Module Flashcards
What is a nucleosome?
Unit of chromatin- DNA wound around 8 histone
proteins 1.65 times
What charge are histones?
positive
What charge is DNA and why?
negative, due to the phosphate groups
What is the function of H1?
stabilising chromatin in higher order chromosomal structures e.g. 30 nm fibres of chromatin
Name 2 mechanisms to make chromatin more accessible:
- Histone modifications e.g. HATs
- chromatin remodelling complexes
What are HATs and HDACs?
- Histone Acetyl Transferases
- Histone Deacetylases
What do HATs do?
transfer acetyl groups to histones,associated with euchromatin, linked to increased gene expression
What do HDACs do?
remove acetyl groups from histones, allow histones to wrap more tightly, less accessible
What are the 3 stages of Transcription?
Initiation
Elongation
Termination
What does RNA Pol I transcribe?
rRNA
What does RNA Pol II transcribe?
mRNA
What does RNA Pol III transcribe?
tRNA
What happens in transcription initiation?
- RNA pol and transcription factors bind to promoter
- form a closed pre-initiation complex
- complex opening separates 2 DNA strands and moves template strand to active site of RNA Pol
- Abortive synthesis
- Promoter escape
What happens in transcription elongation?
- RNA pol travels along template DNA strand in 5’ to 3”
- Synthesises RNA strand 5’ to 3’
- Transcription bubble
In Transcription, what 2 sequences is the cleavage site found between?
AAUAAA - upstream
GU- rich - Downstream
How is transcription terminated when the cleavage sequences have been transcribed?
- CPSF binds to AAUAAA
- CstF binds to GU-rich
- Forms protein complex
- CPSF cleaves downstream of AAUAAA site
- Poly(A) polymerase adds a 3’ polyA tail
List 3 aims of the 100,000 genomes project:
- Increase understanding of genetic variants -> new treatments
- Bring about personalised medicine
- Greater understanding of genomic medicine benefits
What are the aims of the gnoMAD project?
- Bring together exome and genome sequencing data from large scale sequencing projects
- Summarise data for wider scientific community
What are the aims of the EXAC project?
To create a browser to display large population datasets of genetic variation and display gene variation
What Biochemical evidence shows that the non-coding
genome is important?
- Pervasive Transcription
- Functional genomic elements
What Genetic Evidence shows that the non-coding genome is important?
- GWAS
- Non-coding mutations -> mendelian disease
- higher non-coding conservation across mammalian evolution
What is a silencer?
combination of short DNA sequence elements that suppress transcription of a gene
What is an insulator?
DNA element that acts as a barrier or a blocker of enhancers
What is an enhancer?
short region of DNA that can be bound by activators to increase the likelihood of a gene being transcribed
How do enhancers increase gene expression?
promoter-enhancer loops
allow transfer of regulatory elements (TF’s) over a long distance
Give 4 reasons why it is hard to identify enhancers:
- found at various distances from target promoter
- found/regulate upstream and downstream genes
- scattered across 98% of the genome
- many enhancers not evolutionarily conserved
What is gene panel sequencing?
targeted sequencing to detect changes in a selected panel of genes known to cause the phenotype
What is Clinical Exome Sequencing?
targeted sequencing of exons of known disease genes
What is Whole Exome Sequencing?
sequencing of all exons of all genes
How many disease causing variants are found within Exons?
> 85%
What are the 2 Purine bases?
A
G
What are the 2 Pyramidine bases?
T
C
What type of mutation are ‘point mutations’?
Base Substitution
What are Transition point mutations?
purine substituted for another purine
pyramidine substituted for another pyramidine
What are Transversion point mutations?
purine substituted to pyramidine (vice versa)
What is a silent mutation?
mutation that results in a synonymous codon
amino acid sequence stays the same
What is a missense mutation?
base substitution resulting in a different codon
What are the 2 types of missense mutations?
conservative (similar structure+function)
non-conservative (different structure+properties)
What is a nonsense mutation?
base substitution resulting in a stop codon
What are deletions?
deletion of one or more base pairs deleted from DNA sequence
causes altered translational frame
What are insertions?
insertions of additional base pairs, if it’s not a multiple of 3 then causes frameshift
What are INDEL mutations?
length difference between 2 alleles and can’t be known if it’s due to an Insertion or Deletion
How long is the mitochondrial genome?
16,569 bp’s
List 3 features of mtDNA?
- double stranded
- circular
- encodes 37 genes
what is the mutation rate in mtDNA?
1/33 generations
What is Heteroplasmy?
The presence of more than one organellar genome within a cell/individual
What are the risks of mitochondrial transfer procedures?
- mtDNA carryover
- technicality of procedure
- operator dependent
- virsuses used (karyoplast removal)
What are the + and - of Polar body mitochondrial transfers?
+ easier to obtain polar bodies
+ simple procedure-> micropipette
+ lower mtDNA carryover
- more invasive
What ae the relative risks of mTDNA carryover in mitochondrial transfer procedures?
PB1T
What is linkage disequilibrium?
The non-random association of alleles at different lociu
How can you tell when linkage disequilibrium has occurred?
When 2 alleles are inherited together more often than you’d expect by chance
What are 3 characteristics of mendelian disorders?
- Rare
- Specific pattern of inheritance
- Caused by pathogenic variant
List 6 limitations of GWAS studies?
- Large sample size needed
- Effect sizes are small
- Causal pathway not always determined
- SNPs aren’t responsible for all variation e.g. CNVs
- Limited ethnic studies
- Pleiotropy common (variants associated with multiple traits)
What is Y chromosomal testing useful for?
for ancestry DNA testing in men
What is mitochondrial DNA testing useful for?
determining maternal lineage
What are Short Tandem Repeats?
small sequences of the genome that are repetitive and relatively spaced out. Primer site son wither side are the same but no. of repeats between them varies
what characteristic of mtDNA makes it ideal for studying relationships between individuals?
Hypervariable region
DNA lasts longer - double membrane
Constant mutation rate
List 4 uses of autosomal testing:
- paternity
- Relationship e.g. siblings
- DNA fingerprint test
- Inherited Disease
In genetic testing, what do 12-18 markers show?
proves non-relationship
In genetic testing, what do 23-26 markers show?
non-relationship
In genetic testing, what do 37-43 markers show?
family markers become clean (e.g. cousins, 2nd cousins)
In genetic testing, what do 67 markers show?
perfect matches-> related
List 4 disadvantages of DTC Genetic Testing?
- false positives are common
- upsetting results
- little oversight/regulation of companies (privacy)
- Cause decisions based on incorrect info
List 4 advantages of DTC Genetic Testing?
+ promotes awareness of disease (better choices)
+ personalised health info
+ cheap
+ further medical genomics research
What percentage of cancer is sporadic?
80-90% (somatic mutations)
What percentage of cancer is hereditary?
5-10% (germline mutations)
What are driver mutations in cancer?
changes to a gene that drive cancer mutation
What are passenger mutations in cancer?
Mutations that don’t do anything to affect the cancer phenotype
In cancer, what can RT-qPCR be used for?
- Diagnosis + monitoring response to treatment of CML
- Recurrence risk in breast cancer
What is OncotypeDX?
Genomic test that analyzes the activity of a group of genes that can affect how a cancer is likely to behave and respond to treatment
