MCB Lecture 24 ENCODE

Question 0

When did ENCODE occur?

Answer 0

1990-2003

Question 1

What does ENCODE stand for?

Answer 1

Encyclopaedia of DNA elements

Question 2

What is Celera and what effect did it have on ENCODE

Answer 2

This is a private company that started its own project.

This accelerated the completion of the public project ENCODE

Question 3

What were the goals of ENCODE?

Answer 3

1. Complete sequence
2. Identify all genes
3. Physical and genetic map
4. Detailed annotation

Question 4

What is important about Sanger sequencing?

Answer 4

This was used to carry out the ENCODE project

Question 5

Describe the process of Sanger sequencing

Answer 5

1. Single stranded DNA, primers, DNA pol, dNTP and ddNTP are combined
2. The DNA pol elongates the complimentary DNA strand
3. Every so often, a ddNTP will be added in, and no more nucleotides may be added because there is no hydroxyl group on the 3’ carbon
4. This creates DNA fragments of many different lengths
5. The fragments are run on a gel that resolves down to differences of one nucleotide
   6a. Read manually 6b. Automated reading

Question 6

What was the important technical advance with Sanger sequencing that allowed the ENCODE project to occur?

Answer 6

Automated sequencing

Question 7

Describe the change in cost of Sanger sequencing over the years

Answer 7

Reduced in cost
Before: $1 per base
Now: thousands

Question 8

How many bases can Sanger sequencing do per run?

Answer 8

800-1000

Question 9

What are 5 new generation sequencing techniques?

Answer 9

Illumina
454
Ion torrent
ChIP seq
RNA seq

Question 10

Describe Illumina

Answer 10

Imaging detects different colours associated with the different nucleotides

Question 11

Describe 454 sequencing

Answer 11

Fluoretic chambers containing DNA

Detect the length of nucleotides added

Question 12

Describe Ion torrent sequencing

Answer 12

When a nucleotide is added, a proton is given off

This is detected by a very sensitive pH monitor

Question 13

Describe ChIP Seq

Answer 13

Sonic action of the DNA to break it up
Specific proteins bound to DNA are selected out
The protein is degraded.
We now have DNA that is associated with a certain protein
Sequence this DNA

This allows us to determine activity of different bits of DNA at different points in time in different tissues

Question 14

Describe RNA seq

Answer 14

RNAs synthesised from DNA are sequenced

This tells us about transcribed regions in different tissues at different times

Question 15

When did the next generation techniques arise?

Answer 15

After the end of the ENCODE project, 2003

Question 16

What is good about the next generation sequencing techniques

Answer 16

Cheaper
Faster
Quicker

Question 17

Describe 3 cases of personal genomics

Answer 17

Michael Schnyder
Watson
23 and me

Question 18

What do the cancer sequencing projects intent to do?

Answer 18

Sequence many cancers to identify mutations that cause cancer
Also, what sort of mutations they are, how they arose

Question 19

What are some issues to do with the ENCODE project?

Answer 19

A raw sequence is difficult to interpret

What about function?

We don’t need the entire sequence to identify disease linked mutations

Question 20

What did the ENCODE achieve in terms of functional characterisation of the genome?

Which functions are aimed to be characterised? (4)

Answer 20

They were able to characterise the function of 80% of DNA regions

1. Transcription factors
2. Histone modification
3. Regions of transcription
4. Chromatin structure