Cis-regulatory element
A single transcription factor may bind to many CREs, and hence control the expression of many genes (pleiotropy).
[3] Cis-regulatory modules carry out their function by integrating the active transcription factors and the associated co-factors at a specific time and place in the cell where this information is read and an output is given.
[citation needed] The genome of an organism contains anywhere from a few hundred to thousands of different genes, all encoding a singular product or more.
For numerous reasons, including organizational maintenance, energy conservation, and generating phenotypic variance, it is important that genes are only expressed when they are needed.
[1] The original definition presented cis-regulatory modules as enhancers of cis-acting DNA, which increased the rate of transcription from a linked promoter.
[4] However, this definition has changed to define cis-regulatory modules as a DNA sequence with transcription factor binding sites which are clustered into modular structures, including -but not limited to- locus control regions, promoters, enhancers, silencers, boundary control elements and other modulators.
[1] There are two types of transcription factor inputs: those that determine when the target gene is to be expressed and those that serve as functional drivers, which come into play only during specific situations during development.
[citation needed] Additionally, the regulation of chromatin structure and nuclear organization also play a role in determining and controlling the function of cis-regulatory modules.
[4] Thus gene-regulation functions (GRF) provide a unique characteristic of a cis-regulatory module (CRM), relating the concentrations of transcription factors (input) to the promoter activities (output).
[1] Other Boolean logic operations can occur as well, such as sequence specific transcriptional repressors, which when they bind to the cis-regulatory module lead to an output of zero.
[2] Cis-regulatory modules can be characterized by the information processing that they encode and the organization of their transcription factor binding sites.
This model will increase or decrease the amount of cells that transcribe a gene, but it does not affect the rate of transcription.
[4] Rheostatic response model describes cis-regulatory modules as regulators of the initiation rate of transcription of its associated gene.
[5] Only once this region has been bound with the appropriate set of TFs, and in the proper order, can RNA polymerase bind and begin transcribing the gene.
[citation needed] Operators are CREs in prokaryotes and some eukaryotes that exist within operons, where they can bind proteins called repressors to affect transcription.
It has been found that polymorphisms occurring within non-coding sequences have a profound effect on phenotype by altering gene expression.
[1] The layout of cis-regulatory modules can provide enough information to generate spatial and temporal patterns of gene expression.
The program relies on the definition of strict restrictions among the Transcription Factor Binding Sites (TFBSs) that compose the module in order to decrease the false positives rate.
INSECT is designed to be user-friendly since it allows automatic retrieval of sequences and several visualizations and links to third-party tools in order to help users to find those instances that are more likely to be true regulatory sites.
[14] Bayesian Networks use an algorithm that combines site predictions and tissue-specific expression data for transcription factors and target genes of interest.
This model also uses regression trees to depict the relationship between the identified cis-regulatory module and the possible binding set of transcription factors.
This program uses a database of confirmed transcription factor binding sites that were annotated across the human genome.
