Understanding transcription factor activity is critical for defining mechanisms of gene regulation in disease. The traditional view of transcription factors getting recruited to promoters of target genes is too simplistic. We now know that many transcription factors regulate genes from enhancers or cis-regulatory elements that are in some cases, significant distances from the target gene. Furthermore, we know that much of the human genome can be transcribed under one condition or another. As such, our view of transcription factor regulation of gene expression is consistently evolving and is proving to be much more complex than initially thought. Some clarity has been provided by discovering genome-wide patterns in transcription factor binding events, since this information reveals the hidden regulatory regions used to control gene expression. One approach for identifying transcription factor binding events is ChIP-seq, a method that couples Chromatin Immunoprecipitation (for assessing protein-DNA interactions) with high-throughput sequencing. ChIP-seq permits a global, unbiased identification of binding events for a transcription factor of interest. We have used ChIP-seq to explore the underlying biology of Estrogen Receptor binding events that are used to drive gene expression programmes in breast cancer cells. This has revealed remarkable features about our transcription factor of interest. We will discuss how powerful ChIP-seq can be for revealing insight into transcription factors of interest and we will also discuss some of the problems associated with ChIP-seq and the bioinformatics interrogation of the large datasets generated.
Declaration of interest: There is no conflict of interest that could be perceived as prejudicing the impartiality of the research reported.
Funding: No specific grant from any funding agency in the public, commercial or not-for-profit sector.