Gene regulation in Eukaryotes
There are three common ways that the function of regulatory transcription factors can be modulated
1. Binding of a small effector molecule 2. Protein-protein interactions 3. Covalent modification
Three common interactions that communicate the effects of regulatory transcription factors are
1. TFIID-direct or through coactivators 2. Mediator 3. recruiting proteins that affect nucleosome composition
ChIP sequencing
Allows determination of: Where nucleosomes are located Where histone variants are found Where covalent modifications of histones occur
GREs
Are located near promoters of many different genes. B) Are activated in response to increased glucocorticoid levels. C) Are bound by a dimerized regulatory transcription factor.
Zinc finger motif
Composed of one a-helix and two b-sheets held together by a zinc (Zn++) metal ion
the ENCODE project
Encyclopedia of DNA Elements Consortium Isolate and sequence RNA from humans Identify transcription factor binding sites Map DNA methylation sites Identify histone modification sites Map DNaseI cleavage sites
True or False: A CpG island consists of about 2000 copies of the CG dinucleotide.
False
the five histone genes
H1, H2A, H2B, H3 and H4
Changes in function of which of the following proteins by posttranslational modification (such as phosphorylation or acetylation) would be likely to, in turn, affect the expression of specific genes?
IRP
In order for CREB to activate transcription:
It must be phosphorylated.
In comparing effects of regulatory transcription factors that affect TFIID and those that affect mediator:
Mediator allows binding of RNA polymerase but transcription can be prevented by transcription factors binding to silencers.
The best explanation for interference of DNA methylation with transcription factor binding is:
Methylation of the CpG island modifies the shape of the response element to which the transcription factor normally binds.
In the absence of glucocorticoid:
None of these.
coolio
Phosphorylated CREB binds to DNA and stimulates transcription
Eukaryotes have multiple families of chromatin remodelers;
SWI/SNF ISWI INO80 Mi-2
insulators
Since eukaryotic gene regulation can occur over long distances, it is important to limit regulation to one particular gene, but not to neighboring genes Insulators are segments of DNA that insulate a gene from the regulatory effects of other genes Some act as barriers to chromatin remodeling Others block the effects of enhancers May do this by chromosome looping
ATP-dependent chromatin remodeling
The energy of ATP is used to alter the structure of nucleosomes and thus make the DNA more accessible
Gonadocorticoids
These include estrogen and testosterone They influence the growth and function of the gonads
Glucocorticoids
These influence nutrient metabolism in most cells They promote glucose utilization, fat mobilization and protein breakdown
Leucine Zipper Motif
Two a-helices intertwined due to leucine motifs Alternating leucine residues in both proteins interact ("zip up"), resulting in protein dimerization
cAMP
acts as a secondary messenger and activates protein kinase A.
CREB protein
another regulatory transcriptional factor CREB is an acronym for cAMP response element-binding CREB protein becomes activated in response to cell-signaling molecules that cause an increase in the cytoplasmic concentration of cAMP Cyclic adenosine monophosphate
CRE
cAMP response element: CREB protein recognizes a response element with the consensus sequence 5'-TGACGTCA-3' This has been termed a cAMP response element (CRE)
some chromatin modeling thingies
change in nucleosome position histone eviction replacement with histone variants
DNA methyltransferase
converts hemimethylated DNA to fully methylated DNA
heterodimers
formed by two different transcription factors
Homodimers
formed by two identical transcription factors
GRE
glucocorticoid response elements: These function as enhancers GREs are located near dozens of different genes, so the hormone can activate many genes
DNA methylation
is a change in chromatin structure that silences gene expression Carried out by the enzyme DNA methyltransferase It is common in some eukaryotic species, but not all Yeast and Drosophila have little DNA methylation Vertebrates and plants have abundant DNA methylation In mammals, ~ 2 to 7% of the DNA is methylated
hemimethylated
only one strand is methylated
Methylation of CpG islands:
prevents activation of enhancers
recognition helix
recognizes and makes contact with a base sequence along the major groove of DNA
methyl CPG binding protein
recruits other proteins that change the chromatin to a closed conformation
