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Molecular Genetics > TRANSPOSABLE ELEMENTS 2 IN EUKARYOTES > Flashcards

TRANSPOSABLE ELEMENTS 2 IN EUKARYOTES Flashcards

1
Q

LIST Classes of Transposable Elements in Eukaryotes

A
  1. Class I transposable elements
  2. Class II transposable elements
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2
Q

Class I transposable elements: EXPLAIN

A

1 * RETROTRANSPOSABLE ELEMENTS (retrotransposons, retroelements)

2 * require reverse transcription of an RNA intermediate for
movement (transpositio

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3
Q

EXPLAIN Class II transposable elements

A

1 * DNA TRANSPOSONS

2 * no reverse transcription required for transposition

Share an evolutionary history

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4
Q

Class II: DNA Transposons IN DETAIL = 4

A

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

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5
Q

class II transposons 2 TYPES AS WELL

A

Autonomous and non-autonomous

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6
Q

Autonomous class II transposon: EXPLAIN = 6

A

1 ▪ have a simple structure (usually)

2 ▪ a single GENE ENCODING THE TRANSPOSASE, required for transposition.

  1. ▪ 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

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7
Q

Non-autonomous class II transposons: EXPLAIN 4

A

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

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8
Q

Discovery of class II transposons in Drosophila = 3

A
  • P elements in Drosophila
  1. ➢ gene with 4 exons and 3 introns encodes transposase and
    repressor of transposition
  2. ➢ perfect 31 bp INVERTED REPEAT at each end
  3. ➢ 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
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9
Q

Class II DNA transposons in maize: 3

A

It was almost 50 years before the maize
elements Ac and Ds discovered by
McClintock were isolated

  1. ‘Ac’ is AUTONOMOUS – encodes transposase
    Also called ACTIVATOR
  2. ‘Ds’ is NONAUTONOMOUS– does not encode
    transposase thus cannot transpose alone
    Also called DISSOCIATOR
  3. ‘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

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10
Q

Explaining McClintock’s observations of unusual maize phenotypes - 1

= 3

A

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

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11
Q

The Ds transposable element helps cause chromosome breakage = 2

A

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

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12
Q

Explaining McClintock’s observations of unusual maize phenotypes - 2

A

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.

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13
Q

Two subclasses of class I Retrotransposons

A
  1. long terminal repeat (LTR) retrotransposons
  2. non-LTR retrotransposons
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14
Q
  1. long terminal repeat (LTR) retrotransposons = 4
A

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)

  1. Examples: Ty elements in yeast, copia-like
    elements in Drosophila
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15
Q
  1. non-LTR retrotransposons = 4
A
  1. ➢ Lack long terminal repeats
  2. ➢ two sub-types:
  3. ▪ long interspersed nuclear elements
    (LINEs)
    * 17% of the human genome, >99% inactive
  4. ▪ short interspersed elements (SINEs)
    * e.g. Alu in humans
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16
Q

Class 1: long terminal repeat (LTR) retrotransposons:

  1. Ty elements in yeast
A

➢ 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
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17
Q

Class 1: long terminal repeat (LTR) retrotransposons:

  1. copia-like elements in Drosophila
A

➢ 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
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18
Q

Class 1: Non-LTR retrotransposons = 4

A

1 ➢ Most frequent transposons in mammals

2 ➢ Two most abundant are LINEs and SINEs

3.—–1. Long interspersed nuclear elements (LINEs)

  1. —2. Short interspersed nuclear elements (SINEs)
19
Q
  1. Long interspersed nuclear elements (LINEs) = 4
A

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

20
Q
  1. Short interspersed nuclear elements (SINEs) = 4
A

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

21
Q

Retrotransposons – Mechanism of transposition

A

Transpose through a process which
involves the SYNTHESIS OF DNA BY REVERSE TRANSCRIPTION

: RNA to DNA

22
Q

Retrotransposons – Mechanism of transposition - STEPS = 6

A
  1. Transposable DNA used as a
    template to make an RNA COPY
  2. The enzyme REVERSE TRANSCRIPTASE is
    produced using information on the
    RNA copy
  3. Reverse transcriptase uses the RNA
    molecule as a template to synthesise
    a complementary DNA = ‘cDNA’
    * Produces single stranded DNA copy
  4. ssDNA ➔ ‘dsDNA’
  5. dsDNA is INSERTED into target site
  6. Transposition has an RNA and a
    DNA INTERMEDIATE
23
Q

Comparing transposition of Retrotransposons and DNA transposons CLASS 1

= 5

A

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

24
Q

Comparing transposition of Retrotransposons and DNA transposons CLASS 2

A

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.

25
Q

Retrovirus cycle: 5

A

1 * Retrotransposons RESEMBLE retroviruses, but are not viruses themselves

2 * Retroviruses have a ‘ssRNA GENOME’

3 * They employ a ‘dsDNA INTERMEDIATE’ for replication

4 * The RNA is copied into DNA by REVERSE TRANSCRIPTASE

5 * The DNA INTEGRATES INTO HOST GENOME
encodes new virus

26
Q
  • Examples of retroviruses: 2
A

– HIV ➔ AIDS

– HTLV (Human T-Lymphotropic
Virus) ➔ leukemia

27
Q

Comparing retrovirus and retrotransposon structures = 7

A

1 * Retroviruses and retrotransposons are
flanked by LONG TERMINAL REPEAT SEQUENCES (LTRs)

2 * Retroviruses and retrotransposons
contain ‘gag and pol genes’

3 * gag: maturation of RNA genome

4 * pol: reverse transcriptase

    • Retroviruses but NOT retrotransposons
      have ‘env gene’

6—-* env : viral structural protein

    • Retrotransposons lack env genes ➔
      cannot make a virus particle ➔ cannot
      leave the cell
28
Q

Noncoding DNA and Genome Evolution = 6

A

1 * Non-coding DNA makes up ca 98.5% of human genome

  • Why is this apparently superfluous DNA tolerated ?

2 – Some of the non-coding DNA make up promoter regions and other ‘REGULATORY DNA’ elements

3 – Some are important for CHROMATIN STRUCTURE AND GENOME ORGANISATION

4 * Is the rest just ‘junk DNA” or are functions not yet identified ?

5 * Is there no selection pressure to get rid of it ?

6 * A large proportion of this ‘non-coding’ DNA are TRANSPOSABLE ELEMENTS
and introns

29
Q

Transposable elements in the human genome

A
  • about ‘half’ the ‘human genome’ is derived from ‘transposable elements’

Transposable elements in human gene HGO coding for homogentisate 1,2-dioxygenase:
Alus , SINEs, LINEs : ALL ARE IN INTRONS

30
Q

Transposable element content and composition
differs between genomes = 2

A

Variation in transposable element content and composition is largely
responsible for differences in:

1 * genome size seen amongst eukaryotes

2 * genome size between closely related species

31
Q

How do plants and animals survive with so much mobile DNA in their
genomes? = 3

A

1 ➢ Elements insert into both exons and INTRONS
▪ only insertions in introns will be likely to survive

2 ➢ vast majority of transposable elements ARE INACTIVE , and can no longer transpose
▪ most are relics that have accumulated inactivating mutations
▪ some are capable of movement but are inactivated by host regulatory mechanisms

3 ➢ transposons CAUSE ONLY 0.2% OF ALL SPONTANEOUS MUTATIONS IN HUMANS (50% in
Drosophila, 10% in mouse)

32
Q

How do plants and animals survive with so much mobile DNA in their
genomes?

BUT, transposons can also cause problems: 3

A

➢ A few active LINEs and ‘Alus’ escaped host control and have inserted into important genes causing HUMAN DISEASES

2 * LINEs disrupt FACTOR VIII GENE causing HEMOPHILIA

3 * ‘Alus’ cause HEMOPHILIA B, NEUROFIBROMATOSIS, BREAST CANCER

33
Q

Explain Transposable elements can cause chromosome rearrangement

A

Transposons may cause CHROMOSOMAL REARRANGEMENTS:

  1. insertions,
  2. deletions,
  3. duplications:

▪ Example: recombination between two transposon segments leads to
deletion of the region between the two transposons.

34
Q

Transposable elements may influence gene activity

A

The presence of transposons may ALTER GENE ACTIVITY AND FUNCTION:

▪ Example: insertion of a transposon into the promoter region can prevent
gene activation

35
Q

Transposable elements as source for genetic novelty and evolution

A

Transposons may act as a source for GENETIC NOVELTY

in both coding and
noncoding capacities as they can move:

36
Q

Transposons may act as a source for genetic novelty in both coding and
noncoding capacities as they can move: 3

A

1 * Regulatory sequences

2 * Polyadenylation signals

3 * Exons or introns

37
Q

Transposable elements as source for genetic novelty and evolution
EXAMPLES = 2

A
  1. Gene encoding for the mouse SEX-LIMITED Slp
    ▪ ancient RETROVIRAL ENHANCER SEQUENCES now confer HORMONAL DEPENDENCE
    on the ADJACENT GENE
  2. human amylase gene family
    ▪ SALIVARY SPECIFIC EXPRESSION has arisen due to INSERTED SEQUENCES , deriving
    perhaps from a conjunction of two retrotransposable elements
38
Q

What are the functions of transposable elements? = 4

A
  1. selfish

2.Engines of mutation that significantly contribute to evolution/adaptation

3.Mechanisms for genome evolution

  1. In addition, they are useful tools for geneticists
39
Q

What are the functions of transposable elements?

-selfish.. explain

A

“Selfish” DNA of no function other than self-replication (“junk” DNA) ??

40
Q

What are the functions of transposable elements?

Engines of mutation that significantly contribute to evolution/adaptation… explain

A

1 * IS elements in E. coli cause many spontaneous mutations

2 * Transposable elements in animals cause varying proportions of all mutations depending on
species (0.2% - 50%)

41
Q

What are the functions of transposable elements?

A

1 * promote gene duplications, exon shuffling and generation of new combinations of
transcription control sequences

2 * result over time in new functions, new organisms

42
Q

What are the functions of transposable elements?

❑ In addition, they are useful tools for geneticists = 3

A

1 o tag genes for cloning – bacterial transposons and P element often used

2 o create mutations by insertion of element into gene - ditto

3 o study of retrotransposons of yeast may lead to better gene therapy

43
Q

SUMMARY = 9

A

1 * Transposable elements discovered by Barbara McClintock as the cause of unstable mutations in maize

2 * Classes of eukaryotic transposable elements
include:

3 * Class1: retrotransposons

4 * Class 2: DNA transposons

  1. Viral retrotransposons (copia, Ty) resemble retroviruses
    • Non-viral retrotransposons include LINEs and SINEs (Alu)

7* DNA transposons (P, Ac, Ds) resemble bacterial transposons

    • Up to 50% of the human genome is derived from transposable elements
    • How much of our human phenotype is due to the past activity of these elements? Is
      this really “junk” DNA?

Molecular Genetics (21 decks)

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