8 Gene Regulation

Information is encoded in a linear order

For decoration of the information, it is copied into RNA

One gene encodes the information for one protein

DNA -> RNA -> Protein

• Gene expression= amount of product

• genes can be stimulated to get more of the product

• Genes can be repressed to get a low level of the product

• Transport (of mRNA) from nucleus into cytoplasm

• Intron

• 5’ capping

• 3‘ Processing (polyadenylation)

• Transport

Operon: several biosynthesis genes controlled by one promoter

Example: trp Operon

• complete set is needed for trp synthesis

• All genes of the Operon are regulated by the promoter

• If the Tryptophan levels within the cell are low (means trp is needed): the Repressor is inactive -> the trp operon can be active

• If the trp levels within the cell are high (means no trp is needed): the Repressor changes it’s conformation (negative feedback loop: trp binds to Repressor to activate it), so trp Repressor binds to the DNA -> operon is repressed

• The trp repressor is an helix-turn-helix dimer, which needs trp as an activator to change its conformation and then fits into two major grooves of the trp operon

Negative Regulation

• A Repressor Protein bound to the DNA prevents its transcription

• Negative Feedback: Addition of ligand removes repressor (forming bond-> change in conformation) -> switches the gene on

• Removal of ligand switches Gene on by removing the repressor

Positive Regulation

• an activator protein bound to the DNA promotes the transcription

• Addition of the ligand switches gene off by removing the activator

• The removal of the ligand switches gene off by removing the activator protein

• Lambda repressor protein can activate or repress the transcription

• If lambda is places correctly, it can help to recruit the RNA Polymerase (to activate transcription)

• If lambda is being moved only 1 bp closer to the transcriptional start site, it competes with the RNA Polymerase binding and blocks the transcription

Activation

• Formation (actively) of a loop

  allows interactions between distal regulatory sites and the promoter.

  The distance often DNA binding sites affects their probability of interaction

• Promoter: recruits general transcription factors

• Regulatory sequence: can be anywhere. Binds specific initiation /elongation factors

• TF are bulilt modular (activation domain + binding domain)

• The enhancer region is often far away from the activation sequence/ gene

  can interact with/through the mediator or directly with the TF

• The transcription can be activated by altering the chromatin structure

  • remodeled nucleosomes

  • Histone chaperones

  • Exchange of Histone proteins

  • Histone modifying enzymes

• TF can work additive or synergistic to increase the transcription rates

• The RNA Polymerase activity can influence the activation of the gene expression

• The RNA Polymerase activity can influence the activation of the gene expression

  1. Affect initiation (without affecting RNA Pol II recruitment)

  2. Affect promoter clearance by affecting CTD (C-terminal domain) Phosphorylation by CDK7 (TF2H)

  3. Pausing of RNA Pol II after initiation has begun (NELF/ DSIF)

  4. increase RNA Pol II “processivity” (speed of transcription)

     -> Phosphorylation by pTEFb (of Ser 2)

• more possibilities than activation

• Additional: competitive binding

• masking of the activation surface

• direct interaction with general transcription factors

• repression by chromatin remodeling

• Repression by removing positive Histone modifications

• Repression by adding repressive Histone methylations

• there are multiple regulatory methods for one TF

  • Direct vs inidirect effects

  • The specific function of a Tf is often determined by promoter “context” -> the surrounding/environment TF binding sites may influence wether a TF is an activator or repressor

• Principle of Complex assembly: eukaryotic TF usually don’t work alone

  • Often requires enhancosomes (=DNA interactive proteins): formation of a DNA structure with the participation of architectural proteins that bend DNA by a defined angle. It combines all functions of

  • A structural protein induces DNA binding and activates transcription of a nearby promoter

  • In the complex are different effects (inhibitory and activating) that compete with each other. The result is a fine tuning of gene activity. But TF can also work combinatory. The sum of these binding sites determine the end output of the promoter.

• The protein synthesis of the gene regulatory proteins can be regulated (JunB)

• The regulatory proteins can be regulated by ligand binding (Estrogen receptor)

• The regulatory proteins can be regulated by covalent modification (AP1)

• The regulatory proteins can be regulated by the addition of a second subunit (ß-catenin)

• The regulatory protein can be activated by unmasking (E2F)

• The regulatory protein can be activated by the stimulation of the nuclear entry (NFkB)

• The regulatory protein can be activated by a release from the membrane (Notch)

An insulator blocks the ability of an enhancer to activate a specific gene

A barrier prevents the spreading of heterochromatin (dense)

Positive Feedback

• can generate cellular memory

• Autostimulation: product is neededfor reduction of itself. A transient signal can also induce expression and then it can auto stimulate the production

• Gene regulatory network mechanisms:

  • positive Feedback Loop: the product is needed for its own production

  • Negative Feedback Loop: the product inhibits its own production

  • Flip flop device: two products inhibit each others production

  • Feed-forward loop: the product needs a very strong and fast stimulation -> therefore the signal needs an amplification

• Example: Circadian rhythms is generated by a complex gene regulatory network

The circadian rhythm is regulated by light.

PER and TIM regulate their activity of itself.

Through the circle also other genes are influenced, depending on the light

One TF can regulate many genes

Specific factors can promote expression of genes which are already active

MyoD (=TF) uses a very strong positive feedback and feed-forward together

• once the initiation into a muscle cell has begun, there is no way back (bc of cell fusion)

• -> so you need to make sure that the process will be finished -> Programm has to be in a strong way

Different set of TF -> Determination of different fates

Epigenetic information can be transferred to daughter cells.

One important epigenetic control mechanism is the methylation of CG dinucleotides in the DNA.

Tumorigenesis: Tumor cells often misuse the principle of methyl transferase activity in order to mark genes, that should not be marked and inhibit them.

If it's Tumor suppressor-> gets more resistent to stress