Epigenetic Regulation Of Gene Expression Flashcards
What is an epigenetic trait?
A stable, mitotically and meiotically heritable phenotype that results from changes in gene expression without alterations in the DNA sequence
What are epigenetics?
The study of the ways in which these changes alter cell- and tissue-specific patterns of gene expression
What is an epigenome?
This refers to the epigenetic state of the cell
Describe epigenetics as mechanisms
Mechanisms that cause chromosome-associated heritable changes to gene expression that are not dependent on changes in DNA sequence
The phenotype off an organism is a product of the interactio; between the genome and epigenome
What mechanisms would epigenetics use?
- Altering the genome without changing the DNA sequence
- The “epigenome” is a specific pattern of modifications to the DNA that is present in the cell at a given time
- Histone modification controls transcription of genes
- Transcription from only one parental allele
Explain how altering the genome without changing the DNA sequence acts as a part of epigenetics
Includes:
- DNA methylation/demethylation
- Histone modification mainly through acetylation/deacetylation called the “Histone Code”
- Action of non-coding RNA molecules
Explain the epigenome being a specific pattern of modifications to the DNA as a mechanism of epigenetics
Over a lifetime:
- DNA remains the same
- Epigenome may change
Explain how Histone modification controls transcription of genes as a mechanism
Histone modification controls transcript of genes
Either:
-Activating or silencing
Explain how transcription from only one parent acts as a mechanism for epigenetics
Two general ways:
- in a very specific way called “Imprinting”
- In a random way called “Monoallelic Epigenetic Expression”
How are epigenetic traits heritable?
Epigenetic states are transmitted through mitosis and meiosis
- Reversible modification of DNA by the addition of removal of methyl groups to cytosine
- Chromatin remodeling the addition or re,oval of chemical groups to histone proteins
- Regulation of gene expression by non coding RNA molecules
What is the methylome?
DNA Methylation: the methylome
The methylome is tissue specific is cell and tissue specific
- Not “fixed” and is reversible
- Can change as cells respond to changing conditions
When does DNA methylation takes place?
DNA methylation in mammals takes place:
- After DNA replication
- During cell differentiation of adult cells
What is DNA methylation?
DNA methylation involves the addition of a methyl group (-CH3) to the 5’ carbon of a cytosine base base to make a 5-methylcytosine
Explain the catalyzation of methylation
Methylation is catalyzed by a family of enzymes called DNA methyl transferases(DNMTs)
DNMT1-maintains methylation pattern through DNA duplication
DNMT2 and 3- create methylation patterns
How does methylation affect the structure of DNA?
- methylation occurs most often on the cytosine adjacent to a guanosine, CpG doublets in DNA on both strands
- Methyl groups occupy the major grove of DNA and prevent the binding of transcription factors
What are CpG islands?
Methylatable CpG-rich regions are not random but are concentrated
Explain how methylation affects transcript
When methylated, the genes are transcriptionally silent
When unmethylated, the genes are available for transcription
About 70% of human genes have a CpG island in their promoter region
How do ,ethylagion patterns differ among tissues?
Methylation pattern is tissue specific and once established , the methylation pattern is maintained for all cells in that tissue through cell division
Methylation patterns of genes are also tissue specific
What purposes does hypomethylation serve?
Hypomethylation of genes in cells generally involved in housekeeping functions such as cell cycle, transcription and RNA processing
Where are the majority of CpG islands located?
Majority of methylated CpG are located in repetitive DNA sequences located in heterochromatic regions of the genome including the centromere
What is the function of heterochromatin methylation?
-Maintains chromosome stability by preventing translocations and other chromosomal abnormalities from occurring
How X chromosomes in females inactivated?
X chromosomes in mammalian females are inactivated by converting them into heterochromatin
What does CpG methylation in euchromatin regions causes?
-Causes a parent specific pattern of gene transcription
What is Chromatin?
Chromatin is composed of DNA wound around an octamer of Histone proteins to form nucleosomes
Contrast loosely packed and densely packed in terms of transcription
Loosely packed DNA allows for RNA polymerase to access the DNA for transcription to occur
Dense packing is transcriptionally silent
What are dense and loose packing influenced by?
Dense and loose packing can be influenced by post-translational modifications to the amino acids near the N-terminal tail of the histone proteins
Give a brief description of Histone modification
Histone modification alter the nucleosomes
- N-terminal tails become modified by acetylation, methylation or phosphorylation
- his changes the way DNA is wrapped around the histones
- DNA methylation is linked to Histone acetylation
How does the Histone tail interact with the DNA phosphate backbone? Why? What effect does this have?
The Histone tails interact tightly with the negatively charged phosphate backbone of DNA -causes transcription to be repressed
Why- The amino tails of Histone proteins, particularly 3 and 4 have many lysine residues
-Lysines are positively charged
What is Histone acetyltransferase(HAT)?
An enzyme which can add an Acetyl group to the lysine residues
How does acetylation affect transcription?
The Acetyl group masks the charge of the lysine residues and the Histone tails no longer bind the DNA
Transcription can occur
How can Acetyl groups be removed?
The Acetyl group can be removed by Histone deacetylase(HDAC)
-Which is guided to regions of DNA that are methylated
Explain HDAC activity when methylation occurs?
If DNA is methylated:
- Histone deacetylase is recruited to the site
- Acetyl group is removed from the Histone tails by HDAC
- Lysine residues becomes positively charged
- The position charge interacts with the negative charge of the DNA badkbone
- “Closed” configuration
What are writers?
Proteins that add chemical groups to DNA and histones
What are readers?
Proteins that interpret these chemical modifications
What are erasers?
Proteins that remove the chemical groups on histones
DNA demethylase process still poorly understood so no need to memorize figure below…
What are the ncRNA?
Genome transcription doesn’t just produce mRNA
Several classes of RNA are transcribed but never translated into proteins
Differentiate short and long ncRNA
- short RNAs up to 31 nucleotides long
- Long ncRNAs more than 200 nucleotides
What are the 3 classes of short ncRNAs?
- miRNA (microRNA)
- siRNA(short-interfering RNA)
- piRNA(piwi-interacting RNA)
What are miRNA and siRNA?
miRNA and siRNA are processing enzymes within the cell:
-final product are RNA molecules about 25 nucleotides long
What are the functions of miRNA and siRNA?
Biological activity to associate with RISC complex of proteins (RNA induced silencing complex) to repress the translation of specific, targeted mRNA (no protein made)
What is piRNA?
piRNA interact with PIWI proteins (RNA binding proteins):
-Are 21-35 nucleotides long
How much piRNA have been found?
10,000,000
What are the functions of piRNA?
- Silence transposable elements mainly in germ cells
- Promote Both heterochromatin formation and de-novo methylation of DNA
- Some evidence that they help fight viral infection
How were long ncRNA discovered?
Discovered during the Human Genome Project(2000)
How much long ncRNA have been identified?
Over 14,000 long ncRNA
Describe the structure of long ncRNA
Often 5’ caps and poly A tails but no protein coding region
What are the functions long ncRNAs?
Genes often found close to a real gene and can interfere with the real gene and can interfere with the real gene’s expression :
- Interact with chromatin regulating proteins
- Then guide the chromatin regulating proteins to specific locations on the genome
- therefore, participate in chromatin remodeling
- Also involved in post-transcriptional regulation of target mRNA
What are the 4 models of action for long ncRNA?
The decoy model
The adapter model
The guide model
The enhancer model
What is the decoy model of long ncRNA ?
Long ncRNA-binding sites compete with transcription initiation sites on protein-coding genes to prevent transcription
Explain the adaptor model of long ncRNA
lncRNAs act as a platform or adaptor for two or more proteins to form active DNA-binding protein complexes
Explain the guide model of lncRNAs
LncRNAs recruit protein complexes (e.g., chromatin modifiers) and guide them to specific loci.
Explain the enhancer model of lncRNA
LncRNA bind to DNA regions upstream or downstream of genes forming enhancerlike loops to regulate gene action
What is bialleilic gene expression?
- Humans have two copies of each gene. One that is inherited maternally and the other inherited paternally
- Both copies of the genes are expressed equally
Describe epigenetic silencing
Hypermethylation of CpG islands in promoters will silence the genes
- Can be tissue specific
- Can be temporal (specific to a time during development )
- Can be in response to the environment
What is the monoallelic gene express ion?
When only one allele is transcribed and the other allele is silenced, called monoallelic gene expression
What is imprinting?
A type of monoallelic gene expression. Parent of origin monoallelic gene expression -imprinting
In activation of genes can be different on the maternally inherited chromosome vs. the paternally inherited chromosome
What is Random X-inactivation?
Type of monoallelic gene expression
X-inactivation is random in mammalian females, and this compensates for their increased gene dosage of many X-linked genes
(Not all because a fertile female requires biallelic expression of some genes- some genes escape X-inactivation
What is contained in the X-inactivation center?
X-inactivation center contains Xist high is a non-coding RNA that coats the other X chromosome to inactivate it . This is a random process in each female cell
Describe the random pattern of allele inactivation of autosomal genes
A type of monoallelic gene expression
Randim pattern pattern of allele inactivation of autosomal genes
The first identified autosomal genes subject to random monoallelic expression coded for:
- Immunoglobins
- Odorants receptors
- Interlukins
- Many other autosomal genes have since been discovered
What are the 3 types of monoallelic gene expression ?
- X-inactivation
- Parent of origin monoallelic gene expression
- Random pattern of allele inactivation of autosomal genes
Explain the inner workings of parent of origin monoalllelic gene expression
- Parental imprinted genes are methylated in male and female Germ line cells during gamete formation
- the fertilized egg, or zygote, has different methylation patterns on the copies of certain genes that came from either father or mother
- the genes that have hypermethylation associated to it are silenced
- thus, only one allele
When is parent of origin imprinting established?
during gamete formation
First, the development of maternally imprinted genes in oocytes
Next, the development of paternally imprinted genes in sperm
Lastly, parent of origin alleles of the zygote
When are Maternal imprints estaablished?
During oogenesis
Primordial germ cells (2N) —> erasure of methylation patterns in the primordial germ cell(2N) —> established maternal imprints during gametogenesis (each gamete 1N )
When are paternal imprints established ?
Primordial germ cell (2N) —> erasure of methylation patterns in the primordial germ cell (2N ) —> established of paternal imprints during spermatogenesis(each 1N)
How does imprinting affect the zygote?
After fertility, zygotes now will have both maternally and paternally imprinted genes
- Some genes are only expressed from the maternally inherited gene
- Other genes are only expressed from the paternally inherited gene
What could possibly go wrong with epigenetics?
- Environmental agents including nutrition, chemicals, and physical factors such as temperature can alter gene expression by affecting the epigenetic state of the genome
- Artificial reproductive technology can affect the epigenetic state of the genome
How does high maternal nurturing lead to emotional influence of epigenetis in rats?
-High maternal nurturing induces high levels of serotonin in the brain, leading to DNA hypomethylation, Histone acetylation, and increased expression of GR(glucocorticoid receptor)
In adulthood, high levels of GR expression; increase adaptation to stress and, in females, lasses on the high MN phenotype.
How does low maternal nurturing lead to emotional influence of epigenetics in rats?
Rat pups experiencing low levels of maternal nurturing had higher levels of promoter methylation and reduced levels of GR expression
In adulthood, this led to poor stress adaptation and, in females, perpetuation of low levels of nurturing her pups
Explain how the coat color of Agouti mice is controlled (general)
The coat color of mice is controlled by the dominant allele Agouti(A)
Agouti is expressed only for a short time during hair growth which allows yellow pigment to be disposited in the black hair shaft to look brown
Then the promoter of the Agouti gene is methylated and turned off
Agouti mice have non-lethal mutant (A^vy) that allows yellow pigment formation along the entire shaft hair shaft
-there is an insertion of a transposable element near the transcription start site of the Agouti gene that changes gene expression
Explain how the coat of color of Agouti mice is affected by epigenetics
Degree of methylation in the transposon’s promoter is related to how yellow the hair shaft
How can we alter the degree of methylation in Agouti mice?
Feed pregnant Agouti A^(vy) mice methylation precursors
The diet for pregnant agouti mice included methylation precursors like folic acid, vitamin B12, choline
Offspring showed a variation of coat color which was related to the amount of methylation found at the transposon’s promoter
How does methylation affect degree of yellow coat color innAgouti mice?
Lower methylation in transposon’s promoter leads to more yellow color
Explain the Epigenetics of the smoking grandma
A woman who smokes when she is pregnant induces Epigenetic changes in three generations at once
In herself, her unborn daughter and her daughter’s respective cells
What is the Beckwith Wiedemann Syndrome(BWS)?
Beckwith Wiedemann Syndrome is an imprinting disorder on chromosome 11p15.5
- 50% cases from loss of methylation at IC2 on maternal chromosome
- 20% cases from paternal uniparental disomy
IC1- imprinting center 1
IC2- imprinting center 2
In Beckwith Wiedemann Syndrome, what genes are expressed maternally?
H19 nonciding RNA
KCNQ1 is potassium channel
CDKN1C is a cell cycle inhibitor
In Beckwith Wiedemann Syndrome, what genes are expressed paternally?
KCNQ1OT1 is a long noncoding RNA
IGF2 is a growth factor
How often does BWS occur in regular population?
Beckwith Wiedemann Syndrome occurs in the regular population about 1 in 14,000 births
The incidence of BWS is 3-10X higher in children conceived by assisted reproductive technologies than what is seen in the regular population
Express how IC2 affects BWS occurrence
96% of BWS from Assisted reproductive technologies due to loss of maternal IC2 methylation.
What are the clinical features of Beckwith Wiedemann Syndrome ?
- overgrowth disorder
- Macrosomia (large baby, birth weight significantly greater than average)
- Microcephaly(small head)
- Macroglossia (large tongue)
- ear creases or pits
- Nevis flammeus(port wine stain on skin)
- Omphocele (opening of the abdominal wall), umbilical hernia
- Predisposition to tumors
- intellectually normal
How can hypomethylation/hypermethylation lead to cancer?
- DNA hypomethylation turns on genes leading to high transcription of many genes including oncogenes
- DNA hypermethylation at CpG islands leads to inactivation of certain genes found in many cancers including:
- Tumor suppressor genes
- DNA repair genes
- Proteins involved in apoptosis
Give evidence that may lead to epigenetics leading to alterations
- Global hypomethylation May cause genomic and the large-scale chromosomal changes that are a characteristic feature of cancer
- Epigenetic mechanisms can replace mutations as a way of silencing individual tumor-suppressor genes or activating oncogenes
- Epigenetic modification can silence multiple genes, making them more effective in transforming normal cells into malignant cells than sequential mutations of single genes
What chromatin remodeling proteins undergo mutations which are linked to cancer?
Histone Acetyl transferase(HAT) and histone deacytelase(HDAC)
What Rubinstein Taybi syndrome?
Patients with this syndrome have a mutation in HAT which results in the gene silencing of a tumor surpressor protein
-if you do not have histone tails acetylated, the DNA is tightly wrapped around the nucleosome and there is a reduction in tumor suppressor protein made
What is BRAC1? How can this lead to breast cancer?
- BRAC1 normally interacts with HDAC (mechanism still being studied)
- Nornally the promoter for BRAC1 is hypomethylation so it is actively transcribed
- Mutation causes hypermethylation and inactivated in many cases of breast cancer
- inhibitors of HDAC are currently being explored as therapy for breast cancer and other solid tumors
Name an epigenome data base
NIH roadmap epigenome oroject
What are some outcome of the NIH Roadmap Epigeneomics Project?
1000 reference epigenome from a range of healthy and diseased cells
Data is organized in a database called the Human Epigenome Atlas
The roadmap epigenomics project has produced reference epigenomics that provide key information on key functional elements controlling gene expression in 127 human tissues and cell types
