactate dehydrogenase A (LDH-A) promoter was characterized. The involvement of HIF-1, CREB-1/ATF-1, and p300/CREB binding protein (CBP) was demonstrated by techniques documenting in vitro binding, in combination with transient transfections that test the in vivo functional importance of each protein. In both the LDH-A promoter and the erythropoietin 3′ enhancer, formation of multiprotein complexes was analyzed by using biotinylated probes encompassing functionally critical cis-acting sequences. Strong binding of p300/CBP required interactions with multiple DNA binding proteins. Thus, the necessity of transcription factor binding sites adjacent to a HIF-1 site for hypoxically inducible transcription may be due to the requirement of p300 to interact with multiple transcription factors for high-affinity binding and activation of transcription. Since it has been found to interact with a wide range of transcription factors, p300 is likely to play a similar role in other genes, mediating interactions between DNA binding proteins, thereby activating stimulus-specific and tissue-specific gene transcription.

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