lecture 23 Flashcards
(22 cards)
what makes transposable elements recognizable + allows to leave their molecular signature??
what does transposase do?
1) terminal inverted repeats on both ends
2) inserted transposable element is bracketed by flanking direct repreats
generates staggered cuts of the target sequence
what is insertional inactivation by transposable elements?
insertion into a random gene and will make it non functional
what 3 elements do bacteria genomes, plasmids contain?
insertion sequence –
composite transposons – transposase gene, flanking IS region
noncompostie transposons– lack insertion sequence
where are AC and DS elements? what do they contain?
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
what are transposable elements?
what is their size?
how many in the genome?
genetic elements with the capacity to move form one chromosomal location to another
-50bp-20kb
-1 to more than a million
how do TE cause mutations?
-disrupt genes by insertion– cause make stuff stop functoining
-can cause recombination
-can facilitate genome evolution
what are the two mechanisms of transposition ( how they can move around the genome)?
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
mechanism of DNA transposons?
what kind of mechanism is this?
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
mechanism of retrotransposons?
what kind of mechanism is this?
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
what are the transposons in bacteria, yeast, drosophila, and in humans?
bacteria: Tn
yeast: Ty
Drops: P-elements, copia—-> spread by horizontal gene transfer
humans: LINE and SINE
what is the difference between autonomous and non autonomous TEs?
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
in maize, what genotypes gave what phenotypes?
what happens with insertion and excision?
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
why are there two phenotypes in Ac/Ds elements ?
chromosome breakage near centromere of chromosome 9
inactivates C gene
what is Cds/Cds & cAc/cAC producing in wt background and in Ac background?
Cds/Cds:
wt: white bc no transposase
Ac: white with purple spots
cAc/cAC:
wt: white with spots
Ac: with with purple spots
what are the 2 classes of retrotransposons?
LTR/Retrivirus
Non LTr
***each uses different RT
what are the 3 types of DNA transposons?
tyrosin recombinates
Rolling circle– copy paste method
DD type
what does TE diversity span from?
what conserved modules do they all shared?
transposition mechanism
mutation accumulation
horizontal gene transfer
RT
integrase
capsid proteins
tyrosine recombinase
terminal or long terminal repeats (LTRs)
what is the diff between SINE and LINE?
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
how do 2 genomes differ by TE?
de novo germline transition every ____ SINE or ___ LINE?
by 1000 TE insertions
21, 9
how do transposons affect genomes?
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
how does ATAC-seq work to study chromatin structure:
what is the nuclei treated with?
how is Tn5 modified?
Tn5 transpson
insertions will cause DNA breakage
contains sequence adapters
how to interpret ATAC seq?
lots of reads and little reads?
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
