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Transcriptional regulation is often refered to this as turning a gene "on" or "off". Regulating transcription is the job of transcription factors, also known as "trans acting" factors. These are diffusible molecules, often proteins, that act in many different ways to turn up or down the rate of transcription of a particular gene. Some transcription factors bind directly to to cis-regulatory sequences, pieces of DNA usually near the coding region of a gene, and influence the ability of RNA polymerase to bind to the promoter of the gene. They can do this by directly interacting with proteins involved in RNA polymerase recruitment (for example TFIID and Mediator), or by changing the accessibility of the promoter (for example, physically blocking the promoter, adding or removing methyl groups, or interacting with histones and histone binding proteins). Some transcription factors bind to other transcription factors and affect their ability to bind DNA.

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