7-9 Mobile Genetic elements Flashcards
(43 cards)
Give the five classifications of transposable elements found in eukaryotes
Require transcription
- Non-LTR retro(trans)posons
- LTR retrotransposons and retrovirus-like elements (have long terminal repeat for replication by retrotranscriptase).
Don’t require transcription
- Cut and paste transposons (DNA transposons)
- Rolling circle transposons (Helitrons)
Self synthesizing transposons (Polintons)
What happens if a transposable element doesn’t have autonomous elements (eg. Polymerase, reverse transcriptase, transposase etc.)?
They contain sequences that define the element and allow proteins (from other autonomous elements) to recognize it and ‘help’ it.
What is an overlap between transposable elements and repetitive DNA?
DNA transposons (eg. retrotransposons)
Retrotransposons can be LTR or non-LTR type.
Give some general features of all retrotransposons
A retrotransposon is a copy in a region of DNA that is surrounded by a type of element and some protein coding genes (if autonomous)
- Transcribed to RNA
- Translated to produce proteins
- REverse transcriptase will copy RNA into cDNA
- RNA strand is degraded and resulting cDNA strand becomes double stranded
- cDNA is inserted somewhere in genome
The donor site retains the retrotransposon.
The long terminal repeats (LTRs) are able to recognize retrotranscriptase.
How are LTR retrotransposons and retroviruses related?
- A retrovirus has code that is flanked by two LTRs and a number of protein coding genes (eg. for assembly of capsid and genome replicatio and evelope)
- A retrotransposon has the same parts, but lacks the envelope part (or has pseudogenes of it)
During the life cycle of a retrotransposon, once the element is transcribed to RNA, it is also translated to produce retrotranscriptase and other proteins. Some of these proteins make a capsid for the element, but not an envelope (can’t leave cell).
True or false, all ORFs in a retrotransposon are important for transposition?
No, some may just be cellular genes captured by the element.
There are many types of retrovirus and therefore there are many types of LTR retrotransposons. How do LTR retrotransposons compare to non-LTR retrotransposons?
Non LTR RTs are much shorter and propagation is driven by cellular retrotranscriptase.
What is the most important property of LTRs in retrotransposons?
They have DNA elements that make them good promoters for transcription. Transcription will only not occur if the element falls into an inactive region of chromosome (eg. heterochromatin)
Describe the structure (at sequence level) of the following:
- RNA form of retrovirus
- Linear DNA form of virus
- Integrated DNA form of virus
RNA form of virus
- Ends in direct repeats
Free linear DNA form of virus
- Ends in LTRs
Integrated DNA form of virus (provirus)
- Has LTRs that are shortened by two bases each
- Ends at either end with 4-6 bp target DNA repeats
How is minus strand DNA generated during reverse transcription of retrovirus RNA?
Minus strand DNA is generated by switching templates during reverse transcription.
- Retrovirus provides plus strand RNA and primer tRNA anneals to binding site on retroviral RNA
- Reverse transcriptase starts synthesis of minus strand
- Enzyme reaches end of template (end of 5’ repeat on RNA template) generating strong STOP
- 5’ terminal region (including repeat) of RNA strand is degraded
- Single stranded DNA direct repeat region pairs with 3’ terminus in first jump to another retroviral RNA (piece of DNA jumps to the other sided repeat on another molecule and DNA synthesis can proceed)
- Reverse transcriptase resumes synthesis of minus strand
There are great diagrams of this online!
There are other proteins important to retrotransposons beyond reverse transcriptase ofr dsDNA. Describe the activity of integrase.
Integrase catalyzes the insertion of retrotransposons into the genome.
Transcription generates RNA that serves as a template for reverse transcription, yielding a DNA copy.
- Integrase cuts this viral DNA to get 3’ and 5’ sticky ends
- It cuts a sequence in the target chromosome and the viral DNA attacks this target DNA
- DNA is inserted and 5’ and 3’ gaps are filled by DNA repair with short direct repeats of target DNA sequence (these are markers of retrotransposon insertion! 4-6 bp repeats of target DNA)
What are stress granules and how do they relate to replication of non-LTR retrotransposons?
Stress granules are dense aggregations in the cytosol composed of proteins & RNAs that appear when the cell is under stress. The RNA molecules stored are stalled translation pre-initiation complexes - failed attempts to make protein from mRNA.
Replication of non-LTR retrotransposons associated with cellular stress. Stress granules can go back into the nucleus and insert DNA
Describe the distribution of transposable elements in the human genome and how some may have contributed to our evolution.
- Most are non-LTR retrotransposons (eg. L1, Alu, SVA etc.) (about 34%)
- Second most are LTR retrotransposons (8.3%)
- Least are DNA transposons (2.8%), though other animals show the opposite with many DNA transposons.
L1 and Alu are known to have expanded a lot in relatively recent history, which may be important for human evolution.
What is L1?
A non-LTR retrotransposon.
- Similar to a protein coding gene. Has one or two ORFs, thoug none code for retrotranscriptase or anything like that.
- It has flanking UTRs and remains of a polyA tail in genome
What is an Alu element?
A none-LTR retrotransposon
- Has a left and right monomer flanking a A rich region in the centre
- Contains remains of polyA tail
What is a SVA?
A non-LTR retrotransposon
- Known endogenous retrovirus with Alu-like centre.
What are LINES and SINES?
Elements of non-LTR retrotransposons
LINES: Long interspersed nuclear elements (eg. in L1)
- retrotransposons that derive from a selfish DNA sequence that encodes reverse transcriptase.
SINES: Short interspersed nuclear elements (eg. in Alu)
- SINES replicate through an RNA intermediate, but do not encode RT themselves. They utilize RT already in cell
- Evolved from normal cellular RNAs, most often tRNAs, but also RNA that forms a component of the signal recognition particle, which is required for protein translocation across the endoplasmic reticulum membrane.
What RNAs are subject to reverse transcriptase?
Basically and RNA that is able to form hairpin loops. The hairpin loop acts as a primer for reverse transcriptase
What are DNA transposons?
DNA transposons move from one genomic location to another by a cut-and-paste mechanism. They are powerful forces of genetic change and have played a significant role in the evolution of many genomes. As genetic tools, DNA transposons can be used to introduce a piece of foreign DNA into a genome. Indeed, they have been used for transgenesis and insertional mutagenesis in different organisms, since these elements are not generally dependent on host factors to mediate their mobility. Thus, DNA transposons are useful tools to analyze the regulatory genome, study embryonic development, identify genes and pathways implicated in disease or pathogenesis of pathogens, and even contribute to gene therapy.
They have 1 protein coding gene for a transposase, which can excise DNA and integrate it elsewhere in the genome.
What are the three types of eukaryotic DNA transposons?
- Cut and paste transposons
- Helitrons (rolling circle)
- Polintons (self synthesizing)
True or false? DNA transposons are ubiquitous and occur in all three domains of life.
True
We find all the different subtypes of DNA transposons in all the major lineages of eukaryotes. We can assume or infer that when groups share elements, these elements were present in a common ancestor.
However, we know mobile elements can be transferred horizontally, leading us to a simpler explanation.
What are polintons?
Self synthesizing DNA transposons in eukaryotes
- These are pretty variable in structure, which made identifying them difficult.
- Categorized by large size.
- Contain about ten genes.
- Their most conspicuous element is a DNA polymerase gene, making it the only transposon that can copy itself by using its own DNA polymerase.
- Has short inverted repeats that are consistent in size and is present in animals and protists
Describe Polinton transposition
How does this give us hints for the origin of Politons?
- Long internal inverted repeats allow for stems in the dsDNA, which are recognized by enzymes that can excise structure from DNA, which becomes double stranded extrachromosomal DNA
- DNAB (polymerase) proteins function as a primer in absence of oligonucleotides and/or primer.
- Integrase integrates it into the genome
- These proteins have features that are reminiscent of viruses that can infect other viruses (virophages)
Politons originated from virophages.
What are Helitrons?
A new class of DNA transposons. They are usually large and don’t have many conserved structural features, making them difficulut to find and identify.
Helitrons frequently capture host genes, shuffle exons and induce strutural changes in the host chromosomes, generating great structural variability, especially in several plant species.
