02 Intro to the Genome

Question 1

How many bases in the human genome?

Answer 1

3 Gb x 2

Question 2

How much of the genome was sequenced in 2003?

Answer 2

92%. Just 151Mb of sequence that we weren’t sure about

Question 3

How much of the genome is repetitive sequences? (tandem repeats, interspersed repeats, LINES and SINES)

Answer 3

50%

Question 4

How long are SINEs and LINEs?

Answer 4

~400bp and 6kb respectively

Question 5

How do we describe someone’s genome when we look at it?

Answer 5

Just say how it varies from the reference genome

Question 6

How many differences do each of us have from the reference on average?

Answer 6

4-5 million

Question 7

How many SNVs do we have compared to the reference genome?

Answer 7

4-4.5million

Question 8

How many indels (<50bp) do we have compared to the reference genome?

Answer 8

700,000

Question 9

How many structural variants >50bp do we have compared to the reference genome?

Answer 9

25,000

Question 10

What is the Human PanGenome project?

Answer 10

A project trying to capture all the natural variation the exists between the whole diversity of healthy humans

Question 11

What were the initial estimates of the number of human protein coding genes?

Answer 11

65-80,000

Question 12

How many protein coding genes do we actually have?

Answer 12

About 23,000. 19,800 in the main assembly and 3,300 alternative sequences.

Question 13

Where was it found the genes were first broken up in chunks (exons and introns?)

Answer 13

In the ovalbumin gene in chicken

Question 14

Do all genes have introns?

Answer 14

No

Question 15

What’s the most introns in a gene?

Answer 15

360 in Titin

Question 16

What is the primary transcript?

Answer 16

When the whole gene is initially transcribed before the spliceosome makes mature mRNA

Question 17

Do introns have a function?

Answer 17

We don’t think so other than allowing alternative splicing

Question 18

How are alternative transcripts made?

Answer 18

Alternative start and end points, and splicing out whole or partial exons.

Question 19

Are all transcripts that are made functional?

Answer 19

We don’t know. It might be that some are just mistakes

Question 20

What is a Gain of Function?

Answer 20

When a cell gains expression when it shouldn’t, or in the wrong type of cell, or a higher level of expression, or sometimes a new actual function.

Question 21

What inheritance pattern does a gain of function usually have?

Answer 21

Dominant

Question 22

What inheritance pattern does a loss of function have?

Answer 22

Can be dominant or recessive

Question 23

What is haploinsufficiency?

Answer 23

Describes a loss of function that is inherited in a dominant pattern

Question 24

Do we know the functions of all genes?

Answer 24

No! Nor do we know all the functions of single genes

Question 25

Give an example of a gene that we don't understand how a variant can be pathogenic at all

Answer 25

The FFR gene. When LOF in males, they have ID, big facial features, and large testes. But we have no idea why.

Question 26

What effect does ribose have on RNA and why?

Answer 26

It makes it less stable because it has an extra hydroxyl group.H

Question 27

How long can RNA molecules be?

Answer 27

20 - 20,000nt long

Question 28

Why is RNA single stranded normally but not DNA?

Answer 28

There are enzymes that will rapidly turn ssDNA into dsDNA, but that does not exist for RNA.

Question 29

Why does the sequence of RNA's matter? What can it be used for?

Answer 29

As enzymes, to target other RNAs or sequences of DNA, or to make secondary structures in the RNA

Question 30

What secondary structures can RNA make? Give an example

Answer 30

Complex self-annealed structures of stem-loops and hairpins. Examples include tRNA (looks like a clover leaf), and MRP RNA.

Question 31

We used to just think there was mRNA, tRNA and rRNA. But what are some other roles of RNA?

Answer 31

5 RNAs are crucial to spliceosome function. MRP is a ribozyme (RNA enzyme). Many are involved in gene regulation.

Question 32

What role do RNAs have in immunoglobulin genes and t cell receptor genes?

Answer 32

These genes undergo complex rearrangements to create a diversity of antigen receptors. guide RNAs help to target recombinases to the correct cut points for this rearrangement.

Question 33

List some RNAs!

Answer 33

ncRNAs, lncRNAs, piwiRNA, miRNA, snRNA, snoRNAs

Question 34

We have how many cells? A nematode has about 1000.

Answer 34

10^13

Question 35

We have a similar number of protein coding and non-coding genes compared to nematodes. How do we regulate genes in a more complex way?

Answer 35

We have a lot more lncRNAs than them. This may help. Also more pseudogenes, and more transcripts.

Question 36

What do microRNAs (21-25nts) do to regulate gene expression?

Answer 36

Bind to 3'UTRs of specific mRNAs to modulate levels of translation

Question 37

What do piwiRNAs do?

Answer 37

Silence transposons and protect the germline genome intergrity

Question 38

What do long ncRNAs (>200bp) normally do?

Answer 38

Down regulators of gene expression. Act as antisense transcripts.

Question 39

What else do long ncRNAs do?

Answer 39

Can activate gene expression. Can form platforms for assembly of multiprotien complexes.

Question 40

What's a notable lncRNA and what does it do?

Answer 40

XIST is 17kb and it is repsonsible for X inactivation.

Question 41

What groups can you add to histone proteins?

Answer 41

Methyl, acetyl, ubiquitin.

Question 42

What do histone modifications do?

Answer 42

Allow or prevent regulatory molecules binding to the DNA. Might block the protein directly or prevent access to the sequence

Question 43

Are histone modificaitions permanent?

Answer 43

They are fairly permanent, making cells their set cell type. Some are more transient, in response to external cell signals.

Question 44

Where are promoters located?

Answer 44

Upstream of where RNA polymerase binds

Question 45

Where are enhancers located and what do they do?

Answer 45

Up and down strream of where RNA polymerase binds. They are responsible for tissue-specific expression of genes.

Question 46

What does Cohesin do?

Answer 46

Wraps around DNA that is looped to bring RNA polymerase and enhancers close together

Question 47

What is the series of technologies used to capture the information of how DNA is packed together?

Answer 47

Chomatin Conformation Capture (3C, 4C, 5C and Hi-C).

Question 48

What does 3C actually look at?

Answer 48

Looks at DNA sequences lying close together in the interphase cell nucleus.

Question 49

How big are TADs?

Answer 49

500kb-1Mb

Question 50

What does TAD stand for?

Answer 50

Topologically associated domain

Question 51

What defines the boundaries between loops of DNA in TADs?

Answer 51

CTCF bound DNA does not go through cohesin loops so defines the boundaries of the TAD

Question 52

How far away can enhancers act?

Answer 52

Really far! as long as they are in the same TAD

Question 53

What's surprising about TAD boundaries between species?

Answer 53

They are highly conserved despite the sequences not being conserved

Question 54

What's the abilities of all this new Genome knowledge on NGS to sequence new causes of disease?

Answer 54

Can reinvestigate old unsolved problems. Can identify new lethal dominant mutations. Can detect mosaicism where the disease is genetic but not inherited...

Question 55

Whats the point of polygenic risk scores?

Answer 55

Identify people at higher risk of common multifactorial diseases

Question 56

What two things could be do by studying cfDNA?

Answer 56

NIPD for pregnancies, and cancer screening and monitoring

Question 57

How can improved genomics help with DNA forensics?

Answer 57

Confirm or exonerate individuals. identify hair, eye, skin colour, ethnic origin. Do a speculative search for family members (crime runs in families). Could predict facial apperance in the future.

Question 58

What's the effect of deleting repetitive sequences?

Answer 58

Often has no effect. Can have regulatory effects.