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Genomics of Human Dieases > Lecture1 > Flashcards

Lecture1 Flashcards

1
Q

How much DNA sequencing got cheaper since finishing the Human Genome in 2003

A

> 150,000‐fold

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2
Q

What is estimated in 2017 for Nova-seq?

A

2017 Nova‐seq: up to
3 trillion (3x1012) bp
in 40h

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3
Q

How many patients in the Human atlas?

A

11,000

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4
Q

What does Human cell atlas does?

A

International Consortium to
characterize „all“ human
cells with genomic methods

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5
Q

what is Genome project write (GP‐write)

A

an initiative to rewrite the

human genome

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6
Q

what is the major change in

biology in the last decade

A

Genomics and sequencing is maybe

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7
Q

Types of comparisons between healty and dieases genomes?

A 
1)Genetic mapping
in families
2)Genome-wide association
studies (GWAS)
3)Cancer Sequencing
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8
Q

what is Genome annotation?

A 
where are the functional
sites/elements, i.e. where are
The genes and their regulatory
elements, when/where are
they expressed, how do they
interact on cellular, tissue,
organism level
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9
Q

What fraction of the human genome are protein‐coding genes?

A

20,448

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10
Q

What fraction of the human genome are non protein‐coding genes?

A

23,997

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11
Q

What is the averages size of CDS?

A

1500 bp

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12
Q

What is the averages size of 5’UTR?

A

170 bp

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13
Q

What is the averages size of 3’UTR?

A

700 bp

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14
Q

the averages size of 3’UTR is larger than 5’UTR?

A

True

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15
Q

What is typcil Human Pro-coding mRNA?

A

5’Cap, 5’UTR, CDS, 3’UTR, polyA tail

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16
Q

How many precent of the human genome codes for proteins?

A

1%

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17
Q

How many precent of the human genome codes for protein‐coding mRNAs?

A

1.5% (include with 3’UTR and 5’UTR + CDS)

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18
Q

ordinate from larger to smaller? CDS,5UTR and 3’UTR

A

CDS,3’UTR, 5’UTR

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19
Q

only 1 % of the human genome codes for protein?

A

True

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20
Q

Only 5% of genome is regulatory DNA?

A

True

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21
Q

Only 2% of genome is coding region?

A

False 1%

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22
Q

Only 1% of genome is UTR?

A

False 0.5% UTR

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23
Q

Only <1% of the genome is noncoding

RNA

A

True

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24
Q

How many percent of HG are consists of TE?

A 
45% of the human genome
can be readily classified as
transposable element
More sophisticated search
finds 2/3 of the genome to be
derived from TEs
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25
Q

Is The human genome consists mostly of TEs?

A

True

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26
Q

How many percent of HG is consists of Alu?

A

10.6%

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27
Q

How many percent of HG is consist of Dna transposons?

A

2.8%

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28
Q

What is the other name of SDs? explain

A

Low copy repeats (LCRs) = segmental duplications (SDs) are larger
regions (e.g. >1kbp) that are e.g. >90% identical and occur at least
twice

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29
Q

Explain about Highly repetetive DNAs?

A

shorter DNA pieces that make up >50% of the

human genome

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30
Q

What is Repeatmasker?

A

is a program that can serve as a practical

definition

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31
Q

What are Classes of highly repetitive DNA?

A

– High‐copy number tandem repeats (Satellite DNA)
– Transposable elements (or “interspersed repeats”)
• DNA transposons
• Retrotransposons

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32
Q

Duplications of DNA sequences occur by different mechanisms and
have a huge impact on what?

A

shaping a genome

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33
Q

Where are the Tandem repeats?

A

at centromers and telomers

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34
Q

Segmental duplications is basically?

A

Occurrence of duplicated genomic regions-

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35
Q

Define SDs? their lenght? frequency? if they are just TE?

A

Segmental duplications (also termed “low-copy repeats”) are blocks of DNA that range from
1 to >400 kb in length, occur at more than one site within the genome, and share a high level of (>90%)
sequence identity
(note: transposable elements are filtered out, i.e. SDs are not “just” TEs)

36
Q

How many percent of the human genome falls in SDs?

A

5%

37
Q

Are many genes are part of SDs?

A

Yes, Enriched in regions without genes, but also many genes are part of SDs, its also about 10 fold enrichment close to telomeres and centromers

38
Q

Say if its true.
a)SDs are hotspots for disease mutations (that are difficult to detect with short read
technologies)
b) SDs are hotspots for very complex genomic region

A

all true

39
Q

More SDs generate more SDs?

A

Yes!!

40
Q

We have Different types of tandem repeats;what is the most abundant one?

A

alpha satellites at centromers

41
Q

What fraction of the genome is covered by Segmental duplications?

A

5% of the human genome falls in SDs

42
Q

Why are Segmental duplications hotspots for disease mutations?

A

that are difficult to detect with short read

technologies

43
Q

is Segmental duplications matter for genome assemblies?

A

Yes

44
Q

in which chromosomal regions are SDs enriched

A

10‐fold Enrichment close to telomeres and centromers, Enriched in regions without genes, but also many genes are part of SDs

45
Q

What are the other name of TEs?

A

„jumping genes“ or „selfish genetic elements“

46
Q

What are TEs?

A

Transposable Elements are pieces of DNA that can replicate independently within a genome

47
Q

TEs occur in all species
from bacteria to humans
(just like viruses).
True?

A

Yes

48
Q

By who and in whereTEs Originally discovered?

A

in maize
by Barbara McClintock
in the 40‘s (Nobel price 83)

49
Q

Are TEs important?

A

Yes, Transposons are important tools
(Transposon mutagenesis;
Nextera for Illumina)

50
Q

What are selfish DNA good for?

A

TEs can be seen as Selfish DNA or genomic parasites
“The spread of selfish DNA sequences within the genome can be compared to the
spread of a not‐too‐harmful parasite within its host”. Asking what are they good for is like asking what viruses are good for

51
Q

How many types of jumoing do TEs have?

A 
Two types of jumping
1)Via RNA intermediate:
Retrotransposon (reverse trancription will make dna intermediate then integration) 
2)Via DNA intermediate:
DNA transposon
(similar to RNA and DNA
virus)
52
Q

What do Autonomous element encodes?

A

Autonomous element encodes
necessary regulatory DNA and
encodes protein(s) needed for
transposition

53
Q

What do non-Autonomous element encodes?

A

Non-autonomous element encodes
only necessary regulatory DNA
and uses proteins from autonomous
element

54
Q

What are the Direct consequence of A new insertion of a TE?

A

neutral (most likely) => TE insertion will acquire random mutation and eventually
(>300 mio years) mutate beyond recognition
• bad => host and TE insertion die sooner or later
• Advantagous (rare) => TE insertion will be maintained

55
Q

Compare to gene duplication with TE: most often neutral, sometimes deleterious,
rarely adaptive

A

True

56
Q

What is Long-term consequence for the host for TEs?

A

Hosts need to defend themselves against TEs
• Many defense mechanisms of the hosts exist (piwiRNAs. ZnFingers etc.)
• Just like for the immune system there is a constant arms race of TEs and the
host defenc
• This arms race has strongly shaped genomes (origin of epigenetic
mechanisms, RNA regulation)

57
Q

The current content of TEs in a genome is the result of all past TE pandemics and
the following mutations and selection events
T or F?

A

True

58
Q

What are the only transposable elements still active in the human genome?

A

Line1 (L1) and Alu are the only transposable elements still active in the human genome
(~1 TE event every 20 generations)

59
Q

Are The two most common TEs in the human genome are

Retrotransposons?

A

Yes, Line1(autonomous) and Alu (Non-autonomous, needs L1 gene products)

60
Q

1) RNA transcription from internal promotor
L1:
Alu:
For each say which of RNA pol?

A

RNA transcription from internal promotor
L1:RNA Pol II
Alu: RNA Pol III

61
Q

Translation of reverse transcriptase
L1:
Alu:
For each say which?

A

L1: ORF1 and ORF2
Alu: no ORF!

62
Q

Reverse transcription and integration

Often truncated if not ?

A

Reverse transcription and integration
Often truncated if not the full mRNA is reverse
transcribed => new copies are often inactive

63
Q

a) L1 elements can be seen as..

b) Alu elements can be seen as…

A

a) L1 elements can be seen as genomic parasites

b) Alu elements can be seen as parasites of L1 elements

64
Q

Transposition does often lead to full length copies.

True or False?

A

false, Transposition does often not lead to full length copies

65
Q

What is Alus
evolved
from 7SL
RNA?

A

7SL RNA is a RNA Pol III transcribed RNA that is part of the signal recognition particle, which is involved in
translocating peptides during translation into the ER

66
Q

Tell me more about Alu families?

A 
One distinguishes different
families of Alus similar to
different subtypes of a virus
Alu Yc1 is still a little active in
human genome (~1 event
/genome every 20 generations)
67
Q

Are Alu Yc1 still a little active in

human genome?

A

Yes, Alu Yc1 is still a little active in
human genome (~1 event
/genome every 20 generations)

68
Q

How is Emergence, spread and extinction of TEs?

A

Its just like a viral epidemic, but with the difference that the products partly remain (and of
course continue to mutate) in the host genome, i.e. The current genome is a sum of past
epidemics + the mutations that occured since the epidemic

69
Q

another way to

look the history of TE pandemics that hit the germline of the genomes anacestors?

A

Age (=% substitution from a common ancestor sequence or consensus sequence) of TEs

70
Q

The more
substitutions the
older the element !
True or F?

A

True!!

71
Q

certain Alu families more frequent than others in the human genome
T or F?

A

True

72
Q

the average pairwise sequence difference between TEs not homogenously distributed
T or F?

A

True

73
Q

What element of rodents is also evolved from 7SL

RNA?

A

B1 element of rodents
also evolved from 7SL
RNA

74
Q

Different species have (partly) Same histories of TEs?

A

False, Different species have (partly) different histories of TEs

75
Q

SINE elements (non-autonomous
…..) that evolved from a …
gene

A

SINE elements (non-autonomous
retrotransposons) that evolved from a tRNA
gene

76
Q

Maize has more TE than Arabidopsis

A

yes, Maize also has more genome size (Gap)

77
Q

Smallest and largest
vertebrate genome
a) Tetraodon fluviatilis pufferfish
b) Protopterus aethiopicus Lung fish

A

a) 350 Mbp

b) 132 Gbp

78
Q

What is C‐value?

A

haploid nucleus content has most often been measured by weighting the DNA content of nuclei.
Haploid nuclear DNA content
in million bp from ~ 10,000 species (star = human)

79
Q

Genome size correlates with TE content.

T or F?

A

True

80
Q

Genome size, complexity and the

C-value paradox

A

• It has been known for a long time that Genome size varies widely among
species with similar complexity
• This has been called C‐value paradox
• TEs can readily explain this (=> it is not a paradox)
• Seems like a higher DNA content is not such a big disadvantage for slower
growing (multicellular) organisms
• => balance between generating DNA and rate of DNA loss mainly
determines genome size
• Complexity of multicellular organisms is not correlated with genome size
nor gene counts!
• A high proportion of genomes is junk (=non‐functional DNA)

81
Q

Tell me about Junk DNA?

A

Susumo Ohno liked explicit statements
and called this DNA junk DNA in 1972
General term for non-functional DNA that
raised and still raises a lot of emotions

82
Q

WHy its hard to analysis SDS?

A

Because they look similar

83
Q

There is a relationship between Complexity and Genome size?

A

No

84
Q

Onion genome size is bigger bc

A

TE

85
Q

SDS cannot be polymorphics?

A

False

86
Q

SDs are highly copied numbers (classes of repeats)

A

False, Classes of repeats?
High copy tandem ((satellites, minisatellites, microsatellites)
– Low copy (=~ segmental duplications)
– Transposable elements (Tes)

Genomics of Human Dieases (2 decks)

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