Cis-regulatory element

• Cis-regulatory elements (CREs) or Cis-regulatory modules (CRMs)

– regions of non-coding DNA
– regulate transcription of neighboring genes
• vital components of genetic regulatory networks
– control morphogenesis
– development of anatomy
• vicinity of genes that they regulate
– typically regulate gene transcription
• by binding to transcription factors
– A single transcription factor
• may bind to many CREs
• control expression of many genes (pleiotropy)
• The Latin prefix cis means “on this side”
– on same molecule of DNA as gene(s) to be transcribed
• CRMs
– stretches of DNA
– 100–1000 DNA base pairs in length
– where transcription factors can bind
• regulate expression of nearby genes
• regulate their transcription rates
• labeled as cis
– typically located on the same DNA strand as genes they control
• trans
– effects on genes not located on same strand or farther away
• transcription factors
• One cis-regulatory element
– regulate several genes
– one gene can have several cis-regulatory modules
• Cis-regulatory modules carry out their function by
– integrating
• active transcription factors
• associated co-factors at a specific time and place in cell
– where this information is read and an output is given
• CREs
– often but not always upstream of transcription site
• CREs contrast with trans-regulatory elements (TREs)
– TREs code for transcription factors
1 Overview
• genes only expressed when they are needed
– organizational maintenance
– energy conservation
– generating phenotypic variance
• most efficient way-regulate at the transcriptional level
– CREs function
• control transcription by acting
– nearby
– within a gene
– most well characterized types of CREs
• enhancers
• promoters
• Both sequence elements
– structural regions of DNA that serve as transcriptional regulators
• Cis-regulatory modules
– one of several types of functional regulatory elements
– Regulatory elements
• binding sites for transcription factors
• involved in gene regulation
– Cis-regulatory modules
• non-random clusters at their specified target site
• contain transcription factor binding sites