Lecture 3 Flashcards
DNA… Is fixed across the same species but…changes
Quantity
Sequence
DNA. Repair percent
90-99
Methylation is an….that does not…..
Function
Can cause….
What is it..
Epigenetic modification
Follow genetics rules
Controls gene expression
Mutations
Adding methyl group to cytosine
5 methyl cytosine is a ….
Its ….in genomes is…
Associated with gene…
Post synthetic modification
Distribution variable
Repression
Animal cytosine
Plants cytosine
CpG
CNG
What is Dnmt1
Has very strong preference to
DNA methyltransferase enzyme that adds methyl groups to DNA bases
Already methylated CpG on the other strand
Methylation pattern is
Lack of dnmt1 causes
Inherited
Embryonic lethality
Dnmt3a and dnmt3b have the ability to
DeMethylate and introduce de novo methylations in gametogenesis
Absence of dnmt3
Dnmt3b function
Deficiency
Lethal
Methylates centromeric regions
Deficiency causes ICF syndrome
Methylation sequence during mammalian development
Preimplantation low
Implantation high
Rett syndrome
Mutations in MeCP2 gene that reads and binds to methylated DNA
CpG islands are….. regions rich in
Associated with
Exceptions when it is methylated
CG normally unmethylated
Gene promoters
Inactive x chromosome at dose compensation
Imprinted genes that either 1 copy is active (mother or father)
L1 and IAP retrotransponsons are never
DNA sequences that move around the genome but cant once methylated
Unmethylated
Inherited demethylated from mother then methylated
Alu
Why
Inherited methylated from mother but unmethylated from father then remethylated
Gene regulation and genomic stability
Methylation amount in different organisms
Caenorhabditis undetected
Drosophila very low
Mammals 2-7%
Plant 33%
5methylcytosine in vertebrates vs invertebrates
genes in unmethylated
Gene can be found in methylated (invertebrates)
Deamination
Amino grp removed from base
DNA:
cytosine>uracil (not a normal base usually fixed )
5methylcytosine>thymine
4 values of methylation
1.Cancer related (hypermethylation in tumor suppressor or hypomethylation in oncogenes)
2.satellites and heterochromatin DNA heavily methylated demethylated will cause decondensation and genomic instability as well as alter gene expression
3. Transposons inactivation
4. Hybrid marsupials failure of methylation leads to chromosomal remodelling and activation of retroviral elements
Transponsons what are they
Use
Danger
Other name
Replicate and jump from one part to another in the DNA
Evolution and genetic diversity
Too much activity will cause genetic instability and disease
Interspersed repetitive sequence
Failure in methylation in hybrid marsupials can cause
Activation to retroviral elements and cause chromosome remodeling
The C value paradox
DNA is …grams and….m
Variation in … does not equal…
Example
Amount of DNA in a haploid cell does not relate to organism complexity
6-7pg. 2m
Size, variation in general
Syntenic genes in pufferfish and human
Gene number is …..than the total DNA
Percentage
Less than
5800 to 39000
Only 10% of total genome
The larger the genome the….the…
Larger the repetition
Repetitive DNA types
Regarded as
Except
Tandem block
Interspersed throughout but not block
Junk
Telomeres a d drosophila heterochromatin
Satellite types
Mini, VNTR 10-100 0.5-30kb
Micro no more than 6 usually 2 or 3 in all organisms distributed throughout the chromosme
Less common in coding regions and telomeres
Calssiccal
Classical satellites
Number
Percent
Several…can…in the same…
Rich in
Very short repeats cause…
2-7bp
2 crab
6 mammals
7 drosophila
Can be up to half the genome
Types occur block
AT and CG than main band
Strand asymmetry difference between the 2 strands
Some defects
Unequal crossing over due to repeated sequnce
Gene conversion
Replication slippage
What is gene conversion
DNA sequence replaces a homologous sequence so that they become exact
Repeated genes
What are they
Often concentrated in…
Like
RNA/ 5S rRNA/tRNA/ histones
Genes with products req in large quantities which are kept identical
Specific regions of the chromosomes 18s and 28 s
Protein families
Globins each with a distinct function do not form clusters
Homeobox genes are related in function and forms clusters
What is ICF syndrome
Immunodeficiency Centromeric instability and facial anomalies
A disease of DNA methylation
There is….in bothe the amount of DNA between species and its ….within individuals
Extensive variation
Sequence
C value paradox the ..of DNA in…
Amount
Haploid genome
Tandem repeats are referred to as
Satellites
The most common dinucleotide in human and drosophila is…
Plants..
CA
GA/AT
Microsatellites are less common in…
Coding regions
And telomeres
Damage agent repair
Pyrimidine dimer
Alkylation and depurination
Mispaired bases
UV- photorepair
Chemicals-excision repair
Replication errors-mismatch repair
