genomics Flashcards
genomics
study of all nucleotide sequences, including structural genes, regulatory sequences, and non-coding DNA segments in the chromosomes of an organism
structural genomics
physical structure of DNA within genome
what is a genome
single nucleotide sequence of an organisms hereditary info
can be DNA or RNA
range in size
human genome = 3.2 x 10^11
why is human genome project not finished
centromeres largely unsequenced due to repetitive sequences, or being very tightly packaged
comparative genomics
use genomic info from multiple species’ genome and try understand and identify evolutionary conservation
main goal to identify evolutionary conservation of DNA sequences between species
molecular evidence of evolution
DNA incorporates mutations at roughly equal rate so can act as molecular clock
more mutations = more divergent from ancestor
changes in DNA sequence can be ranked, producing branched trees to show species divergence at the molecular level
functional genomics
understanding how the genome is regulated by proteins
how proteins interact with DNA to regulate gene expression
method of DNA footprinting to identify TFBS
piece of DNA with TFBS we want to study, mix with purified set of transcription factors
TFs will bind to TFBS
use DNA-ase1 to cut up DNA
won’t cut where TF is bound so will have fragments of DNA with TF bound
also do control with same segment DNA but no TFs added
PCR and gel electrophoresis
get a gap with no bands where have TF present - where DNA was protected from DNA digestion. allows you to pick out where proteins bind on the DNA molecule
how to perform ChIP-Seq Assay
- treat cell w formaldehyde
- sonicate to break open cell and smash up the DNA
- add antibody specific to TF of interest –> mixture of antibody bound to TF
- use magnetic beads that bind to antibody
- bead-antibody-TF-DNA can now be washed to remove all else
- DNA purified
- now have DNA sample that used to be bound to TF (TFBS)
- sequence it with fancy computer
- will give billions of 50bp sequences
- computer align the given sequences with reference genome
- build up binding site profiles for specific proteins on the genome
epigenomics
study of heritable changes in gene function that can occur without the DNA sequence changing
changes in the way DNA is regulated
DNA methylation
chromatin remodelling
how can DNA methylation be inherited
methyltransferase adds methyl groups to C when in CG sequence that is opposite an already methylated site
If have bit DNA with methylation on both strands and it replicates, the new DNA will both have signal stranded methylation. the other strand will then be methylated to have 2 new DNA both double stranded methylation
how can changes in chromatin be inherited
heterochromatin - tightly bound. heterochromatin proteins coat the surface of chromatin
euchromatin - no coating proteins
when DNA duplicated so are the packaging proteins.
DNA microarrays can give genome wide expression profiles
- two samples (e.g. tumour and normal cells)
- carry out reverse transcription
- carry out PCR with the DNA, and also label it with fluorescent dye, different colour for each sankoe (red and green)
4.mix DNA samples together - hybridise mixture to microarray
- variety of spots with different colours will give info on gene expression
yellow = 50/50 mix so no difference in gene expression between tumour and normal
green = more expression in normal cells
red = more expression in tumour cells
SNPs
single nucleotide polymorphisms
peppered across DNA of the genome
may impact ability of protein to function
Genome wide association studies
can identify variation (SNPs) within genes
could be used to tailor medicine
identify variation between individuals
