Regulation of Eukaryotic Gene Expression (Biochem Ch 5) Flashcards
Result of acetylating lysyl residues in histones
- acetylating certain lysyl residues in the histones decreases the positive charge and weakens the interaction with DNA, which affects chromatin remodeling and ultimately gene expression
- a chromatin remodeling engine binds to acetylated lysyl residues and reconfigures the DNA to expose the promoter region.
- additional transcription factors (i.e. TBP, TFIID, etc) then bind in the promotor region and recruit RNA Polymerase
General Transcription Factor
binds to promotors and is necessary for every gene to be expressed
Specific Transcription Factors
- increase expression of specific genes
- bind to enhancers (enhancers can be upstream or downstream of a gene)
- hold general transcription factors in place at promotor so genes are expressed at a higher rate
- in a few cases bind to silencers
Examples of enhancers (found in Eukaryotes)
Enhancers are binding sites for activator proteins. Ex:
- Glucocorticoid response element (GRE)
- cAMP Response Element (CRE)
- Estrogen Response Element (ERE)
- remember: specific transcription factors bind to enhancers to increase expression of specific genes
Do Histone acetylases favor gene expression or inactive chromatin?
- Histone acetylases favor gene expression (acetylate certain lysyl residues –> decreases + charge–> weakens interaction with DNA)
- histone deacetylases favor inactive chromatin
Upstream promotor elements and location
- a CCAAT box (around -75) that binds a transcription factor NF-1
- a GC-rich sequence that binds a general transcription factor SP-1
Characteristics of enhancers (5)
- they may be up to 1000bp away from the gene
- may be upstream, downstream or within an intron of the gene they control
- orientation of the enhancer sequence w.r.t the gene is not important
- enhancers can appear to act in tissue-specific manner if the DNA-binding proteins that interact with them are present only in certain tissues
- enhancers may be brought close to the basal promoter region in space by bending the DNA molecule
Silencers
sequences that bind repressor proteins in eukaryotes
cis regulators
- cis regulators are DNA sequences on the same chromosome as the genes they regulate
- the DNA regulatory base sequences (i.e. promotors, enhancers, silencers, response elements, etc) in the vicinity of genes that serve as binding sites for proteins
trans regulators
- transcription factors and the genes that code for them are called trans regulators
- trans regulatory proteins can diffuse through the cell to their point of action
- these are on other chromosomes than the genes they regulate
Transcription factors
- transcription factors: the activator proteins that bind response elements
- contain at least 2 recognizable domains: a DNA-binding domain and an activation domain
Examples of DNA-binding domains in transcription factors
the DNA-binding domain binds to a specific nucleotide sequence in the promotor or response element. Ex:
- zinc fingers (steroid hormone receptors)
- leucine zippers (cAMP-dependent transcription factor)
- helix-loop-helix
- helix-turn-helix (homeodomain proteins encoded by homeotic/homeobox genes)
Zinc-fingers
- polypeptide with zinc
- translocates to nucleus when activated
- can bend in major and minor grooves because of the + charge in the zinc ion
- most common protein binding to DNA
- ex) found in steroid hormone receptors (all steroid receptors bind to DNA with zinc fingers)
the function of the activation domain on the transcription factor
the activation domain of transcription factors allows the transcription factor to:
- bind to other transcription factors
- interact w RNA polynmerase II to stabilize the formation of the initiation complex
- recruit chromatin-modifying proteins like histone acetylases or deacetylases
Steroid Receptors
- response element (binding site)
- function
- protein class
- response element (binding site): HRE/GRE
- function: steroid response
- protein class: zinc finger
cAMP response element binding (CREB) protein
- response element (binding site)
- function
- protein class
- response element (binding site): CRE (cAMP response element)
- function: response to cAMP; active when phosphorylated
- protein class: leucine zipper
Peroxisome proliferator-activated receptors (PPARs)
- response element (binding site)
- function
- protein class
- response element (binding site): PPREs (DNA response elements)
- function: decrease serum TG; regulate multiple aspects of lipid metabolism. Activated by fibrates (increase PPAR alpha) and thiazolidinediones (increase PPAR gamma)
- protein class: zinc fingers
- members of this family of zinc-fingers are activated by a variety of natural or xenobiotic ligands including:
- fatty acids, prostaglandin derivatives, vibrates, thiazolidinediones.
NFkB (nuclear factor kappa-B)
- response element (binding site)
- function
- protein class
- response element (binding site): kB elements
- function: regulates expression of many genes in immune system.
ex) glucocorticoids decrease signaling, therefore decrease immune system of patients - protein class: Rel domains
Homeodomain proteins
- response element (binding site)
- function
- protein class
- response element (binding site): none. embryologically regulated factor
- function: regulate gene expression during development
- protein class: helix-turn-helix
- homeobox/Pax gene produces homeodomain protein which affects a number of enhancers, turning on many genes at one time
Gemfibrozil
- what, who
- MOA
- hypolipidemic drug prescribed to patients with elevated blood TG but normal cholesterol and LDL
- acts by stimulating proliferation of peroxisomes and increasing gene expression of lipoprotein lipase, resulting in the induction of the FA oxidation pathway
- more peroxisomes = more burning FA = decrease TG in blood
Zellweger Syndrome
- genetic disease caused by a mutation in any one of several genes (locus heterogeneity) involved in peroxisome biogenesis
- characterized by deficiency of peroxisomes that causes an accumulation of very long chain FA and several unusual FA, such as hydroxylated and branched FA.
- a defect in FA efflux from peroxisomes
MC features of Zellweger Syndrome
- enlarged liver
- high blood levels of copper and iron
- vision problems
- in affected infants there is failure to grow, mental retardation, abnormal muscle tone, and multiple developmental abnormalities
- infants usually die within the first year.
Klein-Waardenburg Syndrome
- defective PAX gene
- all of the tissues involved in KWS are derived from embryonic tissue in which PAX-3 is expressed
- symptoms:
- dystopia canthorum (lateral displacement of the inner corner of the eye)
- pigmentary abnormalities (frontal white blaze of hair, patchy HYPOpigmentation of skin, heterochromia irides)
- congenital deafness
- limb abnormalities
(summary: limb abnormalities, congenital deafness, facial anomalies, HYPOpigmentation of skin, white frontal hair)
methylation of ____ bases in DNA silences genes
- methylation of CYTOSINE bases in DNA silences genes
- involved in down-regulation of gene expression
Prader-Willi syndrome
- cause
- genetic inheritance
- chromosome 15
- result of genetic imprinting
- methylation of DNA silences genes in genetic imprinting
- imprinted so that it is normally expressed only from the PATERNAL chromosome
- if one inherits a paternal chromosome in which this region has been deleted, will get Prade-WIlli syndrome
- can also result from uniparental (maternal) disomy of chromosome 15 (when person receives 2 copies from mom and none from dad)
Symptoms of Prader-Willi
- childhood obesity and hyperphagia
- hypogonadotrophic hypogonadism (hypogonadism due to an impaired secretion of gonadotropins due to problem with pituitary gland or hypothalamus)
- small hands and feet
- mental retardation
- hypotonia
what is the half life of ALA synthase in the hepatocyte?
1 hour
heme increases the initiation of ??
heme increases the initiation of beta-globing translation
Homeotic gene or homeobox gene (HOX)
- regulate the development of anatomical structures
- mutations of these genes can result in multiple developmental abnormalities due to mutation of a SINGLE GENE
- encode for homeodomain proteins
- similar set of gene = PAX genes (paired-box)
- mutations in HOX or PAX might be expected to produce developmental errors
- ie in Klein-Waardenburg Syndrome
Enhancers are transcriptional regulatory sequences that function by enhancing the activity of
RNA polymerase at a SINGLE PROMOTER SITE
- specific transcription factors (i.e. any steroid receptor) bind to specific DNA sequences (enhancers) and to RNA polymerase at a SINGLE promotor sequence and enable the RNA polymerase to transcribe the gene more efficiently
Binding of histone H1 to nucleosomes would result in
down-regulation of gene expression
Mutations in Sonic Hedgehog (SHH) gene
- holoprosencephaly (HPE) is a common developmental anomaly of the human forebrain and mid face where the cerebral hemispheres fail to separate into distinct L/R halves.
- Haploinsufficiency for Sonic Hedgehog (SHH) is a cause of HPE
Homeodomain Protein
- regulatory proteins involved in controlling the sequential and coordinated gene expression necessary for proper tissue and cell differentiation during embryonic life
- each regulatory protein is responsible for activating a different set of genes at the proper time in development
- encoded by genes called homeobox (HOX)
Someone heterozygous for the normal and sickle cell alleles would have
about 50% of the beta-globing chains will contain glutamate and 50% will contain valine at the variable position (specified by codon 6)
Major exceptions to the rule of codominant expression include genes
- on a barr body (inactivated (by condensation to heterochromatin) X chromosome in women)
- in the Ig heavy and light chain loci (ensuring that one B cell makes only one specificity of an antibody)
- in the T-cell receptor loci
Sequence through which Glucagon induces PEPCK gene expression (7 steps)
PEPCK = phosphoenolpyruvate carboxykinase
- glucagon secreted in response to hypoglycemia
- glucagon binds to a receptor in the cell membrane that increases cAMP concentration
- Protein Kinase A becomes active and phosphorylates and ACTIVATES CREB
- activated CREB enters the nucleus and binds to the cAMP response element (CRE) associated with the PEPCK gene
- increases gene expression of the PEPCK gene
- PEPCK concentration increases in the cell
- INCREASES the rate of gluconeogenesis
Sequence through which Cortisol induces PEPCK gene expression (6 steps)
PEPCK = phosphoenolpyruvate carboxykinase
- Cortisol secreted in response to stress is permissive for glucagon in hypoglycemia and acts through an intracellular receptor (zinc-finger protein)
1. cortisol diffuses into the hepatocyte
2. binds to its receptor
3. this complex enters the nucleus and binds (through zinc fingers) to the glucocorticoid response element (GRE) associated with the PEPCK gene
4. this increases gene expression of the PEPCK gene
5. PEPCK concentration increases in the cell
6. INCREASES the rate of gluconeogenesis
