Only a fraction of the genes in a cell are expressed at any one time. The variety of gene expression profiles characteristic of different cell types arise because these cells have distinct sets of transcription regulators. Some of these regulators work to increase transcription, whereas others prevent or suppress it.
Normally, transcription begins when an RNA polymerase binds to a so-called promoter sequence on the DNA molecule. This sequence is almost always located just upstream from the starting point for transcription (the 5′ end of the DNA), though it can be located downstream of the mRNA (3′ end). In recent years, researchers have discovered that other DNA sequences, known as enhancer sequences, also play an important part in transcription by providing binding sites for regulatory proteins that affect RNA polymerase activity. Binding of regulatory proteins to an enhancer sequence causes a shift in chromatin structure that either promotes or inhibits RNA polymerase and transcription factor binding. A more open chromatin structure is associated with active gene transcription. In contrast, a more compact chromatin structure is associated with transcriptional inactivity
Some regulatory proteins affect the transcription of multiple genes. This occurs because multiple copies of the regulatory protein binding sites exist within the genome of a cell. Consequently, regulatory proteins can have different roles for different genes, and this is one mechanism by which cells can coordinate the regulation of many genes at once.