How do you identify a transcription factor binding site?
Prediction of transcription factor binding sites is generally performed by scanning a DNA sequence of interest with a position weight matrix (PWM) for a transcription factor of interest [6, 7] and various pattern-matching tools have been developed for this purpose.
What is the difference between Stat5a and Stat5b?
Stat5a and Stat5b are discretely encoded transcription factors that mediate signals for a broad spectrum of cytokines. Prolactin-directed mammary gland maturation fails without functional Stat5a, while disruption of Stat5b in males mitigates growth hormone effects on hepatic function and body mass.
What sites do transcription factors bind to?
Some transcription factors bind to a DNA promoter sequence near the transcription start site and help form the transcription initiation complex. Other transcription factors bind to regulatory sequences, such as enhancer sequences, and can either stimulate or repress transcription of the related gene.
What activates STAT5?
STAT5 can be activated by various hormones and cytokines, including IFNα, IFNβ, IL-3, GM-CSF, thrombopoietin, and erythropoietin [10,62,91,92]. Interestingly, CrkL has been shown to form a complex with STAT5 under these conditions as well.
How do you identify DNA binding sites?
Representation of DNA binding sites A more accurate way of representing binding sites is through Position Specific Frequency Matrices (PSFM). These matrices give information on the frequency of each base at each position of the DNA binding motif.
What is motif in DNA sequence?
Sequence motifs are short, recurring patterns in DNA that are presumed to have a biological function. Often they indicate sequence-specific binding sites for proteins such as nucleases and transcription factors (TF).
Is STAT5 a transcription factor?
Cell-type-specific STAT5 target gene regulation. STAT proteins act as transcriptional activators upon phosphorylation of a conserved tyrosine residue at the C terminus followed by translocation into the nucleus, where they bind to DNA and activate target gene transcription [2].
What genes does STAT5 regulate?
Activation of the Immune System STAT5 regulates the transcription of the Il4 gene by binding two DNase I hypersensitivity sites, HSII and HSIII, and regulating accessibility to the gene (Zhu et al., 2003; Cote-Sierra et al., 2004).
Why do transcription factors bind to major groove?
These grooves allow proteins to bind to and recognize DNA sequences from the outside of the helix. The grooves expose the edges of each base pair located inside the helix, which allows proteins to chemically recognize specific DNA sequences.
Is p53 a transcription factor?
p53 is a transcription factor that suppresses tumor growth through regulation of dozens of target genes with diverse biological functions.
What is the STAT5 pathway?
STAT3 and STAT5 proteins are oncogenic downstream mediators of the JAK–STAT pathway. Deregulated STAT3 and STAT5 signaling promotes cancer cell proliferation and survival in conjunction with other core cancer pathways.
What is its DNA binding sequence?
DNA binding sites are a type of binding site found in DNA where other molecules may bind. DNA binding sites can be thus defined as short DNA sequences (typically 4 to 30 base pairs long, but up to 200 bp for recombination sites) that are specifically bound by one or more DNA-binding proteins or protein complexes.
How does STAT5 regulate the expression of cytokine genes?
STAT5 regulates the expression of cytokine target genes by binding to gamma interferon-activated sequence (GAS) motifs. Transcriptional activation requires the contact of STAT5 to coactivators and components of the transcription machinery.
What are the enhancer regions of transcription STAT5?
It consists of five enhancer regions (E1–E5) with multiple binding sites for transcription factors. These transcription factors recruit transcriptional co-factors, in particular the BET bromodomain protein BRD4 and the SwItch/Sucrose non-fermentable (SWI/SNF) protein BRG1.
Where does STAT5 bind to the FOXP3 gene?
STAT5 binds directly to the CNS2 region of the Foxp3 gene ( Yao et al., 2007 ), suggesting that STAT5 plays essential roles in nTreg development not only by supporting nTreg expansion and survival but also by promoting the expression of Foxp3. Steven Maltby, Nancy A. Lee, in Eosinophils in Health and Disease, 2013
Where does STAT5 bind to c-Myc super enhancers?
We now show that STAT5 strongly binds to c – Myc super-enhancer regions E3 and E4, both in normal and transformed Ba/F3 cells.