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GenGenMol > 02 Intro to the Genome > Flashcards

02 Intro to the Genome Flashcards

1
Q

How many bases in the human genome?

A

3 Gb x 2

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2
Q

How much of the genome was sequenced in 2003?

A

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

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3
Q

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

A

50%

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4
Q

How long are SINEs and LINEs?

A

~400bp and 6kb respectively

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5
Q

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

A

Just say how it varies from the reference genome

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6
Q

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

A

4-5 million

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7
Q

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

A

4-4.5million

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8
Q

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

A

700,000

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9
Q

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

A

25,000

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10
Q

What is the Human PanGenome project?

A

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

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11
Q

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

A

65-80,000

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12
Q

How many protein coding genes do we actually have?

A

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

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13
Q

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

A

In the ovalbumin gene in chicken

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14
Q

Do all genes have introns?

A

No

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15
Q

What’s the most introns in a gene?

A

360 in Titin

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16
Q

What is the primary transcript?

A

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

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17
Q

Do introns have a function?

A

We don’t think so other than allowing alternative splicing

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18
Q

How are alternative transcripts made?

A

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

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19
Q

Are all transcripts that are made functional?

A

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

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20
Q

What is a Gain of Function?

A

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.

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21
Q

What inheritance pattern does a gain of function usually have?

A

Dominant

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22
Q

What inheritance pattern does a loss of function have?

A

Can be dominant or recessive

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23
Q

What is haploinsufficiency?

A

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

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24
Q

Do we know the functions of all genes?

A

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

25
Q

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

A

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

26
Q

What effect does ribose have on RNA and why?

A

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

27
Q

How long can RNA molecules be?

A

20 - 20,000nt long

28
Q

Why is RNA single stranded normally but not DNA?

A

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

29
Q

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

A

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

30
Q

What secondary structures can RNA make? Give an example

A

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

31
Q

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

A

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

32
Q

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

A

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.

33
Q

List some RNAs!

A

ncRNAs, lncRNAs, piwiRNA, miRNA, snRNA, snoRNAs

34
Q

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

A

10^13

35
Q

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?

A

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

36
Q

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

A

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

37
Q

What do piwiRNAs do?

A

Silence transposons and protect the germline genome intergrity

38
Q

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

A

Down regulators of gene expression. Act as antisense transcripts.

39
Q

What else do long ncRNAs do?

A

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

40
Q

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

A

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

41
Q

What groups can you add to histone proteins?

A

Methyl, acetyl, ubiquitin.

42
Q

What do histone modifications do?

A

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

43
Q

Are histone modificaitions permanent?

A

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

44
Q

Where are promoters located?

A

Upstream of where RNA polymerase binds

45
Q

Where are enhancers located and what do they do?

A

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

46
Q

What does Cohesin do?

A

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

47
Q

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

A

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

48
Q

What does 3C actually look at?

A

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

49
Q

How big are TADs?

A

500kb-1Mb

50
Q

What does TAD stand for?

A

Topologically associated domain

51
Q

What defines the boundaries between loops of DNA in TADs?

A

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

52
Q

How far away can enhancers act?

A

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

53
Q

What’s surprising about TAD boundaries between species?

A

They are highly conserved despite the sequences not being conserved

54
Q

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

A

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

55
Q

Whats the point of polygenic risk scores?

A

Identify people at higher risk of common multifactorial diseases

56
Q

What two things could be do by studying cfDNA?

A

NIPD for pregnancies, and cancer screening and monitoring

57
Q

How can improved genomics help with DNA forensics?

A

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.

58
Q

What’s the effect of deleting repetitive sequences?

A

Often has no effect. Can have regulatory effects.

GenGenMol (15 decks)

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