Genetics Test III Flashcards
(44 cards)
1
Q
Transposable Elements are ?
A
interspersed repeats
known as transposons or jumping genes
2
Q
Transposable Elements originate by a process of ?
A
transposition which is the jumping of a DNA segment to another place of the genome
3
Q
Transposable elements were discovered by ?
A
Barbra McClintock around 1948
4
Q
What are the two types of transposable elements?
A
DNA transposons and Retrotransposons.
5
Q
Retrotransposons.
A
Copy and Paste
6
Q
DNA transposons
A
Cut and Paste
7
Q
What are the classes of transposable elements in the human genome?
A
DNA Transposons
LTR-Retrotransposons -
endogenous retrovirus.
Non-LTR Retrotransposons - LINEs (long interspersed repeats)
Nonautonomous Non-LTR Retrotransposons - SINEs (short interspersed repeat).
8
Q
DNA transposons
A
inactive in the human genome
they accumulated mutations during vertebrate evolution – no loner transpose
we see their ancient remnants or “fossils”.
The transposon moves by a cut-and-paste mechanism and the copy number remains stable.
9
Q
How do DNA transposons function?
A
- the transposable element codes transposase.
- Transposase (when transcribed and translated) binds to the ends of the element.
- The ends of the transposon are formed by inverted repeats
- Inverted repeats exchange DNA strands and stabilize a stem-loop structure
- This allows transposase to bind and act
- Transposase cuts the transposon out and ligates the resulting free DNA ends.
- The complex transposon-transposase binds to a specific sequence motif elsewhere in the genome.
- Transposase cleaves the host DNA and ligates the transposon into the new place.
10
Q
Most important transposable elements in the human genome.
A
Retrotransposons
11
Q
Describe Retrotransposons
A
- most important transposable elements in the human genome.
- directly forming at least 45% of the human genome.
- still active in the human genome.
- Expand in number by a duplication (copy-and-paste) mechanism
- Process of retrotransposition is prone to various mistakes,
- new copies of a retrotransposon are largely inactivated, because of truncation or point mutation.
- Because most of the transposon copies are inactive, the further expansion of the retrotransposon family is governed by the few active full-length elements.
- However, even if all the active elements were lost later during evolution, the genome might be literally overrun with the fossil members of the sequence family.
12
Q
How do Retrotransposons function?
A
- they require cellular RNA polymerases (II or III) to transcribed them into RNA
- the original DNA copy is maintained at the same location.
- The RNA copy is reverse-transcribed into DNA
- the DNA is inserted into the genome at a new location.
13
Q
Endogenous retroviruses
A
• also called LTR retrotransposons
14
Q
Describe LTR retrotransposons
A
- also called LTR retrotransposons
- resemble proviruses of true retroviruses in composition
- they contain:
- long terminal repeats (LTRs), gag, pol, env and prt genes,
- but at least one of the proteins necessary for assembly of infectious viral particles is mutated or actually missing - env in particular.
- they can move only within cells
- their life cycle is similar to infectious retroviruses.
- active in many mammals, including chimpanzee, humans currently contain only fossils (mutated and incapable of transposition), which fill about 8% of the genome.
- Full-length endogenous retroviruses are typically 7-9 kb long.
- Frequently we can find only standalone LTR, because of intrachromosomal recombination between the LTRs or unequal recombination of the homologous chromosomes, leading to deletion of the coding part of the retrovirus.
15
Q
Non-LTR retrotransposons
A
• LINEs (long interspersed nuclear elements)
16
Q
Describe Non-LTR retrotransposons
A
- autonomous retrotransposons.
- They comprise about 21% of the human genome.
- The active elements belong to the most abundant LINE-1 or L-1 family, which alone comprises 17% of the genome.
- Of the roughly half million of L1s in our genome, close to 10,000 are full-length and about 100 are still capable of retrotransposition.
- Active L1 element is about 6 kb long
- contains two open reading frames, ORF1 and ORF2.
- Function of ORF1 is not clear, it is only known to bind to L1 mRNA
- ORF2 contains reverse transcriptase and endonuclease domain and is the enzyme responsible for integration.
- 5´UTR (untranslated region) functions also as a promoter
- 3´UTR contains polyA signal.
17
Q
Nonautonomous retrotransposons
A
• SINEs (short interspersed nuclear elements)
18
Q
Describe Nonautonomous retrotransposons
A
- typically less than 500bp long and have no protein coding potential.
- The main SINE family in humans is formed by Alu elements (the name is derived by their discovery based on a pair of conserved AluI restriction sites).
- The greater than 1 million Alu elements in the human genome account for about 11% of its mass.
- Alu elements share 282 bp consensus
- related to, and presumably derived from the SRP (signal recognition particle) RNA subunit (called 7SL RNA).
- SRP is a ribonucleo-protein complex that recognizes signal peptide, binds to it and translocates the ribosome-mRNA-nascent peptide complex to endoplasmic reticulum (ER) channel, through which the nascent protein is translocated into the ER lumen or integrated into the membrane.
- Alu’s are transcribed by RNA polymerase III.
- Alu RNA can bind two SRP proteins (9 and 14).
- Presumably, Alu then binds to ribosomes and bind nascent ORF2 protein to the Alu’s polyA tail, if the ribosome just happens to translate LINE-1 mRNA
- Once bound to ORF2 protein the Alu forces ORF2 to reverse transcribe and integrate its RNA and not the LINE-1 mRNA
19
Q
What function do transposons have in the cell?
A
From the immediate point of view, transposons have no necessary function in the cel
20
Q
The motility of the retrotransposable elements is important why?
A
for genome plasticity.
21
Q
Occasional insertion into genes results in what?
A
disrupt the gene function and cause an inherited disease.
22
Q
LTR and LINE elements can also change?
A
gene expression, if inserted near a gene, as LTRs and LINE 5´UTR have strong promoter activity in both directions.
23
Q
May lead even to deletions and inversions
A
L1 retrotransposition
24
Q
Very rarely, a cellular mRNA is subject to reverse transcription and transposition by?
A
an enzyme from L1 or other retrotransposons.
25
Describe what happens when a cellular mRNA is subject to reverse transcription and transposition by an enzyme from L1 or other retrotransposons.
•the gene is duplicated and called a processed pseudogene
a. derived from processed mRNA lacking introns,
* usually not functional due to missing promoter.
* Rarely a processed pseudogene can adopt a function under selective pressure.
• Highly expressed housekeeping genes have a higher probability of retrotransposition (find many processed pseudogenes for ribosomal proteins)
a. Not the same as "ordinary" pseudogenes, arose by genomic DNA duplications, retain the original gene structure although with impaired function.
• Several genes were directly derived from a retrotransposon
• Even inactive repeat elements increase plasticity of the genome
a. promoting interchromosomal unequal crossing-over or intrachromosomal recombination, leading to deletions/duplications or inversions.
• transposons are speculated to have some real physiological function
a. their expression is upregulated during stress response.
26
What can LINEs do
* Transpose more LINEs
* Transpose other cellular mRNA (make pseudogenes)
* ORF2 Protein can also transpose SINEs
* Can insert into a gene
* Exon Shuffling (the LINE grabs 3’ end of sequence and moves it around)
* Insertion accompanied by rearrangement
* LINE-1 has a promoter, LINE insertion can provide new promoters for genes
27
How much of the genome is TE?
2/3
28
Most human TE's are ?
retrotransposons
29
How could TE affect gene expression
1. Generate Transcript diversity
a. Provide novel promoters, splice sites, or poly A signals
2. Disperse transcription factor binding sites
a. Linking genes in transcriptional networks
b. Facilitate evolution of complex traits
3. Insertion into ORF
a. Some human diseases
b. Haemophilia A resulting from de novo insertion of L1 sequences represents a novel mechanism for mutation in man
c. A systematic analysis of LINE-1 endonuclease-dependent retrotranspositional events causing human genetic disease.
4. Disperse transcription factor binding sites
a. Linking genes in transcriptional networks
b. Facilitate evolution of complex traits
c. Evolution of the mammalian transcription factor binding repertoire via transposable elements
d. Waves of retrotransposon expansion remodel genome organization and CTCF binding in multiple mammalian lineages.
30
Alu elements
* Alu elements inserted into a gene can provide both splice acceptor and donor sites, creating new exons
* most Alu-derived exons are alternatively spliced, contributing to transcript diversity
* Enriched in the 5’ UTRs of human genes, regulate mRNA translation
* many alternative splicing events of Alu-derived exons are tissue-specific, suggesting TEs contribute to the transcriptome differences that define cell types
31
ATRN gene
* example of how TE induced alternative mRNA processing can enable functional diversification of one gene
* A subset of ATRN transcripts are cleaved and polyadenylated within an L1 element that has retrotransposed into an intron
* Other transcripts splice around the L1 element and incorporate an additional five exons
* A subset of ATRN transcripts are cleaved and polyadenylated within an L1 element that has retrotransposed into an intron
* Other transcripts splice around the L1 element and incorporate an additional five exons
* Transcripts polyadenylated within the L1 element encode a soluble form of Attractin that is released by activated T lymphocytes as part of the basic inflammatory response
* The alternative transcripts encode a protein with transmembrane and cytoplasmic domains that is membrane-bound. This isoform is similar to murine Atrn, which functions as a receptor involved in pigmentation and energy metabolism
32
L1 TE retrotranspose
“other” mRNA
• About 120 retroposed sequences have evolved into bona fide genes in the human genome
• Retrogenes embedded in introns of other genes can influence transcription of that gene, causing upstream transcript polyadenylation.
• This is a mechanism through which TEs can indirectly influence mRNA processing, further promoting transcript diversity.
33
TE and Alternate Promoters
• TEs further promote transcript diversity by providing alternative promoters for host genes
34
TE______ and _____ genes
rewire and link
35
A good example of the importance of TEs in linking genes in a network can be found where?
embryonic stem (ES) cells.
36
Mobilome can facilitate ?
evolution of complex physiological processes
37
TE are important for?
for genome evolution
38
• TE bursts
waves of LTR-RT: long terminal repeat – retrotransposon activity (copy and paste) can increase genome size
• Make genome bigger
39
• Does rate of TE elimination vary from one lineage to another
• If so makes genomes smaller
40
• How are TE’s eliminated
* Recombination between LTRs – create a Solo LTR
| * Small deletions – slowly remove TE
41
• Solo LTR found in all eukaryotes
* Solo to intact ratio, maize 0.2/1, rice 1.5/1
| * Maize genome larger, rice genome smaller
42
Data
* 8 genome sequences based on physical map (necessary to get repeats correct)
* Characterize LTR-RT distributions
* Full copies
* Solo-LTRs
* Truncated or delete copies
43
Findings
* Increase in genome size – accumulation of bursts within last 3 my
* Absence of TE older than 3Mya – must have been rapidly removed
* Deletion are also not lineage dependent
* Elimination process is not genome size dependent (same for all species)
* No correlation between solo/intact ratio and genome size
* S/I varies greatly among LTR-RT families
* This is not lineage specific type of elimination
44
Specifics
* Classified LTR-RT (pretty complicated)
* Dated LTR-RT – 5’ and 3’ LTR part inserted at same time and would have been identical
* Determine age via mutations and a rate of 1.3X10-8
