LIST Classes of Transposable Elements in Eukaryotes
- Class I transposable elements
- Class II transposable elements
Class I transposable elements: EXPLAIN
1 * RETROTRANSPOSABLE ELEMENTS (retrotransposons, retroelements)
2 * require reverse transcription of an RNA intermediate for
movement (transpositio
EXPLAIN Class II transposable elements
1 * DNA TRANSPOSONS
2 * no reverse transcription required for transposition
Share an evolutionary history
Class II: DNA Transposons IN DETAIL = 4
1 ➢ DNA transposons ➔ transposition
INTERMEDIATE is DNA
2 ➢ transpose by CUT AND PASTE
mechanism similar to the mechanism
described for bacterial transposons
3 ➢ structurally similar to bacterial transposons
4 ➢ Example: ‘Ac’ and ‘Ds’transposon in
maiz
class II transposons 2 TYPES AS WELL
Autonomous and non-autonomous
Autonomous class II transposon: EXPLAIN = 6
1 ▪ have a simple structure (usually)
2 ▪ a single GENE ENCODING THE TRANSPOSASE, required for transposition.
- ▪ SHORT TERMINAL INVERTED REPEAT (TIR) ≈10–40 bp (up to
≈200 bp) = CIS ELEMENTS required for transposition
5 ➔can transpose on their own = autonomous
6.▪ Examples: Ac element in corn, some P elements in
Drosophila
Non-autonomous class II transposons: EXPLAIN 4
1 ▪ NO TRANSPOSASE GENE
2 ▪ have required CIS ELEMENTS
3 ➔ can transpose if the transposase activity is
provided by another transposon =NON-AUTONOMOUS
4 * Examples: Ds element in corn, SOME P ELEMENTS in
Drosophila
Discovery of class II transposons in Drosophila = 3
- P elements in Drosophila
- ➢ gene with 4 exons and 3 introns encodes transposase and
repressor of transposition - ➢ perfect 31 bp INVERTED REPEAT at each end
- ➢ discovery:
* crosses of MALE flies bearing P ELEMENTS with FEMALE Flies LACKING P elements (lab strains) produces mutations in progeny flies (sterility)
- P elements able to move, causing mutations, as no Repressor of transposition is present initially in zygote
Class II DNA transposons in maize: 3
It was almost 50 years before the maize
elements Ac and Ds discovered by
McClintock were isolated
- ‘Ac’ is AUTONOMOUS – encodes transposase
Also called ACTIVATOR - ‘Ds’ is NONAUTONOMOUS– does not encode
transposase thus cannot transpose alone
Also called DISSOCIATOR - ‘Ac TRANSPOSASE’ binds the ends of Ac or Ds,
excising the element and cleaving the target site to allow reinsertion at new
location
➔ Ac is required for Ds transposition
Explaining McClintock’s observations of unusual maize phenotypes - 1
= 3
1 * Ds inserts into C gene early in kernel development → suppresses pigment production →
colourless kernels
2 * In a strain with Ac, Ac activates Ds to excise allowing mutant phenotype to revert to wild type
→ produces pigment →purple colour
3 * When Ds leaves C gene EARLY/LATE in kernel development → BIG/SMALL spots of colour
The Ds transposable element helps cause chromosome breakage = 2
1 * Chromosome 9 in maize (Zea mays) is recognizable cytologically by a KNOB at the
end of the long arm
2 * Chromosome breakage “DISSOCIATION” can occur at the Ds locus, with loss of
an ACENTRIC FRAGMENT distal to the breakage point ➔ Ds NAMED DISSOCIATOR
Explaining McClintock’s observations of unusual maize phenotypes - 2
HETEROZYGOUS maize strain with:
1 * One chromosome has a ‘Ds’ element linked to dominant wild-type markers ‘C, Sh, Wx’
2 * The other chromosome lacks the Ds element and has corresponding recessive alleles ‘c, sh,
wx’
3 * CHROMOSOME BREAKAGE caused by the ‘Ds’ element leads to loss of the dominant markers ➔
uncovers EXPRESSION OF THE MULTIPLE ‘RECESSIVE’ MARKERS on the alternate chromosome
4 * Produces distinctive kernel phenotype.
Two subclasses of class I Retrotransposons
- long terminal repeat (LTR) retrotransposons
- non-LTR retrotransposons
- long terminal repeat (LTR) retrotransposons = 4
1 ➢ resemble retroviruses = retrovirus-like
elements
2 ➢ have direct LTRs that range from 100 bp to
over 5 kb
3 ➢ commonly found in high copy number (up to a few million copies)
- Examples: Ty elements in yeast, copia-like
elements in Drosophila
- non-LTR retrotransposons = 4
- ➢ Lack long terminal repeats
- ➢ two sub-types:
- ▪ long interspersed nuclear elements
(LINEs)
* 17% of the human genome, >99% inactive - ▪ short interspersed elements (SINEs)
* e.g. Alu in humans
Class 1: long terminal repeat (LTR) retrotransposons:
- Ty elements in yeast
➢ One of the first eukaryotic transposable elements to be molecularly characterised
- Among 1500 spontaneous mutants in HIS4 gene found, two showed an UNSTABLE
His phenotype (reverted back to His+
very frequently) - mutants contained Ty1 element inserted in HIS4 gene
- yeast genome has ~ 35 copies of Ty1
Class 1: long terminal repeat (LTR) retrotransposons:
- copia-like elements in Drosophila
➢ Certain Drosophila mutations result from insertion of copia-like elements
- e.g. white-apricot mutation for eye colour
- Drosophila genome has ~ 10 to 100 copies of element
Class 1: Non-LTR retrotransposons = 4
1 ➢ Most frequent transposons in mammals
2 ➢ Two most abundant are LINEs and SINEs
3.—–1. Long interspersed nuclear elements (LINEs)
- —2. Short interspersed nuclear elements (SINEs)
- Long interspersed nuclear elements (LINEs) = 4
1 * Up to 6 kb full-length, but most are shorter 1-5 kb
2 * flanked by SHORT DIECT REPEATS
3 * have two ORFs for reverse transcriptase (ORF2) and integration
4 * Autonomous
- Short interspersed nuclear elements (SINEs) = 4
1 * 100-300 bp long
2 * NO GENE TRANSCRIPTASE GENE ➔ cannot transpose independently ➔ non-autonomous
3 * MOBILISED BY LINEs
4 * Most abundant in humans is Alu (so named as contains target site for Alu I restriction
enzyme) = 10% human genome
Retrotransposons – Mechanism of transposition
Transpose through a process which
involves the SYNTHESIS OF DNA BY REVERSE TRANSCRIPTION
: RNA to DNA
Retrotransposons – Mechanism of transposition - STEPS = 6
- Transposable DNA used as a
template to make an RNA COPY - The enzyme REVERSE TRANSCRIPTASE is
produced using information on the
RNA copy - Reverse transcriptase uses the RNA
molecule as a template to synthesise
a complementary DNA = ‘cDNA’
* Produces single stranded DNA copy - ssDNA ➔ ‘dsDNA’
- dsDNA is INSERTED into target site
- Transposition has an RNA and a
DNA INTERMEDIATE
Comparing transposition of Retrotransposons and DNA transposons CLASS 1
= 5
1 ➢ RETROTRANSPOSONS REMAIN PERMANENTLY AT A LOCATION once
inserted into genome
2 ➢ the DNA element transposes
through an RNA copy
3 ➢ the RNA copy undergoes REVERSE TRANSCRIPTION into DNA
that is inserted at new locations In the genome
4 ➔ this INCREASE THE NUMBER OF RETROTRANSPOSONS over time
5➔ copy number of
retrotransposon element in a
genome can be huge
Comparing transposition of Retrotransposons and DNA transposons CLASS 2
1 * DNA TRANSPOSONS transpose
without an RNA intermediate
2 * They move by EXCISION from one site and REINSERTION of the
excised DNA into new site
– See cut and paste in
prokaryotes
3 * The excision of the DNA
element CAN LEAD TO REVERSION OF ORIGINAL MUTATION.
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Lecture 129
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Lecture 2: DNA REPLICATION IN EUKARYOTES AND PROKARYOTES40
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Gene Mutations I and II60
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Mechanisms of Gene Mutation31
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Lecture 325
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Lecture 4: RNA molecules and processing30
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Mechanisms of Gene Mutation 226
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Transgenic 136
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Transgenics 214
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Transgenics 330
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Molecular Techniques31
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Molecular techniques 222
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Molecular Techniques 321
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Transposons I44
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L1 Cancer Genetics Regulated and unregulated cell proliferation49
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Dissection of Gene Function part I: Forward Genetics49
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Dissection of Gene Function part II: Reverse Genetics and Mutant Analysis49
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Immunogenetics 1 and 251
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Cancer Genetics Regulated and unregulated cell proliferation L256
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Mechanisms of DNA Repair L1 AND L259
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TRANSPOSABLE ELEMENTS 2 IN EUKARYOTES43
