cisregulation

Cisregulation refers to the regulation of a gene's expression by DNA sequences that are on the same molecule of DNA as the gene they control. This contrasts with trans-regulatory regulation, where diffusible factors such as transcription factors or RNAs, encoded elsewhere in the genome, affect gene expression.

Cis-regulatory elements include promoters, enhancers, silencers, insulators, and untranslated region sequences. Promoters are typically located near the transcription start site and recruit the RNA polymerase complex. Enhancers can be located far from the gene, can act in either orientation, and modulate transcription by increasing the rate of initiation. Silencers decrease transcription, and insulators can block interactions between enhancers and promoters or protect a gene from neighboring regulatory influences. The activity of these elements depends on the binding of transcription factors and co-regulators to specific DNA motifs, as well as chromatin context and histone modifications.

In bacteria, cis-regulation often involves promoters, operators, and riboswitches that respond to environmental cues. In eukaryotes, regulation is more complex, with multiple cis-elements coordinating tissue- or developmental-stage–specific expression through chromatin looping and combinatorial transcription factor binding.

Mutations in cis-regulatory elements can alter when, where, and how much a gene is expressed, contributing to phenotypic variation, evolution, and disease. Studying cis-regulation involves reporter assays, comparative genomics, chromatin accessibility and binding assays, and genome-editing approaches to dissect element function.