Genomic Regulation Flashcards
euchromatin
Lightly packed form of chromatin- (DNA, RNA and protein)
Highly enriched in genes
Often (but not always) under active transcription
Most active portion of the genome
Approximately 92% of the human genome is euchromatic
heterchromatin
condensed –> Stains darkly throughout the cell cycle, even in interphase
Thought to be late replicating and genetically inactive
Highly concentrated at centromeres and telomeres
Contains very few active genes:
Those that are present are resistant to gene expression
position effect
Activity a gene depends on relative position on chromosome:
Actively expressed genes will be silenced if relocated near heterochromatin
copy number variations detection
Comparative Genome HybridizationProbe Human Genome CHIP with DNA from one
person and with DNA from a ‘normal’ reference DNA
- can detect deletions of genes
long terminal repeats
Repeat hundreds or thousands of times
Found at either end of retrotransposons (proviral DNA)
Formed by reverse transcription of retroviral RNA
Used by viruses to insert their genetic material into the host genomes
Histone Deacetylation
Actively Represses Gene Expression
compressed via HDACs (Histone Deacetylases)
opposed by Histone Acetyl
Transferase (HAT)
DNA methylation
methylate cytosine + adenine
–> At gene promotor –> Represses transcription
associated with: - Genomic imprinting • X-chromosome inactivation • Repression of transposable elements • Aging • Carcinogenesis
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
Direction of DNA synthesis
DNA-dependent DNA polymerase
5’ –> 3’
- requires a primer with a free 3’ -OH to begin
DNA helicase
unwinds DNA Protein with 6 identical subunits
Bind and hydrolyze ATP –> Conformational change
Propels it like a rotary engine
Passing through a center hole
DNA Topoisomerase
Reversible enzyme
• Breaks a phosphodiester bond
• Changes superhelicity
• Relieves supercoiling
anti-cancer agents target this!
–> Block the cell cycle
• Generate single and double stranded breaks
• Harms the integrity of the genome
• Leads to apoptosis and cancer cell death
UV radiation DNA damage
produce a covalent linkage between two adjacent pyrimidines (T-T or C-T)
• Pyrimidine dimers
non-ionizing radiation
bases bond (thymine-thymine)
ionizing radiation
DNA protein crosslinks are induced
ex: thymine-tyrosine bind
spontaneous DNA damage
–> Depurination: 5000 purine lost, bases/day
–> Base deletion or substitution
–> Deamination:
adenine –> hypoxanthine
guanine –> xanthine
cytosine –> uracil
Why are Methylated Cytosine Residues in CpG Sites/Islands problematic?
CpG Sites/ CpG Islands (Adjacent Cytosine-Phophate-Guanine)
Associated with inactive genes
T mismatches with G
Methylation of CpG islands stably silences genes (Cancer/DNA Repair Genes)
Cross-linking chemical agents
prevents DNA replication and transcription nitrogen mustard cisplatin mitomycin C carmustine
alkylating agents
attach akyl group dimethy sulfate (DMS) methyl methanesulfonate (MMS)
intercalating agents
insert into DNA b/t pairs -> unwinding, separation of bps ethidium bromide **thalidomide doxorubicin daunomycin
deamination
adenine -> hypoxanthine
guanine -> xanthine
cytosine -> uracil
ionizing damage
strand breaks
modify bases
DNA-ptn crosslinks
*recombination repair
nonionizing DNA damage
thymine dimers
covalent linkage b/t adjacent pyrimidines (T-T)
- direct repair
- nucleotide-excision repair
base-excision repair
single base mismatches
small non-distorting alterations
depurination
altered base flipped out detected by DNA glycosylases endonuclease cleaves bond lyase removes phosphate DNA pol adds correct nt ligase
nucleotide excision repair
chemical adducts -> distort DNA
pyrimidine dimers
BPDE-guanine adducts
cisplatin adducts
NER complex recognizes distortion
create nicks, remove stretch
DNA pol, ligase
mismatch excision repair
mismatched base in daughter strand
MER complex (detects error) helicase/endonuclease (cuts out wrong base) DNA pol, ligase
