II. Post-transcription | 22. Epigenetic regulation of eukaryotic transcription: the role of DNA methylation and histone modifications Flashcards
- Epigenetics
a/ Definition of epigenetics
- The study of inherited changes in the phenotype of a cell that do not result from changes in DNA sequence
- the hereditary transmission of information by means other than the sequence of nucleotides that comprise the genome.
- Epigenetics
b/ List epigenetic modifications
DNA methylation and chromatin condensation
- Epigenetics
c/ What is the purpose for the use of inherited epigenetic modification?
- Eukaryotic cells can use inherited epigenetic modification (DNA methylation and chromatin condensation) as additional gene expression mechanisms, without altering the DNA sequence.
- DNA methylation and histone modifications are complementary processes in determining the chromatin structure.
- DNA methylation
a/ Definition of DNA methylation
It is the addition of a methyl group (CH3) to a DNA molecule.
-> Methylation can change the activity of a DNA segment without changing the sequence.
- DNA methylation
b/ What are the 4 features of DNA methylation?
- Transcription factors able to bind only to non methylated binding sites (true for silence genetic regions).
- Another option is instead of inhibiting the binding of transcription factor, repressor protein would bind and compete with transcription factor.
- Some transcription factor favour the methylated DNA and leads to demethylation of methylated sequences and allows the binding of further transcrioption factors that can only bind to unmethylated regions.
- Some transcription factor which has different binding sites depending on the methylation characteristic of the binding site itself.
- DNA methylation
c/ What are CpG islands?
These are regions of DNA where a cytosine (C) is followed by a guanine (G) nucleotide in a linear sequence of bases along its 5’ -> 3’ direction (aka dinucleotide sequence)
- DNA methylation
d1/ What is the general mechanism of DNA methylation?
1/ Methylation usually occurs at the CpG (CG) islands.
2/ Many genes have CpG islands associated with the start of the gene (promoter regions)
3/ Active CpG island promoters have C’s in its sequence that are unmethylated -> unmethylated CpG island promoters have reduced affinity for histone octamers
- DNMT (DNA methyltransferase) will covalently modify a (5-)methyl-group to the C pyrimidine on the CpGs
-> {S-adenosyl-methionine (SAM) -> S-adenosyl homocysteine (SAH)}
-> SAM = methyl donor
4/ MBDs (= proteins with DNA sequences rich in 5- methylcytosine) binds to the 5-methylcytosine marked promoters, and associates with HDAC (histone deacetylases) + repressive chromatin remodeling complexes -> condense chromatin -> transcription repression
- DNA methylation
d2/ What is the mechanism of DNA methylation at promoter?
Left:
- trimethylated histone H3 Lys4 (H3K4me3), which marks active promoters, prevents binding to chromatin of the ATRX-DNMT3-DNMT3L (ADD) domain of DNA (cytosine-5)- methyltransferase 3A (DNMT3A) and DNMT3B (and also of DNMT3L), thereby causing it to bind to the methyltransferase (MTase) domain and auto-inhibit the DNMT3 enzymes.
Middle: in the absence of H3K4 methylation, the ADD domain binds to H3K4 and the auto-inhibition is relieved, thereby allowing the MTase domain to methylate the DNA.
Right:
- DNA methylation at gene bodies.
- In gene bodies, the ADD domain binds unmethylated H3K4, thereby releasing the auto-inhibition of the DNMT3 enzymes.
- H3K36me3 is deposited in gene bodies of actively transcribed genes and serves as a recruitment module for the DNMT3 PWWP domain.
- DNA methylation
d3/ How is DNA methylation at promoter maintained?
DNA methylation is maintained through mitosis
Left:
- E3 ubiquitin-protein ligase UHRF1 is recruited to replicating DNA through its SET- and RING-associated (SRA) domain, which binds hemimethylated CpG sites, and through its TUDOR (TTD) domain, which binds H3K9me2.
- The RING domain of UHRF1 ubiquitylates the histone H3 tails (Ub). The replication foci targeting sequence (RFTS) of DNMT1 folds into the MTase domain, thereby preventing its catalytic activity.
- UHRF1 recruits DNMT1 through an interaction between its ubiquitin-like (UBL) domain and the DNMT1 RFTS.
Right:
- the auto-inhibition of DNMT1 is released when the RFTS binds to ubiquitylated H3 tails, which enables the maintenance of symmetrical DNA methylation at CpG sites.
- DNA methylation
e/ What is the position and role of methyl groups on methylated cytosines?
The methyl groups on methylated cytosines lie in the major groove of DNA and interfere directly with the binding of proteins (ex: TFs) required for transcription initiation.
- DNA methylation
f/ What is the 2 applications of DNA methylation?
- X chrome inactivation
- Genomic printing
- DNA methylation
g/ What are the definition and role of X chromosome inactivation?
- X chromosome inactivation is a process by which one of the copies of the X chromosome is inactivated in female mammals.
- It prevents females from having twice as many gene products as males, who only have a single copy of the X chromosome
- DNA methylation
h1/ What is genomic imprinting?
It is an epigenetic phenomenon by which certain genes are expressed in a parent-of-origin-specific manner
-> an epigenetic process that involves DNA methylation and histone methylation without altering the genetic sequence
- DNA methylation
h2/ How does genomic imprinting occur?
1/ if the allele inherited from the father is imprinted, it is thereby silenced and only the allele from the mother is expressed
2/ if the allele from the mother is imprinted, then only the allele from the father is expressed.
- DNA methylation
h3/ What are examples of the disorders associated with genomic imprinting?
o Prader Willi syndrome: parental deletion of specific loci – inherited from father (chromosome 15)
o Angelman syndrome: maternal deletion of specific loci – inherited from mother (chromosome 15)
- What is DNA demethylation?
It the process of removal of a methyl group from cytosines. It can either be =
- (1) passive: process takes place during several replications of a new DNA strand that is absent of methylations
- or (2) active: occurs via direct removal of a methyl group through an enzymatic process.
- Histone modification
e1/ How does Histone acetylation + deacetylation occur?
- Histone-tail lysines undergo reversible acetylation + deacetylation by enzymes that act on specific lysines in the in the histone N-terminal
- Lysine (K) H3K27ac, H4K5, K8, K12
- Histone modification
e2/ What are the characteristics of Histone acetylation and deacetylation forms?
1/ Acetylated form: the (+) charge of lysine is neutralized -> less attraction to the (-) charged DNA -> chromatin forms less condensed ‘’beads-on-a-string’’ conformation -> open gene = activate transcription.
+) Done by histone acetyl transferases (HATs)
2/ Deacetylated form: (+) charge of lysine goes back -> increased attraction to the (-) charged DNA -> further chromatin condensation -> closed gene.
+) Done by histone deacetylases (HDACs)
- Histone modification
j/ How does histone phosphorylation occur?
- The oxygen in hydroxyl groups (-OH) of serine + threonine side chains can be reversibly phosphorylated, introducing 2 (- ) charges.
- Each of these posttranslational modifications contribute to the binding of chromatin-associated proteins that participate in the control of chromatin folding and the ability of DNA + RNA polymerases to replicate/transcribe the associated DNA
- Usually occur on H3S10
- Histone modifications
l/ Examples of writers
- Histone modifications
m/ Examples of erasers
- Histone modifications
n/ Examples of readers
