LECTURE 7 Flashcards
By what date were genes being linked to disease
1980’s
Human genome project goal ?
Obtain the entire DNA sequence of the haploid human genome
main guy in the HGP
Francis Collins
Two ‘players/organisations’ in the human genome project?
IHGSC (international human genome sequence consortium ) Francis Collins, and Celera genomics (Craig venter
Difference in techniques used by both organisations?
- Mapping overlapping clones method
- Shot-gun sequencing
Public effort strategy?
Human genome (haploid) was partitioned into mini yeast chromosomes. Each chromosome was then sequenced. And assembled using human genome map (genetic)
Sequencing method?
1- Partial digestion of DNA which leads to overlapping fragments which is cloned into bacteria
2- This is analysed for markers or overlapping sites into a contig (continuous DNA sequence)
3- assembled stretching
4- A subset of overlapping clones that cover the entire chromosome are selected and fractured and the pieces are cloned
5- put together large large clones and filling any gaps
Second human genome project
Player b Celera Genomics - Craig venter. Privately funded and used shot gun sequencing
Method for shotgun sequencing ?
1- Genomic DNA is cut into small numerous fragments and cloned into bacteria
2- Each is sequenced
3- overlap in sequence is used to order the cloned
4- Computer programming is used to assemble the DNA sequence
Second human genome project compared to first
No markers
no mini chromosomes
when was the haploid genome first sequenced?
2001-draft
2004- no gaps
first free living organic to be sequenced
Haemophilas influenza
1993
Genomics
Study of the genomes
Were the expectations met for the human genome project?
No,
we still don’t understand the function of all genes and all genes.
Diagnosis and cure to diseases (genetic) still lots of research to be done.
What does genomics avoid
pre-selecting genes based on their function but looking for trends and patterns in DNA sequences
structural genomics
Looking at the structure of genes and sequencing (organisation)
comparative genomics
Comparing genomes between different species. Evolution
functional genomics
use techniques for accessing levels RNA
Expected size of genome?
50,000-1000,000 genes
how much of the human genome is coding?
1.4%
Transposons ?
short sequences found within DNA in multiple copies. Contain genes which allow the conversion to RNA and back to DNA
Majority of our DNA?
Has an unknown function.
Other genomes which were sequenced around the time of sequencing the human genome
influenza- first - 1995 yeast- 1995 worm -1998 2000-fruit fly 2002- mouse
Homologous
Genes which are evolutionarily related
Orthologs
homologous genes found in different species which have evolved from the same gene in a common ancestor
Paralogs
Homologous genes which have duplicated within the same organism
Accelerate evolution indicates? Low rates of evolution indicates what about a gene?
gene under selective pressure to change to become better suited to an organism
highly conserved gene= importance
Example of accelerated evolution?
Myoglobin, in aquatic animals to increase capture of oxygen
transcriptome?
All RNA molecules which were transcribed from a genome
Proteome
All proteins encoded for by a genome
ways in which we can analyse the transcriptome?
- Micro array
- Next generation sequencing
Method of next generation sequencing
Sequence RNA fragments against genome. Shred RNA into smaller fragments. .
Microarray method?
DNA probes fixed to glass slide. Each spot had a different DNA probe. RNA is extracted from cells, reverse transcriptase to form cDNA which pairs with complementary probe. After hybridisation, colour of the dots which show up on the screen a indicative of the volume of the mRNA present
Use of microarray in cancer
Can compare the difference of expression of genes between cancer patients and ‘normal’ patients. See where genes expressed which are in control of cell growth replication rates etc
