Abstract
BackgroundThere is considerable interest in identifying target genes and chromatin binding sites for transcription factors in a genome-wide manner. Such information may become useful in diagnosis and treatment of disease, drug target identification, and for prognostication. In cancer diagnosis, patterns of transcription factor binding to specific regulatory chromatin elements are expected to complement and enhance current diagnostic predictions of tumor behavior based on protein and mRNA analyses. Signal transducer and activator of transcription-5 (Stat5) is a cytokine-activated transcription factor implicated in growth and progression of many malignancies, including hematopoietic, prostate, and breast cancer. We have explored immunoaffinity purification of Stat5-bound chromatin from breast cancer cells to identify Stat5 target sites in an unbiased, genome-wide manner.ResultsIn this report, we evaluate the efficacy of a Stat5-bound chromatin library to identify valid Stat5 chromatin binding sites within the oncogenome of T-47D human breast cancer cells. A general problem with cloning of immunocaptured, transcription factor-bound chromatin fragments is contamination with non-specific chromatin. However, using an optimized strategy, five out of ten randomly selected clones could be experimentally verified to bind Stat5 both in vitro and in vivo as tested by electrophoretic mobility shift assay and chromatin immunoprecipitation, respectively. While there was no binding to fragments lacking a Stat5 consensus binding sequence, presence of a Stat5 binding sequence did not assure binding.ConclusionA chromatin library coupled with experimental validation may productively identify novel in vivo Stat5 chromatin binding sites in cancer, including abnormal regulatory sites in tumor-specific neochromatin.
Highlights
There is considerable interest in identifying target genes and chromatin binding sites for transcription factors in a genome-wide manner
We identify novel Signal transducer and activator of transcription-5 (Stat5) binding sites from a genome-wide chromatin library and validate the sites by prolactin-inducible Stat5 binding by electrophoretic mobility shift assay (EMSA) and chromatin immunoprecipitation (ChIP)
In contrast to transcription factors that bind to chromatin in a constitutive manner, Stat5 is a latent cytoplasmic transcription factor that is activated by tyrosine phosphorylation and binds tightly to DNA in response to extracellular cytokines, such as prolactin [13]
Summary
There is considerable interest in identifying target genes and chromatin binding sites for transcription factors in a genome-wide manner. Such information may become useful in diagnosis and treatment of disease, drug target identification, and for prognostication. Tumor-specific patterns of transcription factor binding to target chromatin are expected to enhance diagnostic information beyond what is achieved through protein and mRNA analyses. Such added diagnostic information may directly improve disease prognostication and prediction of tumor responsiveness to therapy
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