The Epigenome Flashcards
What is the genome?
→ The complete set of genetic material in a cell
→ DNA sequence present in a full set of chromosomes
What forms the first level of packing?
→ Histone proteins forming nucleosomes
What are the features of euchromatin?
→ Gene rich
→ transcriptionally active
→ nucleosomes are far apart
What are the features of heterochromatin?
→ Gene poor
→ less transcriptionally active
→ condensed appearance
→ repetitive DNA
Describe the packaging of DNA
→ Nucleosomes wound to make 30nm fibres
→ fibres wound up further with scaffold proteins
→ chromosomes are most densely packed
What is the epigenome?
→ the sum of all the heritable changes in the genome that do not occur in the primary DNA sequence that affect gene expression
What does an epigenetic change result in?
→ A change in the phenotype but not genotype
What are the 4 epigenetic mechanisms?
→ DNA methylation
→ histone modification
→ X inactivation
→ Genomic imprinting
What is DNA methylation and what does it require?
→ The addition of a methyl group in the 5’ position of cytosine
→ DNA methyltransferase
→ S-adenosyl methionine to provide the methyl group
How is DNA methylation done?
→ DNA methyltransferase enzymes
What are the DNA methyltransferase enzymes?
→ DNMT1
→ DNMT3a
→ DNMT3b
In differentiated cells where does DNA methylation occur?
→ in CpG nucleotides (C next to a G)
When does passive demethylation occur?
→ During replication
What is passive demethylation done by?
→ TET enzymes - ten eleven translocation enzymes
→ TDG - thymidine DNA glycosylase
What is the function of TET enzymes?
→ They catalyse the movement from 5 methylcytosine to hydroxy methyl cytosine to formyl to carboxy
What is the effect of DNA methylation?
→ Turns transcription off by preventing the binding of transcription factors
What is a CpG island?
→ A region of DNA where CpG is more frequent than normal
What is histone modification?
→ The addition of chemical groups to proteins that make up the nucleosome
What are common histone modifications?
→ Acetylation and methylation
What are modifications named based on?
→ Histone
→ amino acid
→ actual modification
What does a H3K4Me3 mean?
→ on histone 3
→lysine at position 4 is trimethylated
What are the three types of histone modification enzymes?
→ Writers
→ Erasers
→ Readers
What are examples of 2 writer enzymes?
→ Histone acetyltransferase - HAT1
→ Histone methyltransferase - EHMT1
What are 2 examples of eraser enzymes?
→ Histone deacetylase - HDAC1
→ Histone demethylase - KDM1
What are 2 examples of reader enzymes?
→ Bromodomain and extra terminal (BET) proteins - BRD2
→ Chromodomain proteins - CBX1
What is the effect of histone acetylation at lysine residues?
→ Relaxes the chromatin structure and makes it accesible to transcription factors
Why does chromatin relax when acetyl is added at lysine residues?
→ Lysine is basic
→ if you add an acetyl (acid) group it relaxes the chromatin
What is the effect of histone methylation?
→ Can repress or activate transcription depending on where it occurs
How can histone modifications occur and what happens as a result?
→ at the same time (concurrently)
→ their effects can interact or modify each other
Why does X inactivation occur?
→ ensures that every somatic cell in humans has the same number of active copies of every gene
Why is X inactivation needed?
→ Y chromosome has virtually no genes
→ only one copy of X in males
Describe how X inactivation occurs?
→ Xist gene is transcribed as long noncoding RNA from the X inactivation centre
→ It then binds all over the X chromosome
→ histone acetylation is removed and histone methylation occurs
What are inactive X chromosomes called?
→ inactive X chromosomes are heterochromatic - Barr body
What is Tsix and what does it do?
→ It is derived by transcription in the opposite direction and antagonises Xist RNA to keep one X active
Give an example of X inactivation in cats
→ all tortoiseshell cats are female
→ they have one X with an orange fur allele and one X with a black fur allele
→ Random X inactivation results in patches of orange and black fur
What is imprinting?
→ the ability of a gene to be expressed depends upon the sex of the parent who passed on the gene
→ functionally hemizygous
Willis syndrome
Where do imprinted genes tend to be found?
→ in clusters
What are imprinted genes mediated by?
→ Imprinting control regions
What mechanism causes imprinting?
→ One copy is silenced by DNA methylation
→ catalyzed by DMNT3a and histone methylation leading to inactivation
→requires SAM which is involved in methylation reactions.
When are imprinting patterns reset?
→ During gamete formation
How are epigenetics altered in cancer cells?
→ hypermethylation of tumor suppressor genes
→ hypomethylation of tumor activating genes
What enzymes are mutated in tumor cells?
→ DNMT3a and TET1/2
→ Histone acetyltransferases
→ Histone methyltransferases
→ Histone kinases
→ histone readers
→ histone demethylases
What are 2 DNA methyltransferase inhibitors?
→ 5 azacytidine
→ Myelodysplastic syndrome
What are 2 histone deacetylase inhibitors?
→ Romidepsin
→ Cutaneous T-cell lymphoma
What is the role of histone readers?
protein complexes that read combinations of marks: chromodomains specifically recognize methylated residues, while bromodomains bind acetylated residues.
