Genomic Regulation Flashcards
• Euchromatin
Lightly packed form of chromatin, highly enriched in genes, often under active transcription, most active form of the genome
• Heterochromatin
very condensed, genetically inactive, contains few active genes, position effect: Activity of an active gene is silenced if moved near heterochromatin
• Histone Acetylation
modifying enzymes involved in histone acetylation are called histone acetyltransferases, promotes gene expression
• Histone Methylation
the transfer of one, two, or three methyl groups from S-adenosyl-L-methionine to lysine or arginine residues by histone methyltransferases
• Phosphorylation-
compaction is achieved by repeatedly folding chromatin fibers into a hierarchy or multiple loops and coils, accomplished by phospholylation of Histone H1
• Helicase
Unwinds DNA helix, bind and hydrolyze ATP, 1000bp/sec
• Topoisomerase
Relieves overwound supercoils, every 10 bp replicated corresponds to one turn, used as a target in anti-cancer drugs
Nucleoside analog inhibitors (Correlation box)
- DNA synthesis involves the formation of 3’ to 5’ phosphodiester bonds, nucleoside analogs that lack the 3’-OH group act as drugs that inhibit DNA replication
- Such nucleosides need to be converted to dNTPs before they can act as inhibitors of DNA polymerase
- Ex: arabinosylcytosine (treatment of leukemia)
i. Ionizing radiation (X-rays)
- 40 to 60 chemically distinct base damages
- Direct strand breaks
- DNA-protein cross-links
ii. Non-ionizing (UV light)
- Inducing formation of a covalent linkage between adjacent pyrimidine bases
- There are two outcomes
- Pyrimidine cyclobutane dimers (common)
- 6-4 covalent linkage of two pyrimidines (p53 cells)
iii. Spontaneous Mutation
- Depurination: 5000 purine lost
- Deamination: C to U change 100 bases/day
- Adenine becomes hypoxanthine
- Guanine becomes Xanthine
- Cytosine becomes Uracil
- Outcomes: DNA Replication Ensues or Base deletion or substitution
i. Direct repair
- Type of damage repaired: Pyrimidine dimers, O6-methylguanine
- Enzymes associated: DNA photolyase, Methylguanine methyltransferase
ii. Base excision repair
- Type of damage repaired: Single-base mismatch
* Enzymes involved: DNA glycolases, AP endonuclease, AP lyase, DNA polymerase, DNA ligase
iii. Nucleotide excision repair
- Type of Damage repaired: Chemical adducts (Nitrogen mustard, cisplatin, DMS, MMS) that distort DNA
- Enzymes involved: NER protein complex, DNA polymerase, DNA ligase
- Disease: Xeroderma pigmentosum
iv. Mismatch repair
- Type of damage repaired: mismatched base in daughter strand
- Enzymes involved: MER complex, helicase/endonuclease, DNA polymerase, DNA ligase
- MutS binds while MutL scans for nick and triggers degradation of the nicked strand
- Disorder: Hereditary nonpolyposis colorectal cancers
v. Recombination repair
- Types of damage repaired: double-strand breaks
- Enzymes involved: Exonucleases, DNA polymerase
- Mechanism involved: damaged ends filled in and joined, some base pairs may be missing
- Disorder: BRCA1/2 breast cancer
i. MSH 2,3,6, MLH1, PMS2
- Colon cancer
* Mismatch repair
ii. Xeroderma pigmentosum
- Skin cancer, UV sensitivity, neurological abnormalities
* Nucleotide excision-repair
ii. Hereditary nonpolyposis colorectal cancer
- Individuals with inherited mutations in one of the alleles of genes in the MER complex have an increased susceptibility
- An acquired mutation in the remaining good copy of the gene would then render the MER system non-functional and allow for tumor development
iii. Cockayne syndrome
- Rare autosomal recessive disorder
- Mutant genes involved are ERCC-6 and ERCC8 proteins
- Developmental and neurological delay, photosensitivity
- Death occurs in the first two decades of life
Epigenetics
Mechanism for regulating gene activity independent of DNA sequence that determines which genes are turned on or off
i. Methylation
- Methyl groups added to the DNA molecules by methyl transferase enzymes
- Changes the activity of a promoter region that mediates gene regulation
- Represses gene transcription when at gene promoter
- Essential for normal development
- Alternations of DNA Methylation…important component of cancer development
- Transcriptional silencing
- Can be inherited by daughter cells following cell division
- Occurs at the 5 position of pyrimidine ring of cystosine residues within CpG sites
- Hypomethylation- chromosomal instability, loss of imprinting
- Hypermethylation- associated with gene promoters, can arise secondary to gene (oncogene suppressor) silencing, might be a target for epigenetic therapy
• HATs
acetylate core histones to neutralize the positively charged lysines and facilitate chromatin condensation, DNA repair, and gene transcripton (activation of expression)
• HDACs
remove acetyl groups from the lysine on core histones and nonhistone proteins, cancer cells are very sensitive to HDACs inhibitors (valproic acid and vorinostat) (Repression of expression)
