Promoters, Activators, Enhancers, Mediators

GENE CONTROL ELEMENTS

GENES AND REGULATORY ELEMENTS

Structural genes – proteins used in metabolism or biosynthesis

Regulatory genes – products are either RNA or proteins, interact with other sequences and affects transcription and translation.

Regulatory elements – expression of sequences to which they are physically linked.

LEVELS OF REGULATION 1) Alteration of gene structure – modification to DNA, its packaging - DNA methylation, changes in chromatin2) Transcription3) mRNA processing Eukaryotic mRNA modified -5’ cap, 3’ end

polyadenlyated, introns removed. Determines : Stability of mRNA, whether mRNA can be

translated, the rate of translation, and the amino acid sequence.

Growing evidence that eukaryotic cells operate at the level of mRNA processing

4) Regulation of RNA stability – rate of synthesis and degradation.

5) Translation – complex process requiring large number of enzymes, protein factors, and RNA molecules.

6) selectively activating or inactivating proteins after they have been made.

LEVEL OF REGULATION - EUKARYOTES

TRANSCRIPTIONAL LEVEL Promoters include an initiation site 50 nucleotides upstream a sequence

for binding of RNA polymerase Regulatory DNA sequences are used

to switch the gene ON and OFF. In bacteria – 10 nucleotide pairs long In eukaryotes - >10,000 sequences –

molecular microprocessors – integrating information

Regulatory DNA sequences must be recognized by proteins called transcription regulators

Proteins inserts into major grooves of DNA helix.

Proteins form hydrogen bonds, ionic bonds, hydrophobic interactions with the edges of the bases.

Fits into the DNA in the form of dimers.

Dimerization doubles the area of contact with the DNA – ensures only limited number of proteins have access to the DNA

GENES SWITCHED ON AND OFFRepressor proteins – in its active form,

switched off the gene or represses it.Promoters are able to marginally bind and

position RNA polymerase Activator proteins – enhances the promoter by

binding to a nearby DNA site and contact RNA polymerase to initiate transcription.

- Able to bind to another molecule before binding with DNA.

EUKARYOTIC TRANSCRIPTIONAL REGULATORS Both activators and repressors to

regulate the expression of genes. Enhancers – Regions of DNA where

eukaryotic gene activators are bound. Activators enhance transcription even

when bound thousands of nucleotides away from gene’s promoters.

DNA between enhancer and promoter loops out allowing protein bound to an enhancer to interact with the proteins in the vicinity of the promoter.

Mediators – large complex proteins aiding in the assembly of the general transcription factors and RNA polymerase at the promoter.

Eukaryotic transcription regulators – attract proteins that modulate chromatin structure and thereby affect the accessibility of the promoter

PACKING OF PROMOTER DNA Nucleosomes – highly folded structures of DNA. Can inhibit transcription if positioned over

promoter, because it blocks the assembly of the general transcription factors RNA polymerase.

Chromatin structure altered by - chromatin – remodeling complexes and Enzymes that covalently modify histone proteins Gene activators – recruits histone acetylases –

attach an acetyl group to lysine tail of histone proteins – greater accessiblity to DNA.

Gene repressor proteins – modify chromatin to reduce efficiency of transcription initiation.

Repressors attract histone deacetylases – removes acetyl groups from histone tails – reversing the effects.

COMBINATORIAL CONTROL OF EUKARYOTES

Combinatorial control refers to the way that groups of regulatory proteins work together to determine the expression of a single gene.

Specialized cells – differentiate into a specific cell type and cell memory is a prerequisite for the creation of organized tissues.

A mammalian skeletal muscle cell is a highly distinctive cell type.

Large cell formed by fusion of many muscle precursor cells – myoblasts distinguished by the presence of actin, myosin, receptor proteins, ion channel proteins in the cell membranes.

Genes encoding these muscle –specific proteins are all switched on coordinately as the myoblasts fuse.

POST-TRANSCRIPTIONAL CONTROLS Operate after RNA is synthesized. Alternative splicing Self- regulating mRNA have -riboswitches Short sequences of RNA that change their

conformation when bound to small molecules. Economical, because they bypass the need for

regulatory proteins. UTR can control translation – ribosome

recognition forms base pairs with the RNA in the small ribosome subunit – ideal target for translational control.

Eukaryotes – 5’cap helps guide the ribosome to AUG.

Repressors can inhibit translation initiation by binding to the specific sequences in 5’UTR.

microRNA (miRNA) – non coding RNA found in plants and animals.

- regulates protein coding genes. - control gene expression by base-pairing with

specific mRNAs. MiRNA is assembled with specialized proteins

to form an RNA-induced silencing complex RISC

Searches for target mRNA in the cytoplasm – base pairs regions in 5’ and 3’ UTR- mRNA destroyed by nuclease.

RNA interference (RNAi): Viruses and transposable genetic

elements – produce dsRNA. Targeted RNA degradation

mechanism helps to keep these potentially dangerous invaders in check.

dsRNA triggers RNAi by attracting protein complex containing nuclease - Dicer

Dicer cleaves dsRNA intro short fragments and sends to RISC.

RISC discards one strand and with another strand searches for complementary foreign RNA molecule.

RNA I activity can spread from tissue to tissue by movement of RNA between cells.