Gene Regulation in Eukaryotes

1. Gene Regulation in Eukaryotes Same basic idea, but more intricate than in prokaryotes Why? • Genes have to respond to both environmental and physiological conditions • Developmentally triggered genes that organize cells into tissues, tissues into organs, and organs into an entire organism

2. Transcription and translation overlap in prokaryotes New polypeptides

4. RNA polymerase IV synthesizes siRNA in plants • RNA polymerase V synthesizes RNAs involved in siRNA-directed modification of chromatin in plants

5. There are many opportunities for regulation of eukaryotic gene expression! • Eukaryotic DNA is closely associated with proteins with the resulting chromatin structure playing a role in determining which genes are available for transcription. • Among those genes that are available for transcription, the presence of proteins referred to as transcription factors determines which genes will be transcribed. • Following transcription, processing of the RNA transcript exerts another level of regulation. • Transport of the mRNA to the cytoplasm and its stability in the cytoplasm represent additional levels of control. • When and how long a protein is active in the cytoplasm represents a post-translational level of control.

6. Gene expression can be regulated by chromatin remodeling! • DNA that is highly condensed with histone proteins is referred to as heterochromatin in contrast to the more diffuse euchromatin. • Genes contained in the heterochromatin regions of a chromosome are usually not expressed because the packaging of DNA into nucleosomes can make DNA physically inaccessible to RNA polymerase for transcription. • In a process called chromatin remodeling, specialized proteins can cause the nucleosome forming histone proteins to disassociate from the DNA molecule exposing genes for transcription. • The presence or absence of chromatin remodeling proteins represents an important mechanism for global regulation of many genes on large segments of chromosomes.

7. Chromatin Remodeling protein WT mutant Gene 1 Green fluoroscent protein Gene 1 promoter

8. Exposing the DNA does not ensure transcription of its genes! • To initiate transcription eukaryotic RNA polymerase requires the assistance of proteins called transcription factors. • Transcription factors are produced in response to environmental and developmental signals to elicit an appropriate change in gene expression. • There are additional control elements on genes which interact with activators and regulators to further enhance or otherwise modify transcription. • The result is a combination of factors that form a complex that determines the rate at which the RNA polymerase transcribes the gene.

9. Eukaryotic Promoter Site where other regulatory proteins bind to enhance transcription A site where regulatory proteins can bind to enhance transcription Sequence recognized by a transcription factor Sequence where DNA is denatured determining where transcription starts

10. Transcription factor binds to the core promoter region

11. Different transcription factors bind with the RNA polymerase This holoenzyme complex recognizes the original transcription factor

12. Enhancers act as transcription activators

13. Can have inhibitors – negative regulators that prevent the binding of the transcription factors

15. Regulatory proteins are specifically structured to interact with certain nucleotide sequences on the DNA molecule. • The regulation of gene expression in eukaryotes requires the binding of specialized proteins to the DNA molecule. • Thus far, research has revealed four kinds of structural motifs for DNA binding proteins. • As noted to the right, each type of binding protein is capable of activating or inactivating certain categories of genes (e.g. genes expressed at certain stages of development). • Notice that the structural motifs fit into the major and minor groves on the DNA, have amino acids that fit into the interior of the double helix, or amino acids that form hydrogen bonds with bases inside the DNA molecule.

16. Environmental responses and developmental changes requires coordinating the expression of multiple genes • Recall that in prokaryotes related genes are linked together in an operon. • Eukaryotes do not have operons, but do have the need to turn on (or off) groups of genes at the same time. • This can be accomplished because groups of related genes have the same regulator sequences in their promoter and respond to the same regulator protein. • As shown to the right, a regulator protein produced in response to an environmental stress interacts with a stress response element (SRE) in the promoter of those genes needed for responding to the stress even though the genes may be scattered on different chromosomes throughout the genome. • Some of the proteins produced during developmental changes are transcription factors which trigger cascades of expression of developmental genes. Stress response proteins

17. Eukaryotic gene expression can be regulated after translation! • There are opportunities to alter the activity of a protein after it is made by chemical modification (protein processing) as well as by how quickly the protein itself is degraded (protein degradation). • With respect to protein degradation, eukaryotic cells can earmark a protein for destruction by tagging it with a special molecule called ubiquitin (see below). Once tagged, the ubiquinated protein will enter a polypeptide shredder called the proteasome. The proteasome shreds the protein into small peptide fragments that can be further broken down to component amino acids to be used again to build new proteins.

18. Molecular genetics • Previous discussions focused on the individual. • Focus has now shifted to genes • How are they encoded -DNA structure • How do they replicate - DNA replication • How are they expressed - transcription • How are they expressed - translation • Review on these topics (4/12, 4/14) • Relationship between phenotype and genotype - pathways • How are they regulated - Gene regulation • How we study them - individual genes (4/23, 4/26) • Review on pathways, gene regulation and recombinant DNA (4/28) • Exam IV (4/30) • How we study them - global studies (Genomics-4/26, 5/3, 5/5) • Final Exam 5/10