Brainscape's Knowledge GenomeTM


Top Flashcards (Certified)
All Flashcards

Molecular Genetics 3 > 15. + 16. Transposable elements in eukaryotes > Flashcards

15. + 16. Transposable elements in eukaryotes Flashcards

(77 cards)

Start Studying
1
Q

What is a transposable element?

A

Transposable element (TE) - jumping genes - mobile DNA fragments which can copy themselves around the genome
- can jump in/out -> affect expression of nearby genes

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
2
Q

What are the types of TEs in eukaryotes?

A

TEs types:
Class I: retrotransposons / “Copy & Paste” / RNA->DNA
Class II: transposons / “Cut & paste” / DNA

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
3
Q

Can TEs affect other gene expression?

A

Yes, TEs moving around the genome can change/block expression of nearby genes

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
4
Q

Do TEs make up a large proportion of human genome?

A

Yes, TEs make up around 50% of human genome - mostly Alu (SINE) and L1 (LINE)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
5
Q

What are Alu and L1s TEs?

A

L1: LINE - encodes own reverse transcriptase
Alu: SINE - uses LINE reverse transcriptase for transposition

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
6
Q

Are TEs proportion in genome constant between species?

A

No, proportion of TEs in genomes highly variable - corn up to 85% - C. elegans 15%

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
7
Q

What are the reason why TEs proportions in genomes variable between species?

A

The reason underlying TEs genome proportion variability and ability to change % proporiton quickly within a species because of:
- different transposition rates (moving)
- different acquisition rates of new TEs (new TEs introduced)
- different efficiency in removing TEs

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
8
Q

How do TEs spread in populations more quickly than normal genes?

A

TEs have different inheritance patterns compared to normal genes:

TEs spread more quickly in populations because are inherited at >50% frequency (cheat Mendelian genetics) - even if TE is harmful - if reproduction fitness is not reduced more than TE gain -> TE will spread in population

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
9
Q

Explain how retrotransposons increase their copy numbers

A

Retrostransposons - “copy & paste”:
- TE transcribed as RNA
- reverse transcriptase RNA->DNA
- DNA incorporated into new location in the genome => new TE copy

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
10
Q

Explain how transposons increase their copy numbers

A

Transposons - “cut & paste” - if only cut no extra copy created:
1) Copy by repair using sister chromatid
- after replication 2 chromatids - TE in one chromatid cut - jumps to new location
- ssDNA gap repaired using sister chromatid as template => 3 TE copies

2) Copy by moving ahead of replication
- during replication - when TE location doubled - 2 chromatids
- TE from one chromatid cut - jumps ahead of replication fork - replicated again - in both chromatids => 3 TE copies

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
11
Q

What are the two mechanisms used by transposons to copy themselves?

A

Transposons use “cut & paste” method - need somehow copy:
1) Copy by repair using sister chromatid
2) Copy by moving ahead of replication fork

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
12
Q

What are the possible consequences of transposition? Give examples

A

Transposition consequences for the host can be both:
- harmful: changed protein expression - disfunctional gene
- beneficial: acts instead of telomeres in Drosophila

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
13
Q

Why are TEs transposing in the germline and not somatically?

A

Host-parasite relationship:
If TEs transposed somatically - bad for both host and TEs:
- somatic transposition (mutation) could harm the host
- TEs would not spread if hapenned somatically
=> bad for both

When TEs transpose in germline - bad only for the host:
- germline transposition doesn’t affect host - only passing of its genes
- TEs can spread if transpose in germline
=> good for TEs, bad for host
==> TEs transpose in germlines

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
14
Q

How does transposition affect the host’s gene expression?

A

Transposition can:
- break coding genes by breaking the ORF / promoter
- TEs carry promoters / enhancers - affect neighbouring gene expressions

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
15
Q

How is the effect of transposition been characterised in rodents?

A

Transposition effect event only strong for new insertions - fades over time => expression change of neighbouring genes is associated with TE insertion event

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
16
Q

Give an example how TE can affect human behaviour?

A

HK2 - retrotransposon - recently active in human germline - present in 5% - HK2 transposition affects RASGRF2 expression level (associated with dopaminergic signalling) => people with this transposition respond to dopamine differently - carrying the allele doubles the chance of being chronic injection drug user

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
17
Q

Can transposition cause disease?

A

Yes, certain TE insertion can cause severe developmental disorders

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
18
Q

What is an ectopic recombination?

A

Ectopic recombination - atypical recombination event which happens between homologous sequences at non-allelic chromosome positions

–VS non-homologous allelic recombination (NHAR)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
19
Q

How TEs allow ectopic recombinations?

A

TEs sequences don’t diverge fast (at normal mutation rate) - when TEs move - homologous sequences in random chromosome places - recombination possible - within a chromosome / between 2 chromsomes

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
20
Q

Explain ectopic recombination within one chromosome

A

Ectopic recombination within a single chromosome:
- two identical TEs on one chromosome - pair - form a loop
- recombine genetic info - chunk of the sequence is lost -> sequence DELETION (harmful)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
21
Q

Explain ectopic recombination between 2 chromsomes

A

Ectopic recombination between 2 chromosomes:
- two identical TEs on two chromosomes - pair - loops formed because alignment incorrect - based on TEs not chromosome lengths
- recombination ->
1) sequence DUPLICATION (not as harmful)
2) sequence DELETION (harmful)

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
22
Q

Although sequence duplication because of TE ectopic recombination is not as harmful, what risk increases upon duplication?

A

When sequence duplicated in ectopic recombination because of TEs - # of TEs also increases => if TE # increases - chance of next ectopic recombination increases at (# TEs)^2

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
23
Q

Can transposition have beneficial effects?

A

Yes, more rare than harmful - mutation introduced by TEs can be beneficial and go to fixation

Example: Doc non-LTR retrotransposon inserted upstream of TSS -> increased cytochrome P450 expression - higher detoxification of DDT - insecticide => flies with insertion became resistant - mutation selected for - spread in population

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
24
Q

What is TE domestication?

A

TE domestication - adaptation of inserted TE within the genome to serve novel functions in a host cell

How well did you know this?
1
Not at all
2
3
4
5
Perfectly
25
Give an exaple for TE domestication
In **Drosophila telomeres** have been **lost** in evolution -> **TEs** transpose on **chromosome ends** - repeats **used as telomeres**
26
How can TEs insertions be identified in the genome?
TE insertions can be identified using **DNA sequencing** - from reads and read-pairs: - analyse **reference sequence**: cut - read - **construct back reference genome** - analyse sample in terms of reference sequence: cut - read - **see if match** to reference - **new reads** = **new TE inserts**
27
How can TE insertion (transposition) rates be identified?
Estimate transposition rate **by sequencing families** (parents-offspring) **over time** - comparing genomes - figure out **TE insertions** from **mutation accumulation lines**
28
Are transposition rates identical within species?
Transposition **rates vary between species** / **families** / **individuals** - specific factors affect transposition rates in each individual + in each tissue
29
How are locations of new TE inserts identified?
Difficult to identify - **remove host supression mechanism against TEs** (selected against) - **activate** TEs - **compare** TE **insertions** with previous generations => identify new locations of TEs
30
What is the evidence that TE insertions is highly selected against?
Strong selection against TE insertion is proved - **only low number is passed to offspring** from **de novo TEs in parent**
31
What are the genomic locations where transposition occurs?
New TE inserts occur in: - **promoters** - **exons** - **introns** - more rare More common in promoters and exons - especially **in TSS** => transposition common in **highly expressed genes**
32
Why is transposition more common in promoters and exons than in introns?
TE insertion **depends** on **chromatin accessibility** - **euchromatin** - open chromatin **more accessible for transposition** => **highly expressed genes** are **more common** in new **TE inserts**
33
Differentiate between de novo TE insertions vs surviving TE insertions
**De novo** TEs - **new TEs** in host that have occurred **in the host somatic/germline** - common in highly expressed genes **Surviving** TEs - TEs that are **passed on to offspring** (only from **germline**) - **introns** - more **commonly allowed** to be passed on because **less risk of damage**
34
Are there specific locations where TEs insert?
**Some TEs** have **specific target sites** for insertions - ex short sequence motifs Usually **TEs target low impact regions** - reduce their cost of inserting into host - **increase TE fitness** to be **passed on** to offspring
35
Give two examples how TEs have specific target sites and why
1. **Ty LTR retroelements** transpose in **yeast** **upstream of tRNA genes** - **essential gene** but there are **many copies** - if TE **break** one copy - **little reduction** in host **fitness** - will be **passed on** to offspring 2. **R2 non-LTR retrotransposons** insert in **animal 28s rRNA genes** - ribososmal genes **essential** but there **many copies** - if TE insertion **breaks** one gene copy - **little reduction** in fitness of the host - TE can be **passed on**
36
What is the strcuture of Mariner-like TEs?
Mariner-like TEs - **"cut & paste" DNA** transposons consist of: - **single gene** - encodes **transposase** - **inverted terminal repeats** on **both ends** of the gene Short direct repeats **flanking** TE
37
What is the mechanism of transposition in DNA "cut & paste" TE?
DNA "cut & paste" (**P-element**, **Mariner-like** transposons, **piggyBac**): - TE expresses **transposase** - transposase **cuts TE out** (with terminal inverted ends) - **OH** on TE **attack target site** - TE **inserts** - **staggered ends** - DNA **repair needed** - DNA repair **fills in gaps** - new DNA = direct repeats - **ligation**
38
Explain Mariner transposition mechainism in detail
**Mariner** and Mariner-like transposons - **DNA** "**cut & paste**" (the mechanism follows the overview of DNA "cut & paste" transposition mechanism): - TE expresses **transposase** - transposase **binds to TE** - **cuts** **at** **terminal inverted repeats** (leave them out) - **second transposase** binds - **dimerize** - **TE sequence** forms a **loop** - transposases **cut again** - **loop released** - bound by 2 transposases - **OH attacks target sites** in the genome - TE **integrates** - **gaps** - **repaired** - regenerate direct repeats
39
What is the main differences between transposases activity?
Main difference - **where transposase cuts TE** - for **different TE** - **different transposase**
40
Are all DNA transposons "cut & paste"?
**No**, not all DNA TE are of "cut & paste" transposition mechanism - cut only one ssDNA - leave other to repair - cut out migrates
41
What are therecently discovered groups of DNA TEs?
Recently discovered DNA TEs groups: - helitrons - polintons - cryptons
42
Explain how helitrons transpose
Helitron transposition - very different from Mariner transposition: - **transposase** expressed - transposase **cuts only one ssDNA** from two - the left ssDNA **gap repaired** - dsDNA TE remains - the e**xcised ssDNA TE circularizes** - **rolling circle replication** -> **multiple TE copies**: 1) **integrate** into new site 2) further **replicate**
43
Explain how polintons are thought to transpose
Polintons - **larger TEs** - encode **polymerase**, **integrase** - have particular end sequences Only **model** for transposition - **not sure** yet: - one **ssDNA excised** - forms a **loop** - **replicated** into **dsDNA** - **integrate** into genome
44
What are the subclasses of RNA retrotransposons?
RNA retrotransposons: - **non-LTRs** - **LTRs** LTR - long terminal repeat
45
What are RNA retrotransposons?
RNA retrotransposons - "**copy & paste**" TEs that retrotranspose through **RNA intermediate** and using **reverse transcriptase**
46
Explain what are non-LTRs
Non-LTRS - **RNA retrotransposons** that **don't have long terminal repeats** (LTRs) **Express mRNA-like product** encoding **reverse transcriptase**
47
What is the structure of a non-LTR retrotransposon?
Structure of non-LTR retrottransposon: -**1-2 ORFs** + **TSS** - **not long terminal repeats** - could have **polyA tail**
48
What is non-LTR mechanism of retrotransposition?
Non-LTR retrotransposition involves **transcription**, **nuclear export**, **translation**, ribonucleoparticle formation (**RNP**) - **expressed RNA** binds at **cleaved target site** - **base pairs** with one ssDNA - **OH** of cleaved DNA - **target site** of DNA **synthesis** using **RNA as a template** - DNA synthesis - top strand **cleavage**: 1) **downstream** of primery cut: - **synthesised DNA bends** and **base pairs** to **protruding** cut end of **ssDNA** - exposed **OH** - for **second DNA** strand **synthesis** using **first ssDNA** as **template** - RNA **released** - **gaps** left - **repair+ligation** - **target site duplication** => new TE insertion 2) **upstream** of primary cut: - **ssDNA base pairs** to **protruding end** - **RNA released** - **overlapping** flaps of original sequence left - **degraded** - **target site deletion** => new TE insertion
49
Explain RNA transposon LTR subclass
LTRs - **RNA retrotransposons** - TEs - have **long terminal repeats** (LTRs)
50
What is the strcuture of an LTR?
LTR - RNA retrotransposon - "copy & paste" strtcture: - **2-3 ORFs** - **TSS** - **long terminal repeats** at **both ends** (LTR) - some may have **additional codon** for **envelope** proteins LTRs encode **pol gene** (integrase, reverse trancriptase, RNAse)
51
Explain how LTRs retrotranspose
LTR retrotransposition mechanism
52
What is the currently new proposed update on LTR retrotransposition mechanism?
LTR replication occurrs via **circular intermediate**
53
Why do TE have to synthesise their own proteins?
Because **host cell doesn't have necessary proteins for transposition** - ex **reverse transcriptase** (RNA->DNA)
54
Why is nuclear export and then import needed for TE genes?
TE genes code for proteins not present in host cells - **express mRNA** - **export** out of nucleus into cytoplasm - get **translated** into **proteins** - have to **re-enter the nucleus** to **act on TE** **sequences** in the genome
55
Why are TEs and viruses alike?
Features making TEs (retroelements) and viruses alike - same gene at same order: - **capsid protein** production - ability to **integrate** into the **host genome** - **specific activation** in certain tissues - high **mutability** - existence of virophages propagating only with another virus - similar to **non-autonomous transposons** - **use expression products of autonomous**
56
How TEs and viruses differ?
Features making TEs and viruses different: - **LTR** elements - **no horizontal transmission** - **envelope** genes
57
Did viruses evolve from TE or TEs from retroviruses?
**Retroviruses likely evolved from LTR elements** (RNA retrotransposones) However - endogenous retroviruses, polintons - not known which way
58
What is the classification of TEs
59
What is Gag gene?
Gag gene encodes **Gag proteins** - **LTR transcripts** - act in **virus-like particle formation**
60
What is Env gene?
Env gene encodes **Env proteins** - for envelope formation - **LTR** retroelement (**Gypsy**) - **cross-species transmission** **Gag+Env** proteins form **virus-like particles**
61
What role do Gag+Env proteins play?
Gag+Env expressed proteins **form virus-like particles** - formed by **Gypsy** retroelement - structure very similar to LTR => **makes question if LTRs <-> retroviruses** evolved one from another
62
What is the structure of retroviruses, ex Gypsy?
Structure very **similar to LTR**: - **long terminal repeats** - **Gag proteins** +**Env gene** added
63
Whate are endogenous retroviruses? Give example
Endogenous retroviruses - **TE in genomes that highly resemble retroviruses** - encode **capsid** Ex: **KoRV-A** endogenous retrovirus - resembles **Koala KoRV virus** - can be **horizontally transmitted** even **without infection** - KoRV-A can **make viral particles**
64
Why are polintons considered a potential virus cross-over?
Because polintons (DNA "cut&paste" TE) are: - **large** sequences - **widely distributed in eukaryotes** - have **virus-like DNA pol** - synthesise own DNA - many polintons encode **capsid** proteins => polintons - viral origin in genome? (not determined)
65
Are polintons derived from retroviruses?
**Not determined** - two possible mechanisms: 1) **unknown virus donated capsid** - polintons gained capsid proteins (can horizontally transmit) 2) **virus integrated into genome** - lost capsid function - became polinton
66
What are autonomous vs non-autonomous elements in genomes?
**Autonomous** elements: **transpose themselves** - perform excision + integration proteins **Non-autonomous** elements: **need help from autonomous element to transpose** - needs enzymes => TEs that **lost all structures** (genes) due to **mutation** - except inverted terminal repeats - important in transposition to get help from autonomous element protein - ex MITEs
67
What are SINE elements?
**Short interspearsed nuclear elements** (SINEs) - **non-autonomous** - not because lost genes - because **gained inverted terminal repeats** to **be transposed by autonomous** elements - ex **Alu** elements in human genome
68
What are Alu elements?
Alu elements - **SINEs** in **human genome** 10.6%: - derived **from RNA of SRP** - has **RNA pol II promoter** - transcription initiation - **3' end A-rich region** - **used** in transposition to **mimic LINEs** - use LINE mechanism to **transpose**
69
How does the host defend againts TEs? What are the mechanisms?
**Immune system** against TEs - protect against parasites - several mechanisms: - **KRAB domain zinc fingers** - **piRNA pathway**
70
Explain KRAB domain zinc fingers as defence mechanism against TEs
**Kruppel-associated box zinc-finger proteins** (KRAB-ZFPs) - largest **TF** family - **bind DNA** via tandem zinc-fingers - form **complexes** - **recruits repressors** - together **induce inactive chromatin** (accessibility of chromatin important for transposition)
71
Explain piRNA pathway as defence mechanism against TEs
piRNA - **RNA interference supresses TEs** in animals: 1) **piRNA** generating **cluster** 2) piRNA **maturation** in **somatic cells** / **Ping-pong amplification** in **germline** 3) **TE transcription silencing** by mature piRNA **Long transcripts produced** from piRNA generating clusters: neighbouring + non-functional TEs in heterochromatin - sequence used in **recognising TE** -> **methylating**
72
What is the piRNA maturation process in somatic cells?
73
What is the piRNA Ping pong amplification process in germline?
In Drosophila germline:
74
What is the piRNA induced transcriptional silencing of TEs?
Common in both **somatic** and **germline**:
75
Quiz 1
76
Quiz 2
77
Quiz 3

Molecular Genetics 3 (17 decks)

Brainscape helps you reach your goals faster, through stronger study habits.
© 2025 Bold Learning Solutions. Terms and Conditions