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One distinct feature of transcription factors is that they have DNA-binding domains that give them the ability to bind to specific sequences of DNA called enhancer or promoter sequences.

First, transcription is controlled by limiting the amount of mRNA that is produced from a particular gene. The second level of control is through post-transcriptional events that regulate the translation of mRNA into proteins. Even after a protein is made, post-translational modifications can affect its activity.

Transcription elongation is controlled across gene bodies by a wide variety of factors, including transcription factors, chromatin modifiers, chromatin assembly factors and chaperones, RNA processing factors, and histone variants.

The activity of a transcription factor is often regulated by (de) phosphorylation, which may affect different functions, e.g. nuclear localization DNA binding and trans-activation. Ligand binding is another mode of transcription-factor activation. It is typical for the large super-family of nuclear hormone receptors.

At the level of chromatin state The highest level of transcription regulation occurs through the rearrangement of histones in order to expose or sequester genes, because these processes have the ability to render entire regions of a chromosome inaccessible such as what occurs in imprinting.

During elongation, nucleic acid signals and regulatory proteins modulate concurrent RNA-processing events, instruct RNA polymerase where to pause and terminate transcription, or act as roadblocks to the moving enzyme.

The DNA-dependent multi-subunit RNA polymerase is the central component in the regulation of transcription initiation in bacteria. Sigma factors bind to the RNA polymerase to produce a holoenzyme that is competent for transcription.