Genomics - lecture 6

Question 1

What is the goal of the human Genome project?

Answer 1

Obtain the entire DNA sequence of the haploid human genome

Question 2

who were the two organisations that funded the Human Genome Project?

Answer 2

• International Human Genome Sequence Consortium ,headed by Francis Collins
• Celera Genomics, headed by Craig Venter

Question 3

Funding type and technique used by the International Human genome Sequence Consortium

Answer 3

• Public funding , free access to all

- Used mapping overlapping clones methods

Question 4

Funding type and technique used by Celera Genomics

Answer 4

• private funded

- used whole genome shotgun strategy

Question 5

What was the public effort strategy?

Answer 5

• The human genome was partitioned into large sequences and stored in yeast mini chromosomes
• Each mini chromosome sequenced
• sequences then assembles

Question 6

What as the technique used by public funded strategy?

Answer 6

Human genome sequencing strategy

Question 7

An overview of the human genome strategy

Answer 7

• partial digestion of DNA
• large- insert clones are analysed for markers or overlapping restriction sites
• These can then be assembles into a contig (continuous stretch of DNA)
• A subset of overlapping clones that cover the entire chromosome are selected and fractured , these pieces are then cloned.
• Each of these small- insert clones is sequenced and overlap to determine the structure

Question 8

Why was the human genome sequencing strategy not useful?

Answer 8

Progress was very slow

Question 9

The second human genome project, used Whole- genome shotgun sequencing

Answer 9

• Genomic DNA is cut into small overlapping fragments and cloned in bacteria
• Each fragment sequenced
• overlap is used to sequence the clones , the entire genomic sequence is assembled by powerful computer programs

Question 10

What is structural Genomics?

Answer 10

Determines the DNA of sequences of entire genomes

Question 11

What is the aim of structural genomics?

Answer 11

To understand the organisation and sequence of genetic information contained within a genome

Question 12

What was the big discovery, in regards to gene number.

Answer 12

estimated that there would be 50,000 to 100,000 genes

Roughly 20-22k genes

Question 13

What is the difference between nuclear and mitochondrial genomes?

Answer 13

nuclear genome only 1.5% protein coding vs mitochondrial genome is 93% protein coding

Question 14

What are transposons?

Answer 14

• half our genome is made up of them , no one knows exactly what they do

Question 15

What is comparative genomics?

Answer 15

Refers to the comparison of genomes to understand evolution of genes and species and the function of genes

Question 16

What are the aims of comparative genomics?

Answer 16

• To annotate genes and identify conceived and functional areas
• To understand how genomes evolve
• To understand how species relate to each other
• To understand the function of genes

Question 17

What are homologous genes

Answer 17

Genes that are evolutionarily related through speciation

Question 18

What are orthologs

Answer 18

Homologous genes in different species that evolved from th same, gene in a common ancestor

Question 19

What are paralogs

Answer 19

Homologous genes arsing by duplication of a single gene in the same organism

Question 20

Sequence evolution and functional relevance

Answer 20

Genes can show accelerated rates of evolution or unusually low rates of evolution .

e.g accelerated evolution = myoglobin shows accelerated evolution to increase oxygen capture

Question 21

Definition of the transcriptome

Answer 21

All the RNA molecules transcribed from a genome

Question 22

Definition of the proteome

Answer 22

All the proteins encoded by the genome

Question 23

Transcriptomics; the techniques to understand the gene activity

Answer 23

• Microarrys : nucleic acid hybridisation - using a known DNA fragment as a probe to find a complementary sequence
• Next generation sequencing : Sequencing RNA fragments which are then annoyed by aligning them to a reference genome sequence

Question 24

What were the expectations from the human genome sequencing project ?

Answer 24

Within 10 years:

• We will understand the function of genes
• We will understand the genomic basis of many diseases including cancer
• We will be able to use this knowledge to diagnose and cure these diseases…