Human Genome and Karyotype Flashcards
Genome size
Dna, genes, #chroms
# genes in mito
3.2 billion bps
22,000 genes
23 pairs of chroms
37 genes known
Chromatid
After DNA is replicated, form a pair of sister chromatids attached by a centromere
C-value enigma
some single celled organism have larger genome size than humans
Ploidy
Chrome number does not correlate with genome size/complexity
Mechs that lead to increased genome comlpexity/size
Duplication of existing sequences (evidenced by multilane families)
Lateral transfer-incorporation of DNA from other species
RNA vs DNA
RNA may have preceded DNA
- more complex and diverse in functions
- BUT DNA is stable
ENCODE Project
Essentially mapped genome for 80 different cell types for exons, histone mods, regions where dna cleaves, binding of many tf factors
Encode projet conclusions
80% of genome is functional and noncoding regions may be more important than protein coding in determinants of health and disease
CTCF encriced
insulated-no interactions with enhancers or promoters
enchancers
open, h3k4me1, h3k28ac, bound tf’s
Promoters and tf start sites
h3k4me3, bound pol 2/3 and proximal binding tfs
transcribed regions
h3k36me3, elongationg form of polymerase, polyA+ RNA
Repressed
H3k27Me3, bound polycomb group proteins
Functional states of chromatin
cell type specific
Functional DNA
sequences that display a reproducible biochemical signiture
Encode on evolutionary genome
a lot of baggage through evolution but doesn’t hurt us enough to be eliminated through evolution
Variation in genome
Much is of unclear significance-try to find ones that affect phenotype
Tandem repeats
ancient repeats have diverged in nucleotide over time. recent rrepates have over 90% sequence identity
repeats of genes or blocks of genes
repeats homology make hot spots for recombination
-can cause inversion, duplication or deletion
% of genome that natural selection operates on
10%
red green color blindness
Recombination of duplicate genes that are almost same sequence on x chromosome
- misalingment in meiosis followed by recombination
- may lose a single receptor gene -cant distinguish between red and green
red(long), green(medium_)
males with deleted x have only 1 receptor-cant distinguish
Contiguous gene syndromes
Microdeletion or segmental aneuplidy syndromes
recombination in large repeates deletes a block of dna with multiple genes
Satellite sequences
microsatellites
short repeats
Tandem repeats of sequences a few hundred bp long-around centromeres and telomeres
Repeats of few nucleotides, copy number highly variable-used to identify parents
Called satellites because when dna fractionated-repeats form satellilite seen next to DNA peak
Retrotransposons
mRNA that is reversed transcribed and put somewhere else in genome
-25% of complexity of human genome
insertion into a gene can disrupt function
LINE, SINE, Pseudogenes
LINE-long interspersed nuclear elements-mRNAs encoding reverse transcriptase
SINE-copies of a short cellular RNA
-Alu sequences-most abundant-restriction site for Alu
Copies of cellular mRNAs that ar not transcribed b/c no promoter
When should you consider diagnosis of chromosome abnormality
hysical or menetal dev delayed
infertitly, sponaenous abortion, stillbirth
prenancy in woen over 35
cancer
G banding
cells incubated with colchicine, cells consense, stain with dye
dark-g bands
can identify chrome by size, banding pattern, centromere position
cochiicine
binds tubilin, prevents spindle function, arrests cell in metaphase
p vs q arm
p is short, q is long
metacentric, sub metacentric, acro centric, telocentric
middle of chrome
somewhat high on chrome
very high on chrome
at end of chrome-not in humans
g banding resolution
CAN ONLY SEE PROBLEMS OF MUTATIONS THAT ARE SAME AS TEST
Detects large changes in chrom structutre
lower resolution limit is like 45 genes-cant detect small changes
FISH
Chromatin fixed to slide, probe binds to DNA of complimentary seqeucen
Fast when done to interphase cells-lower resolution b/c dna not condensed vs metaphase
metaphase need to amplify cell number and use colchicine
prentnatal diagnosis
NEEDS SPECIFIC PROBE
+
ONLY DETECT TO POSITION WHERE YOU KNOW PROBE BINDS
-cant rule out genetic defects elsewhere
FISH resolution
better in metaphase
does not reveal single nucleotide deletion or changes somewhere else in genome
useful for detecting monosomes and translocations!
-can make more specific with more specific probe (small deletions, but not single base pair deletions)
Resolution decreases as number of probes increases
CGH
Comparitive Genome Hybridization
Array of oligonucs immobilized at different positions on glass slide (mercury)-completementary to sequenced spaced across genome
-compare PCR amplified patient genome with reference
Tells deletions, duplications
Can plot to see gain/ lose of chromatin
Limitation-can detect deletions or duplications but not inversions or translocations
CGH strength/weaknesses
detects very small changes in genome-anywhere
Detects only icnreases/cecreases in copy number
Cannot detect rearramgents without gain or loss (inversion/translocation)
Human polyploidy
not viable
Euplody vs aneupoidy
normal # vs more or less (trisomy and monosomy)
Aneuplodiy lethal for most except X, Y, small autosomes
Trisomy 21/13 designation
47 XY +21 or 47 XX +13
Kleinfelter syndrome designation
47, XXY
Turner syndrome designation
45, X
Translocations (2 types)
Recipricol
Non-recpircol
Abnormalites in chroms
translatiocs, inversion, duplications, deletions
Causes of chromosome alterations
dsbreaks in DNA, NHEJ, carcniogenesis, increased by radiation
How to identify + of chromasomes
Number of centromeres and then identify centromere to identify chromosome
Where are most common translocations?
Between afrocentric autosomal chromosomes
-conceptions with extrachroms usually die, but those with extra D or G group may survive because small
Short p arms of these chrome contain only genes for rRNA (rDNA gene copy number is very large)
Robertsonian translocations and designation
45, xx, 14,21 +rob(14q, 21q)
breakpoints occur within centromeres of D and g group chromosomes, with fusion of chromosomes and loss of p arms
carrier has normal phenotype
no loss of DNA in q arms
- short arms often lost, but nonlethal
- also have normal chr 14 and 21 from other parent
Results of meiosis in carrier of robertsonian translocation
normal
balanced carrier
trisomy 14
monosomy 14
monosomy 21
trisomy 21
at meiosis- 1 robertsonian, 1 normal chrome 14, 1 normal chrome 21
isochromasome 21
both arms from 21q
viable since diploid for 21q
but gametes receive either 1 21 q or no 21 q
trisomy 21 (down syndrome or lethal) or monosomy 21 (lethal)
Pericentric inversion
Dna between two breakpoints in the same arm are flipped (only in middle of chromosome but tips are okay)
