Lecture 6 'Archaic genomes & our genome under attack: origin of repetitive DNA elements''

Question 1

Neanderthals and homo sapiens, some of the humans do have Neanderthal DNA and some don’t. But how do we now that the substitution is not already in our common ancestor?

Answer 1

They looked to the genome from Afrika and compared this with the other parts in the world. And the substitution was not seen in Arika then it is likely that it comes from Neanderthals because they don’t live in Arika. So not present in Afrika suggests that it is from Neanderthals DNA.

Question 2

Bottleneck situation

Answer 2

Bottleneck situation means when you have a large situation and by, for example a virus, the population will shrink to a small population.

Question 3

Interbreeding

Answer 3

the action of breeding or causing animals to breed with members of another breed or group:
Neanderthals simply disappeared through interbreeding with the modern newcomers.

Question 4

What did Neanderthals contribute?

Answer 4

HLA genes, immuunsystem correlated.
Disease-risk alleles
Many other features that we don’t know the function of

Question 5

what did we learn from the archaic hominis?

Answer 5

• Finetuning of hominin evolutionary events
• Finetuning of ancient hominin-phylogenetic tree and branchpoints
• Insights into population sizes (+ bottlenecks) of hominin species
• We have not undergone apparent dramatic differences in the last 400 thousand years
• Some traits we consider ‘human-specific’ were contributed to homo sapiens by interbreeding with Neanderthals and Denisovans
• An unknown archaic hominin species (Erectus?) has interbred withDenisovans

Question 6

Classes of Transposable Elements

Answer 6

DNA transposons
LTR retrotransposons
SVAs
Non-LTR retrotransposons

Question 7

LINE1

Answer 7

Long Interspersed Nuclear Element
- can intergrates somewhere else in the genome and they are self-filling
- active troughout promate evolution
- active in humans
- Now 20% of our genome!

Question 8

Composition LINE1

Answer 8

ORF1, ORF2, 5’UTR, own promotor, autonomous retrotransposons

Question 9

SINE

Answer 9

Short Interspersed Nuclear Elements
non-autonomous: Needs L1 for retrotransposition
still active in human genome
Alu belongs to SINE

Question 10

SVA

Answer 10

consist of: SINE-VNTR-Alu
Newest retrotransposons in our genome
Active and polymorphic in humans
non-autonomous: needs L1 for retrotransposition
has a strong enhancer function, effect the gene next to it

Question 11

Long tandem repeats (LTR)

Answer 11

Are promotors for the transcription of the viral proteins
Solitary LTRs are present in our genome

Question 12

Human endogenous Retrovirusses (HERVs)

Answer 12

HERV-K has been active recently in human evolution but are
now thought to be extinct (=not able to retrotranspose)
HERVK-proteins are expressed in pathological conditions

Question 13

Genomic Implications of transposable element insertions

Answer 13

• Direct gene regulation
• Creation of new transcripts
• Creation of new promoters
• Inducing splice variance
• Affecting mRNA stability
• Genomic Instability
• Changing epigenetic environment
• Changing the 3D genomic structure (G4)

Question 14

What is de cause for the huge variation in the sequence in the human population?

Answer 14

Mostly SNPs, but also deletions, insertions, segmental duplications, and copy number variants

Question 15

what happends by an attack of a retrovirus

Answer 15

the gene will be copy paste a couple of times