1. Gene Expression Control
Cell Biology
Lecture 9
Dr. Frances Santiago-Schwarz
ECB Chapter 8(cont)
Gene Expression Control
And selected topics from ECB Chapter 9

2. SUMMARY : Differences in the initiation of transcription between eukaryotes and prokaryotes. These differences are fundamental and you should be able to describe them!!!

3. Assembly of Eukaryotic Transcriptional Initiation Complex
Eukaryotic RNA polymerase II requires general transcription factors. The general transcription factors assemble in the promoter region (on the TATA box) and help RNA polymerase II to bind and start transcription.
ECB Fig 8-10

4. of RNA pol II allows RNA processing
Phosphorylation
of RNA pol II allows RNA processing
proteins to assemble
on its tail
ECB Fig 8-12

5. Eukaryotic genes can be controlled from a distance
Eukaryotic genes can be controlled from a distance. The DNA sequences bound by gene activators are called enhancers. These enhancers sites can be located thousands of bps away from the gene. They can also be located down stream of the gene.
ECB Fig 8-13

6. Hormones Signaling molecules
Stimulate or inhibit activity in target cells
Mechanism of action varies
May bind to cell surface
May enter cell and bind to regulatory proteins
May bind with enhancers in DNA
Some have widespread effects
Somatotropin (growth hormone)
Others signal only certain cells at certain times
Prolactin stimulates milk production

7. A single gene regulatory protein can coordinate the expression of many different genes.
EXAMPLE: Glucocorticoid receptor protein -Group of genes regulated by the binding of the hormone-Glucocorticoid receptor protein complex to a regulatory site in the DNA of the gene -Response to stress

8. A single gene regulatory protein can coordinate the expression of many different genes.
Activator
Proteins bound
Regulatory region
ECB Fig 8-20

9. Nucleosomes are able to inhibit or activate the initiation phase of transcription when they are positioned at the promoter region.
Nucleosome
Methylation (-CH3) of DNA can inactivate genes
Acetylation of histones allows activation of genes by DNA unpacking and transcription
Starr Figure 15.2 Page 240

10. Covalent modification of core histone tails.
Figure 4-35 Mol Bio Cell

11. Nucleosomes are able to activate the initiation phase of transcription when they are positioned at the promoter region.
ECB Fig 8-14

12. Gene regulatory proteins and the location of their binding
sites relative to the promoters are different for different genes
Same for all
RNA Pol genes
ECB Fig 8-15

13. DNA methylation
The addition of methyl groups to the 5’ carbon of cytosine occurs at a frequency of up to 1 in every 100 bases
This method of control is found in vertebrates & plants, but not in invertebrates such as flies or round worms
Methylation occurs through the action of enzymes called methyltransferases
Methylation is concentrated into GC-rich islands of DNA which are found in promoters
Methylation of promoters is strongly correlated with gene repression

14. Methylation of Cytosine
5-methyl cytidine is referred to as the 5th deoxynucleoside

15. - Changes in the methylation state of a promoter alters the level of expression of a gene
- Important during development (genes that do not contribute to particular path become permanently shut down through methylation)

16. Methylation is the mechanism by which X-inactivation occurs
Recall that women are XX while men are XY
In order to even out the dose of the genes on the X between the sexes women have one X randomly shut down in each cell
The mechanism of this dosage compensation is through methylation as well as permanent chromosome compaction
This results in the Barr body found in female cells
Once either Xp or Xm has been inactivated, it remains silent throughout all subsequent cell divisions of that cell and its progeny, indicating that the inactive state is faithfully maintained through many cycles of DNA replication and mitosis.

17. X-inactivation
(64 cell embryo)

18. Gene Expression Control: Emerging Concepts
double-stranded RNA molecules (dsRNA) efficiently and specifically inhibit gene products on a posttranscriptional level (gene silencing)
RNA interference is the phenomenon in which double-stranded RNA (dsRNA) can specifically suppress expression of a target gene, and was originally discovered in C. elegans
Host cells can detect the presence of dsRNA (frequently of viral origin) and initiate a program of drastic responses in attempt to eliminate it.
dsRNA-directed ssRNA destruction is the basis of the technique of RNA interference (RNAi) that is used by researchers to block specific gene expression

19. RNAi is a two-step mechanism.
-First, long dsRNAs are cleaved by an enzyme known as Dicer in nucleotides (nt) fragments, called siRNAs for small interfering RNAs.
-Second, siRNAs are recruited to a ribonuclease complex (termed RISC for RNA Induced Silencing Complex) which in turn mediates the cleavage of the target mRNA.

20. Double-stranded RNA-binding proteins could suppress RNA interference-mediated antiviral defences
Zsuzsanna Lichner, Dániel Silhavy and József Burgyán
Agricultural Biotechnology Center, Plant Biology Institute, P.O. Box 411, H-2101, Gödöllö, Hungary
RNA interference (RNAi) is a double-stranded (ds)RNA-inducible, sequence-specific RNA-degradation mechanism that operates as a natural antiviral system in plants and animals. Successful virus infection requires evasion or suppression of RNAi. Indeed, RNAi suppressor proteins have been identified in plant and animal viruses, although the molecular mechanism of silencing inhibition is still poorly understood. Because many RNA viruses encode dsRNA-binding proteins (dsRBPs) and as RNAi is triggered by the accumulation of dsRNAs, dsRBPs were examined to see if they inhibit RNAi. Here, it is shown that heterologous dsRBPs suppressed RNAi in plants, indicating that in natural host-virus interactions, pathogen-encoded dsRBPs could inactivate RNAi-mediated host defences.

21. Curr Opin Chem Biol. 2003 Aug;7(4):516-23.  
MicroRNAs: key participants in gene regulatory networks. Ke XS, Liu CM, Liu DP, Liang CC. National Laboratory of Medical Molecular Biology, Institute of Basic Medical Sciences, Chinese Academy of Medical Science & Peking Union Medical College, Beijing , China. microRNAs (miRNAs) are a newly identified and surprisingly large class of endogenous tiny regulatory RNAs. They exhibit various expressional patterns and are highly conserved across species. Recently, several regulatory targets of miRNAs have been predicted. Functional analysis of the potential targets indicated that miRNAs may be involved in a wide range of pivotally biological events. The nature of miRNAs and their intersection with small interfering RNAs endow them with many regulatory advantages over proteins and make them a potent and novel means to regulate gene expression at almost all levels. Here we argue that miRNAs are key participants in gene regulatory network.

22. Altering of Genes and Genomes
ECB Fig 9-3

23. www.pitt.edu/ ~heh1/research.html
                  
                  
Horizontal gene transfer is any process in which an organism transfers genetic material (i.e. DNA) to another cell that is not its offspring. By contrast, vertical transfer occurs when an organism receives genetic material from its ancestor, e.g. its parent or a species from which it evolved.
~heh1/research.html

24. Horizontal gene transfer
and evolution