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lecture 23 Flashcards

(22 cards)

1
Q

what makes transposable elements recognizable + allows to leave their molecular signature??

what does transposase do?

A

1) terminal inverted repeats on both ends

2) inserted transposable element is bracketed by flanking direct repreats

generates staggered cuts of the target sequence

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2
Q

what is insertional inactivation by transposable elements?

A

insertion into a random gene and will make it non functional

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3
Q

what 3 elements do bacteria genomes, plasmids contain?

A

insertion sequence –

composite transposons – transposase gene, flanking IS region

noncompostie transposons– lack insertion sequence

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4
Q

where are AC and DS elements? what do they contain?

A

AC: contain transposase gene that helps activated transposition
-autonomous
-conservative mechanism of transposition

DS: moves around the genome , cause of unstable kernel mutation
- do not contain transposase gene and require and Ac element to activate their transposition
-non autonomous
- conservative mechanism

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5
Q

what are transposable elements?
what is their size?
how many in the genome?

A

genetic elements with the capacity to move form one chromosomal location to another

-50bp-20kb

-1 to more than a million

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6
Q

how do TE cause mutations?

A

-disrupt genes by insertion– cause make stuff stop functoining

-can cause recombination

-can facilitate genome evolution

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7
Q

what are the two mechanisms of transposition ( how they can move around the genome)?

A

1) replicative (copy paste)– TC is copied and the copy is inserted somewhere in the genome

2) conservative (cut paste): TE is excised and inserted into a new location

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8
Q

mechanism of DNA transposons?

what kind of mechanism is this?

A

1) transposase is translated from the transposons’ sequence– its a trans factor (in cytoplasm)

2) transposon is flanked by TIRs (cis elements)– needed for the transpose to regonizeand cut the elements

3) transposase binds to TIRs and excises the transpose from the original site

4) transposon inserted into new site in the genome

1) cut/paste (conservative)– no copy is make, the element moves directly

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9
Q

mechanism of retrotransposons?

what kind of mechanism is this?

A

1) retrotransposons are transcribed into RNA

2) RNA is RT into DNA via Rt (trans element)
-RT is translated in the cytoplasm

3) new DNA is inserted into new genomic location

4) retrotransposons have LTRs (long terminal repeats)—which are cis and are required for recognition and insertion

1) replicative mechanism– original element stays put + new copy is made and inserted

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10
Q

what are the transposons in bacteria, yeast, drosophila, and in humans?

A

bacteria: Tn

yeast: Ty

Drops: P-elements, copia—-> spread by horizontal gene transfer

humans: LINE and SINE

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11
Q

what is the difference between autonomous and non autonomous TEs?

A

autonomous: encode the protein required for their own movement
-Ac in maize

non: lack genes and rely on enzymes from autonomous elements
-Ds in maize

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12
Q

in maize, what genotypes gave what phenotypes?
what happens with insertion and excision?

A

C+ : purple
c-: colorless

-insertion of Ac or Ds into C gene inactivates it, producing white kernels

-excision restores C function in some genes (reversion), causing purple spots on a white background

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13
Q

why are there two phenotypes in Ac/Ds elements ?

A

chromosome breakage near centromere of chromosome 9

inactivates C gene

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14
Q

what is Cds/Cds & cAc/cAC producing in wt background and in Ac background?

A

Cds/Cds:
wt: white bc no transposase
Ac: white with purple spots

cAc/cAC:
wt: white with spots
Ac: with with purple spots

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15
Q

what are the 2 classes of retrotransposons?

A

LTR/Retrivirus

Non LTr

***each uses different RT

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16
Q

what are the 3 types of DNA transposons?

A

tyrosin recombinates

Rolling circle– copy paste method

DD type

17
Q

what does TE diversity span from?
what conserved modules do they all shared?

A

transposition mechanism
mutation accumulation
horizontal gene transfer

RT
integrase
capsid proteins
tyrosine recombinase
terminal or long terminal repeats (LTRs)

18
Q

what is the diff between SINE and LINE?

A

LINE:
-non LTR
-only 100 copies are active and autonomous
-copy paste method

SINE:
non autnomous
derived from tRNA
highjack LINE 1 (uses its activity for transposition)

-potential driver of somatic variation

19
Q

how do 2 genomes differ by TE?
de novo germline transition every ____ SINE or ___ LINE?

A

by 1000 TE insertions

21, 9

20
Q

how do transposons affect genomes?

A

cause mutation by disrupting gene sequences

can lead to chromosomal rearrangements

create new genes or alter gene expression

impact RNA processing (splicing)

leave footprints after excision

21
Q

how does ATAC-seq work to study chromatin structure:
what is the nuclei treated with?
how is Tn5 modified?

A

Tn5 transpson

insertions will cause DNA breakage
contains sequence adapters

22
Q

how to interpret ATAC seq?
lots of reads and little reads?

A

lots:
inaccessibility by DNA
occupied by nucleosomes- heterochromatin
-will have lots of stuff there

little:
accessible DNA,
no nucleosomes
TF or RNA pol binding possible