Eukaryotic genomics - 1

Question 1

When was the first genome sequenced?

Answer 1

1990s

Question 2

When was the human genome project?

Answer 2

1990-2003

Question 3

When was the ENCODE project?

Answer 3

2003-2012 - more functional info than the human genome project

Question 4

When was the 10,000 genomes project?

Answer 4

2012-present

Question 5

How many protein coding genes are there?

Answer 5

20,000 protein coding gene - 4% of human genome

Question 6

How man lncRNA genes are there in the human genome?

Answer 6

15,000

Question 7

How many genes in prokaryotes compared to eukaryotes?

Answer 7

P - 700-5000 genes

E - 12,000- 3,200,000 genes

Question 8

What is the difference in transcripton location in Eukaryotes and Prokaryotes?

Answer 8

E - mRNAs process in nucleus and translated in cytoplasm

P - mRNAs translated at same location as transcription

Question 9

What is the difference in genome structure between eukaryote and prok?

Answer 9

P - circular plasmid

E - linear chromosomes

Question 10

What proportion of the genome is protein coding?

Answer 10

The higher the eukaryote - the portion becomes smaller

Question 11

What gene features are important to consider

Answer 11

splicing
alternative splicing
Alternative transcription start sites
Alternative PolyA sites 
Alternative translation start sites

Question 12

Facts about model organism Saccharomyces cerevisiae?

Answer 12

12.1 mil bp
16 chromosomes
31% genes have human orthologs
0.05 introns per gene

Question 13

Facts about model organism Schizosaccharomyces Pombe?

Answer 13

14.1 mil bp
3 chromosomes
69% protein coding genes - human orthologs
0.9 introns per gene

Question 14

Facts about model organism C. elegans?

Answer 14

103 mil bp
12 chromosomes
26% of genome is introns

Question 15

Facts about model organism D. melanogaster

Answer 15

143 mil bp
60% of protein coding genes have human orthologs
2.5 introns per gene

Question 16

Facts about model organism Zebrafish?

Answer 16

1.7 bil bp
25 chromosomes
69% of protein coding genes have human orthologs

Question 17

Facts about model organism Must musculus?

Answer 17

3.5 bil bp

40 chromosomes

Question 18

Facts about Human

Answer 18

3.6 bil bp 
46 chromosomes
humans are 99.8% similar to each other 
8 introns per genes 
95% genes alternative spliced

Question 19

Facts about plant Arabidopsis thaliana?

Answer 19

136 mil bp
28000 p coding genes
5 chromosomes
4.8 introns per gene

Question 20

Facts about plant Zea mays?

Answer 20

2.1 bil bp
390000 protein coding genes
20 chromosomes
85% genome = transposons

Question 21

As complexity increases in eukaryotes…

Answer 21

coding % decreases
non-codifying % increases
repeat region % increases

Question 22

What is the NGS workflow?

Answer 22

Purified RNA/DNA

Library prep

Lanes on flowcell

Clusters of each DNA molecule

Sequencing by synthesis - every time nucleotide added, different colour emitted

Question 23

What is the RNA-seq workflow

Answer 23

Sequencing

Mapping/aligning reads to genome

calculate mRNA transcription levels

assemble transcripts de novo

build new mRNA transcript models

Question 24

What is exome sequencing?

Answer 24

sequence 1% of genome - corresponds to protein coding content
85% of disease causing mutations identified are found in exam

Question 25

What is ribosome profiling?

Answer 25

NextGenSeq of ribosome footprints

isolation of cyclohgeximide “frozen” mRNA-ribosome complexes

Ribosome footprinintg - RNaseI treatment

Footprint purification

Preparation for NGS linker ligation, RT, circularisation, PCR

28-34nt RNA fragment protected by ribosome

Question 26

What are single cell genomics?

Answer 26

sequencing individual cells separately rather than population in bulk

Question 27

What is nanopore sequencing?

Answer 27

direct sequencing - RNA or DNA of interest is being fed through the pore

change current as result of different sequences going through - can identify which nucleotide is going through based on changes in current

Question 28

Long read vs short read sequencing?

Answer 28

short read - get a snapshot of what is connected with what