Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are often spatially located near the gene they regulate due to the tight packaging of DNA in the chromosome. The ones that are close in the sequence regulate the initiation of gene transcription, while those further away, enhance or silence gene transcription. The effects of several cis-regulatory sequences transcriptionally regulate most genes; however, occasionally, a single cis-regulatory sequence regulates the transcription of a gene.

Transcription factors bind to cis-regulatory sequences when DNA in is its double-helical form. Transcriptional regulators bind specific sequences but are capable of binding closely related sequences, as well.The double helix hastwo types of groove:the smaller, minor groove, and the larger, major groove.Regulatory factors are more likely to bind to major DNA grooves because of theirsize. Transcription regulators recognize specific cis-regulatory sequences by the characteristic chemical features present at the edges of the nitrogenous base pairs.For example, the bases have different hydrogen bond donors and acceptors exposed along the groove that can form hydrogen bonds with the transcriptional regulators. Because many non-covalent interactions are also involved in this binding, the association is highly stable.