Regulation of Gene Expression

• Gene expression can be regulated at many levels.

Transcription Initiation

• Access of RNA Polymerase to DNA is a point of regulation.
• Chromatin and nucleosome structures in eukaryotes affect this access.
• Regulation occurs via binding of RNA Polymerase to the promoter, forming an open complex.
• How RNA Polymerase escapes the promoter affects Gene expression.

RNA Processing

• Alternative splicing affects Gene expression.
• Export from the nucleus affects Gene expression.

RNA Stability

• Regulating RNA half-life (turnover) affects Gene expression.

Protein Synthesis

• Protein synthesis is usually regulated before translation initiation.

Protein Modification

• Protein modification is a point of regulation.
• The phosphorylation of RNA Polymerase CTD is an example of regulation this way.

Protein Stability

• Protein half-life is a point of regulation.

Protein Localization

• Protein localization is another point of regulation.
• Transcription is typically the most highly regulated step in gene expression.
• Constitutive or "basal" expression refers to genes that are "always on."
• Basal expression of housekeeping genes like enzymes of basal metabolism and ribosomal RNA is always required.
• Basal levels may be low or high based on the function of a gene product
• Expression levels are mainly determined by the intrinsic affinity of RNA Polymerase for the promoter
• Regulated by accessibility of DNA in chromatin structure
• Expression can be constitutively expressed and still be either activated or repressed

Repression/Negative Control

• If a gene is naturally on, it is turned off via a repressor protein
• Efficient RNA Polymerase binding to promoter is prevented
• Open complex formation is prevented
• Promoter escape is prevented

Activation/Positive Control

• Genes are expressed only when an activator protein is present.
• RNA Pol binding to promoter is facilitated, probably by recruitment.
• Open complex formation is facilitated.
• Promoter escape is facilitated.
• Induction vs. Repression are defined by small molecules (effectors) as well as metabolites and hormones

Induction

• Is when a small molecule, an inducer, helps turn a gene on.

Repression

• Co-repressors help turn a gene off.
• Negative and positive control can utilize either inducers or co-repression.
• Effectors, or small molecules, operate in both positive and negative regulation.

Negative Regulation

• Effectors can cause dissociation of a repressor from DNA, inducing transcription
• Effectors can cause binding of a repressor to DNA, inhibiting transcription

Positive Regulation

• Effectors can cause dissociation of an activator from DNA, inhibiting transcription.
• Effectors can cause binding of an activator to DNA, inducing transcription.

Activators and Repressors

• In bacteria, activator binding sites are usually just upstream of the promoter.

• In eukaryotes, activator binding sites can be upstream or downstream and thousands of base pairs away.

• Repressors can influence expression.

• In Bacteria, the DNA site where a repressor binds is called an operator.

• Eukaryotes do not have operators, the chromatin structure itself is repressive.

• Some co-repressors block the activity of activators.

• Most eukaryotic genes would be "OFF" without activators and repressors and most bacterial genes would be "ON" without them.

• Eukaryotic genes are typically regulated by 5+ regulatory sequences (eg enhancers) outside the core promoter.

• One activator or repressor is generally sufficient to promote transcription in bacteria, but not in higher eukaryotes

• If a regulatory protein bound its proper site 10^6 -fold more tightly than to random DNA, 10 molecules would be sufficient to ensure that one was usually at the proper location in bacteria

• Using multiple enhancers helps ensure that transcriptional activation is very specific.

• A limited number of TF can regulate many genes

DNA Looping

• DNA looping (repression) prevents RNA Polymerase from interacting with a promoter.
• DNA-Looping (activation) can occur when enhancers are thousands of base pairs from the promoter, however, are very close in 3D space.
• Architectural regulators may be required to promote DNA looping
• Not all Transcription Factors (TF) bind directly to DNA (Co-Activators).
• Co-Repressors influence transcription.
• The "Mediator" is a protein complex of greater than 20 proteins, and is highly conserved.
• The mediator is required for activated transcription in vitro and in vivo.
• Mediates interaction between enhancers, Polymerase II, and general transcription factors.
• Mediator functions as a giant co-activator.
• Transcription in eukaryotes takes place in chromatin and requires dozens to hundreds of other factors.
• Mediator brings distal regulatory elements to core promoter via interaction with TFs and RNA Pol
• Modulates interaction of proteins bound to enhancers with RNA polymerase and modulates chromatin remodeling.
• Integrates regulatory signals
• Insulators prevent unwanted cross talk between regulators of different genes.