Lecture 2 Flashcards
Mutation rates differ across the genome, between species and by type. Methods of calculating mutation rates can be based on..
(2)
- the number of neutral sequences
- divergence between neutral sequences between two species
Types of neutral sequences include..
5
- junk DNA
- pseudogenes
- four fold degenerate sites
- ancestral repeats
- fraction deleted which reflects deletion rate
Four fold degenerate site:
2
- The situation in which any nucleotide in the third position still encodes the same amino acid.
- eg) The third base in the codons that encode glycine: GG and A, C, G or T.
Mutation rate is not even across chromosomes.. why?
3
- X chromosome mutation rate is lower than in the Y chromosome
- This is because there are more cell divisions in spermatogenesis than oogenesis in females.
- This means there are more opportunities for mutations to occur.
Mutation rates differ between species. A comparison between mice and humans showed
(2)
- 67% identity and 33% divergence
- This is an underestimation of divergence because parallel mutations and revertants can occur.
Dukes and Kantor model:
2
- Corrects for multiple hits
- We have diverged X, and we can figure out how many changes have happened over time, including parallel revertants, but excluding CpG’s (which can be biased)
Species have different mutation rates eg)
2
- Point mutations (single nucleotide mutations) have occurred twice as frequently in rodents than humans.
- Use an out-group species to
Indels (insertion/deletion of nucleotides) occurrence:
2
- Deletions occur more frequently than insertions
- Deletions are bigger than insertions.
How long ago did humans and mice diverge?
65-100 mya
2012 data, the Encyclopedia of DNA elements (the ENCODE project) showed that not only the protein coding sequences are functional. What else is functional?
(4)
- cis and trans regulatory elements
- DNA replication sites
- Histone modification sites
- The transcriptome was produced, and 75% of the genome is transcribed
What is the definition of function?
2
- if a TF binds, a transcript is produced, chromatin state is alters, does this imply function? (as ENCODE seems to think)
OR - if you were to lose it, would there be a fitness cost
How can you determine what type of selection is occurring?
2
- calculate divergence rates, synonymous sites, introns, intergenic regions, coding sequence etc.
- compare them to determine whether purifying selection or negative selection is occurring and whether there is any selective constraint
Divergence studies between D.melanogaster and D.simulans allowed calculation of.. and showed..
(3)
- divergence rates of CDS, synonymous sites, untranslated regions, introns, intergenic regions and pseudogenes.
- this showed that there is a lot of selective constraint acting on CDS and UTRs, and this is why they are evolving slower.
- Mutations may arise there, but they are purified out by negative selection because they are deleterious.
Phylogenetic footprinting:
2
- looking across different sequences to determine whether there is a transcription
- Test putative regulatory elements with transgenic experiments
DNAse1 footprinting steps
6 steps
Flourescently label one end of the gene.
- Region of DNA bound by DNA binding protein
- Random cleavage by nuclease or chemical
- Removal of the protein
- Separation of the DNA strands
- Separation by Gel electrophoresis
- A footprint will show where no cleavage occurred, because of the binding of the DNA binding protein
