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Chromosome Structure and Translocations
Terms in this set (35)
Cancer can be the result of...
-too many Chromosomes (too many genes)
-Translocations (moving a bit of one chromosome to another)
In order to mechanically be a chromosome, all you need is...
1) Telomeres (stabilize the two ends of the linear chromosomes)
2) Centromere (allows for accurate mitotic segregation)
3) Replication Origins (many needed because DNA Polymerase can only move so fast)
Genes not needed! They do not do anything that contributes to the mechanical properties of the chromosome
The density of Chromatin Packaging varies and is a reflection of...
Gene Density and Transcriptional Activity
More Compact, Less Active
Less Compact, More Active
What percent of the Human Genome encodes protein?
-these look like they used to be an RNA.
-remnants of mRNAs that were integrated into the genome
-they are mistakes that get carried along and, if they don't cause a negative consequence, there is no sense in deleting it.
-elements that "lived" in one part of the genome and moved to another place in the genome.
-some are able to physically cut themselves out of the genome and insert somewhere else. Then, they fill in the gap they just made with the same information.
LINEs and SINEs are...
LINEs are transcribed by...
...RNA Pol II, the mRNA is copied into DNA by reverse transcriptase, and the DNA is integrated into the genome at a new site.
SINEs do not...
...encode any genes.
Retroposon and Transposons Schematic
-Reverse Transcriptase is encoded by the RNA
-Pseudogenes "piggy back" on the Retrotransposon Mechanism.
Alpha-Satellite Repeats are usually associated with...
-intervening sequences processed out of primary transcripts during the production of mRNA
Microsatelites (VNTRs or HVRs)
-can be in coding regions or not; they are useful to us as markers for genetic variation but we don't know functions for them in general.
-help us assure that someone's DNA is working properly (utilized in diagnostics)
Translocation from Chromosome 8 to 14 t(8;14)
-puts the normal open reading frame for c-Myc under the control of the very strong IGH promoter/enhancer, leading to overexpression of c-Myc.
-caused by DNA Damage
What is involved in the Translocation process?
Double-Stranded Breaks (DSBs)
A human chromosome must have...
...a single centromere/kinetochore for accurate mitotic segregation
...an adequate number of replication origins to be copied
...telomeres protecting the linear ends of the DNA molecules.
Human chromosomes contain many sequences that don't serve known functions, such as......as well as many repeated sequences, non-coding RNAs and intergenic regions whose functions are known in some cases but not in others.
...pseudogenes, transposons, microsatellites
Translocations occur when...
...DNA molecules break and are rejoined inappropriately during repair in a way that fuses sequences from different chromosomes.
Translocations can join the regulatory or functional features of one gene with another gene, leading to...
...inappropriately regulated normal genes, or genes with new, inappropriate functions
Translocations can be detected by...
...FISH or PCR, but only if their approximate location is known in advance (good for common events)
Microarray-based methods like Comparative Genomic Hybridization or whole genome sequencing can detect...
...increased or decreased copy numbers of genes without prior knowledge of the type of event being sought, but reciprocal translocations are difficult to detect with these methods.
Figuring Out Which Technique to Use
-Do you know where/what the sequence of the mutation is?
.....if yes, OLIGONUCLEOTIDE to find the specific seq or PCR
.....if no, Microarray
What do you need to know in order to do PCR?
-the sequence you are looking for.
PCR tells us what two things?
-whether a template is present (and if so, how much)
-how far apart the two primers are on the template.
Quantitative PCR Reaction Product Tracings
-the farther to the left, the more effective the treatment (because farther left means less templates of the certain cancer causing translocation are being made)
-the more ng of template, the less cycles it takes to cross the Crossing Point. 2^#=Fold Difference on How Much Template there is
-PCR IS EXTREMELY SENSITIVE
PCR vs RT PCR?
-PCR: Template is DNA and we are looking at Genome to find answer to questions about a Translocation, etc.
-RT PCR: Template is RNA and we are looking at how many TRANSCRIPTS are in a Cell.
RT PCR Process
Amplified RNA means...
...a strong PROMOTER was placed in front of the gene
Amplified RNA AND DNA means...
...there are too many copies of the GENE
-c-Myc translocation can be detected by FISH with a set of "split apart" probes
Excess c-Myc drives what two processes?
1) transcription of genes involved in cell cycle progression
2) prevents repression of genes involved in maintaining quiescence
-High levels of c-Myc promote formation of c-Myc-Max complexes, and prevent formation of Mad-Max complexes
Splitting in the MIDDLE of a gene causes...
...an aberrant protein product to be made.
Split Apart FISH Analysis uses what probe to detect what target?
It uses a DNA Probe to detect a Chromosomal DNA Target.
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