7a Transposable Elements

7/22/2019 7a Transposable Elements

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Mobile &Transposable Elements

Jum

ping

Genes


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Ethnobotany


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mosaic kernels


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1938: Marcus Rhoades reported odd

phenotypic ratios in corn.

Self pollination of a

pigmented corn kernel

yielded:

12 : 3 : 1pigmented : dotted : colorless


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A hypothesis:

Two mutations at

unlinked loci: 1. pigment

geneA1 mutated to

colorless mutant a1, and

2. a dominant allele fordotting (Dt) appeared.

The presence of the Dt

allele caused spots of

pigment to appear.


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Barbara McClintock

1902-1992


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Barbara McClintock

1902-1992


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Transposition = the movementof genetic information from one

chromosomal location, thedonor site, to another, the

target site.


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DNA sequences that can change

their genomic locationintragenomically either

autonomously or non-autonomously

are called transposable elements.


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copy-and-paste

cut-and-paste


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Retrotransposons can be divided into five

orders on the basis of their mechanisticfeatures, sequence organization, and reverse

transcriptase phylogeny: LTR

retrotransposons, DIRS-like elements,Penelope-like elements, LINEs, and SINEs.


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When a transposable element is insertedinto a host genome, a small segment of the

host DNA (usually 4-12 bp) is duplicated at

the insertion site.


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Transposition = the movementof genetic information from one

chromosomal location, thedonor site, to another, the

target site.


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DNA sequences that can change

their genomic locationintragenomically either

autonomously or non-autonomously

are called transposable elements.


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Classifications of

Transposable Elements


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Transposition may be replicative or

conservative. Replicative transposition

will result in two copies of the element,

one at the donor site and one at the

target site. Following conservativetransposition the transposable element

will only be found at the target site, with

no change in copy number.


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Conservative transposition =

cut-and-paste transposition


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Duplicative transposition =

copy-and-paste transposition


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DNA-mediated and RNA-mediated

transposable elements:

1.Class I transposable elements

(retrotransposons).

2.Class II transposable elements (DNA

transposons).


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Autonomous and nonautonomous transposable elements

Autonomous transposable elements encode all the

components of the transposition machinery.

Nonautonomous transposable elements appropriate the

transposition machinery of autonomous transposable

elements.


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Active and fossil transposable elements

A transposable element is defined as active if it contains

all the necessary sequence elements foreither

autonomous or nonautonomous transposition.

Active elements may be rendered defectiveby different

types of mutation, in which case they are referred to as

fossil transposable elements.


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Active and fossil transposable elements

A transposable-element family may contain different

combinations ofactive autonomous, active

nonautonomous, fossil autonomous, and fossil

nonautonomous transposable elements.

For example, the human genome contains approximately

50,000 fossil autonomous and 200,000 fossil

nonautonomous DNA transposons.

Intriguingly, the human genome seems to contain NO

active DNA transposons.


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According to the numbers and kinds of

genes they contain, DNA-mediated

transposable elements are divided into

insertion sequences and transposons.


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FoundinEscherichia coliandShigella dysinteria.

Length = 770 nucleotides, including two inverted

terminal repeats, 23 bp each.

Contains two out-of-phase reading frames, insA and

insB, from which a single protein is produced by

translational frameshifting at a run of adenines.

The N-terminal is an inhibitor of transposition; the C-

terminal is a transposase, an enzyme that catalyzes the

insertion of transposable elements into insertion sites.


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Carriers and non-carriers of the insertion sequence can

be separated by centrifugation because the carriers are

heavier.

INSERTION SEQUENCES (IS)


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galE = UDP-galactose 4-epimerase

galT = galactose-l-phosphate uridylyltransferasegalK = galactokinase

galM = mutarotase

Galactose (gal) operon

galEgalT galK galM

INSERTION SEQUENCES(IS)Insertion sequences were first discovered in thegal

operon ofE. coli.


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Insertion of an IS affects only the transcription of the genes

downstream from the insertion. For example, if the IS occurs

in thegalT gene, thegalT,galK andgalM genes will bedisrupted, butgalE will not be.

This phenomenon is known as a POLARmutation.

Galactose (gal) operon

galE galT galK galM

IS


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Stupidity


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Hypercomposite transposons contain two or

more transposons.

Composite


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(symmetrical-inverted) Tn3 fromE. coliconfers

streptomycin resistance. tnpR and bla are transcribed on

one strand; tnpA on the other. Tn3 is flanked by 38-bp-long inverted repeats.

(asymmetrical) Tn554 fromStaphylococcus aureus lacks

terminal repeats and contains 8 protein-coding genes.

Three of the genes are transcribed as a unit and encode

transposases (tnpA, tnpB, and tnpO). The spc and ermA

genes confer spectinomycin and erythromycin resistance,

respectively.


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Composite transposon Tn9 from

Escherichia colicontains two copiesofIS1 flanking the catgene, which

encodes a chloramphenicol-resistance

protein.


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Some mobile elements can transpose

themselves in all cells; others are cell-specific.

Tc1 elements in the nematode

Caenorhabditis elegans andPelements

inDrosophilamelanogasterare usually

mobile only in germ cells.


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Transposition of many elements is

regulated by developmental stage.

From an evolutionary point of

view, the developmental timing of

transposition is particularly

important, because it affects the

propagation of the transposableelement to future generations.


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LINE-1 transposable elements in mammals are

particularly active during leptotene and

zygotene, when DNA-strand breakages occur.This offers an opportunity for transposable

elements to insert themselves into new sites.


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Genomic locations of target sites for

transposition:

Exclusive genomic preference: In the vast majorityof cases IS4 incorporates itself in the galactosidase operon

ofEscherichia coli, and thus each bacterium contains

mostly one copy ofIS4.

Complete randomness: BacteriophageMu transposesitself at random within the genome.

Intermediate genomic preference: 40% of all Tn10transposons inE. coli are found in the lacZ gene, which

constitutes a minute fraction of the host genome.


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transposition:

Affinity for a particular nucleotide

composition:IS1 favors AT-rich sites.

Affinity for a particular sequence:IS630 has aspecial affinity for 5'CTAG3' sequences.

Chromosomal preference:TRIMelements inDrosophila miranda exhibit a preference for the Y

chromosome.


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Hotspots forPelement insertion in the X

chromosome ofDrosophila melanogaster


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transposition:

TheDIRS-1 transposable element in the

slime moldDictyostelium discoideum


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transposition:

Self affinity:DIRS-1 preferentially inserts itself intootherDIRS-1 sequences.D. discoideum contains, on

average, ~40 intact copies ofDIRS-1 and ~300 fragments.

oldest oldestnewest

ActiveDIRS


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Species specificity:

DIRSinDictyostelium discoideum

only.

marinermoves from species to

species, even if the species belong to

different taxonomic kingdoms.


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Retroelements are sequences that contain a

gene forreverse transcriptase, which

catalyzes the synthesis ofcDNA from anRNA template.

Not all retroelementspossess the intrinsiccapability to transpose. Therefore, not all

retroelements are transposable elements.

Retroelements that transpose do so by

retroposition.


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Central Dogma


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Modified Central Dogma


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Not the Central Dogma


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That would have been nice


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That would have been nice

Joanna Masel


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R t l t


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Retroelements

Retroelements are DNA or RNA sequences that contain a gene

encoding the enzyme reverse transcriptase, which catalyzes thesynthesis of DNA from an RNA template. The resulting DNA

molecule is called complementary DNA (cDNA). Not all

retroelements are transposable ormobile.

Retroelements can be divided into three categories:

(1) transposable elements that move within a genome by replicative

RNA-mediated transposition (but may also move

intergenomically)(2) mobile nontransposable elements that only move

intergenomically

(3) non-mobile elements


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Masayori Inouye

Rutgers University

R t id l di t ib t d b t i l


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Retrons are widely distributed among bacterial

species.

Within each bacterial species retrons tend to be

rare.

Natural populations of retron-carrying genomes

possess a single retron copy, either in the intergenic

part of the genome or inside a prophage (a viral

genome that had became integrated into thebacterial chromosome).


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multicopy single-stranded DNA (msDNA)

TERT genes


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Human telomeres consist of the sequence TTAGGG tandemly

repeated many thousand times. Because of asymmetrical DNA

replication, a few of these repeats are lost from the tips of thechromosomes each replication cycle.

TERT


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TERT genes

Telomerases are nucleoproteins whose function is to add DNA-

sequence repeats to the 3' end of the DNA strands in the telomeres atthe ends of linear eukaryotic chromosomes.

The de novo addition of TTAGGG repeats by the enzyme telomerase

partially or wholly compensates for telomere shortening.

Telomerases in all eukaryotic species share at least two components

essential for catalytic activity: a telomerase reverse transcriptase

protein (TERT) and a telomerase RNA.

The TERT encoding gene is a retroelement. In humans, this

retroelement is located on chromosome 5.

R t l id


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Retroplasmids

Extragenomic DNA and RNA molecules (plasmids) are

frequently detected in fungal mitochondria. They can be

divided into:

- Genomically derived plasmids (similar in sequence tothe mitochondrial sequence)

- Autonomously-replicating true plasmids that exhibit no

sequence similarity with the host mitochondrial genome.


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Group-II introns


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p

Group-II introns are a subclass of self-splicing introns.

Some group II introns contain protein-coding genes forendonuclease and reverse transcriptase. The latter may act

as retrotransposable genetic elements.


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Group-II introns

Group-II introns can integrate into the homologousposition of an intronless allele of the same gene (homing),

and at much lower frequencies into other sites

(retroposition).

Retroposition


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Twintrons are introns-within-introns excised by

sequential splicing reactions.

Group II twintrons have presumably been formed by the

insertion of a group II intron into an existing group II

intron.


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Group-III introns are short ORF-less introns found in a

small number of protist eukaryotes, such asEuglena

gracilis. They appear to be group-II introns from whichthe central ORF-containing portion has been removed.

Thus, group-III introns are essentially nonautonomous

group-II introns.

Group III twintrons are known.

Retrotransposons are transposable elements that use RNA


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Retrotransposons are transposable elements that use RNA-

mediated transposition, but do not construct virion particles,

i.e., they lack the env (envelope) gene, and so, unlike retroviruses,

cannot independently transport themselves across cells.

Initially, the retrotransposons were divided into LTR

retrotransposons and non-LTR retrotransposons (or

retroposons) according to whether or not their coding sequences

were flanked by long terminal repeats (LTRs).

Subsequent evolutionary studies indicated that while most non-

LTR retrotransposons constitute a monophyletic group, the

LTR-retrotransposons are paraphyletic.

Some LTR-retrotransposons have secondarily acquired env-like

reading frames that may enable them to move from cell to cell (i.e.,

they are in practice viruses).


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LTR retrotransposons

Non-LTR retrotransposons


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Integrase


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Pararetroviruses:


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1.HepaDNAviruses, e.g., hepatitis B virus

Pararetroviruses:

Pararetroviruses:


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2. Caulimoviruses, e.g., cauliflower mosaicvirus

Pararetroviruses:


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Pararetroviruses are not transposable elements


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RETROSEQUENCES


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RETROSEQUENCES

Restrosequences (orretrotranscripts) are

genomic sequences that have been derivedthrough the reverse transcription of RNA and

subsequent integration of the resulting cDNA

into the genome.

Retrosequences lack the ability to produce reverse

transcriptase, and have been produced through theuse of a reverse transcriptase from a retroelement.


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Diagnostic features of mRNA der ived retrosequences


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g

1. lack of introns

2. precise boundaries coinciding with

the transcribed regions

3. stretches of poly(A) at the 3 end

4. short direct repeats at both ends

5. truncations6. posttranscriptional modifications


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many

many

few

Retrosequences:


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Retrosequences:Retrogenes

Processed genes

Semiprocessed genesRetropseudogenes

Processed pseudogenesSemiprocessed pseudogenes


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umber of human retropseudogenes and number of parental functional genes

_________________________________________________________________________

N b f N b f


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Number of Number of

Gene genes retropseudogenes

_________________________________________________________________________

argininosuccinate synthetase 1 14-actin 1 ~20-tubulin 2 15-20Cu/Zn superoxide dismutase 1 >4

cytochrome c 2 20-30

dihydrofolate reductase 1 ~5

G3PD 1 ~25lactate dehydrogenase A 1 10

lactate dehydrogenase B 1 3

lactate dehydrogenase C 1 6

laminin 1 >20

nonmuscle tropomyosin 1 >3

nucleophosmin B23 1 7-9phosphoglycerate kinase 1 2

prohibitin 1 >4

prothymosin 1 >5ribosomal protein L32 1 ~20

triosephosphate isomerase 1 5-6

_________________________________________________________________________

G t d t b b d


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Genes tend to bombard

the genome with dead copiesof themselves.

The Vesuvianparadigm


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How do you get reversetranscribed sequences to

become incorporated into the

germline genome if the gene

itself is not transcribed in the

germline?


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Pseudogenes are affected by two evolutionary


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Pseudogenes are affected by two evolutionary

processes:

Compositional assimilation: The accumulationof mutations which obliterate the similarity

between the pseudogene and its functional

paralogue. The nucleotide composition of thepseudogene will come to resemble its

surroundings, eventually blending into it.

Abridgment: Due to the excess of deletions overinsertions, pseudogenes become increasingly

shorter compared to the functional gene.

It takes on average 400 million years


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It takes on average 400 million years

for a mammalian retropseudogene to

lose half of its length.

Mammals are ~200 million years oldand, therefore, the mammalian

genome is expected to contain

reptilian pseudogenes. These ancientpseudogenes have by now become

unrecognizable.

Mammalian processed


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Mammalian processed

pseudogenes are created ata much faster rate than the

rate by which they areobliterated by deletion.

Processed pseudogenes are


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ocessed pseudoge es a e

abundant in mammals.

Processed pseudogenes are

rare in amphibians, rarer in

birds, and even rarer in

Drosophila.


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Creationrates

Deletionrates


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Hypothesis: Retroposition occurs

mainly in the female germline

Spermatogenesis is similar among

animals.

Oogenesis in mammals differs fromthat in the other animals by a

prolonged lambrush stage (=

suspended animation) that lasts from

birth to ovulation (up to 40 years in

humans).

Lampbrush chromosome

Creation rates are determined by


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y

the length of the suspended

animation during oogenesis

20-40 years in humans.2-4 months in amphibians.

Less than 3 weeks in birds.

Less than 1 day inDrosophila.

Prediction:


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Retrosequences should be found in highnumbers on the X chromosome, in

intermediate numbers on autosomes, and be

rare on the Y chromosome.

Prediction:


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Retrosequences should be found in high

numbers on the X chromosome, inintermediate numbers on autosomes, and be

rare on the Y chromosome.

Density of Processed Pseudogenes in Human Chromosomes

(from Bischof et al. 2006)

Mean Density Density in Density inin Autosomes X-chromosome Y-chromosome

2.28 0.40 3.01 0.74

Differences among organisms in


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numbers of retropseudogenes can also

be due to deletion rate.

DNA loss inDrosophila is ~75 timesfaster than that in mammals.

This high rate may explain thedearth of pseudogenes in

7a Transposable Elements

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