We also compare the DNA-binding properties of the three best-studied type 11 DNA-binding proteins, Escherichia coli HU, E. coli integration host factor, and TF1, and discuss them in the context of the structure and properties of chromatin in prokaryotes....
Table S4. DNA Shape Profiles for TF1- and TF2-Preferred Sites, for All TF Pairs in This Study, Related to Figure 4 Table S5. ChIP-Seq Data and iMADS Predictions Used in the Comparative Analyses of Differential In-Vivo -Binding- versus In-Vivo -Binding-Preferences Predictions, Related to ...
Under stress condition and prolonged competition, Tf1 integration was beneficial to its host by creating a pool of new alleles, linked to TOR and other stress response pathways. Similarly, in wild isolates of S. pombe integration clustered next to genes important for sporulation efficiency and heat...
The significance of overlap between TF-pairs determined by pY1H assays and those presenting ChIP-seq peaks within the same promoter was evaluated by a network randomization analysis. First, we built a directed network graph where the source node was (TF1–TF2), and the target node was cytokine...
Natural mitochondrial DNA (mtDNA) mutations enable the inference of clonal relationships among cells. mtDNA can be profiled along with measures of cell state, but has not yet been combined with the massively parallel approaches needed to tackle the compl
replication fork barrier. He used an elegant two-plasmid transposition assay to determine that Sap1 is important, but not necessary, for targeting Tf1 insertion, and that the fork barrier activity of Sap1 binding sites is an important secondary requirement for Tf1 transposition at stalled ...
These factors are involved in transcriptional regulation not only by binding to the promoter region of DNA with sequence specificity but also by interacting with one another on DNA. It has also been revealed that some factors bind to DNA indirectly to regulate transcription. These factors, which ...
A fission yeast TE termedTf1is a retrotransposon prevailing in the specific yeast genome.Tf1insertion predominantly occurs closer to the 5′ end of genes, in regions known to have relatively open chromatin [78,79]. These studies clearly argue for the relationships between open chromatin and prefere...
m.h. sayre et al. effects of mutations at amino acid 61 in the arm of tf1 on its dna-binding properties j. mol. biol. (1990) f. saitoh et al. arginine-55 in the beta-arm is essential for the activity of dna-binding protein hu from bacillus stearothermophilus biosci. biotechnol. ...
TF1 cells require GM-CSF for proliferation and will undergo differentiation down the erythroid lineage upon exposure to EPO. However, with expression of mutant WT1, TF1 cells failed to upregulate fetal hemoglobin upon exposure to EPO (supplemental Figure 5E), indicating that expression of mutant WT1...