DOSTIE - LECTURE 3 Flashcards
GENOMIC IMPRINTING AND 3D CHROMATIN ORGANIZATION
how can DNA methylation repress transcription
H3K9 and HP-1 and transcription control
how can HP-1 create silencing over long distances
HP-1 can also recruit H3K9 HMTs
what are the elements that prevent the spreading of long distance transcription silencing
boundary elements
rich in CTCF and cohesin binding sites
depleted in nucleosomes: full of G and C, not very foldable
electron micrograph of a nucleus and the organisation inside
what is level 1 of genome organization
what is level 2 of genome organization
what is level 3 of genome organization
organization of the chromatin in the nuclear space
1. the 10nm fiber into the 30nm fiber
2. there are only in vitro folding models, very little is known about the 3D organization in vivo
3. packaging is essential, combining 1 meter into something very small
4. packaging is not random, it is functional
how do various chromosomes localise in the nucleus
what techniques were used to study genome organization and what are their shortcomings
–> need to develop a high resolution technique
because the functional organization is not strictly linear
suggests an extensive communication within and between chromosomes
example that shows that the functional organization of genes and elements is not linear along chromosomes
the LCR enhancer, despite being near the olfactory receptor genes, does not affect them at all
how does chromosome conformation capture (3C) work
what does a graph of 3C results look like and how can we interpret it
what can we know from mapping of the genome network
what were the shortcomings of the 3C method and what was developed to counter that
what was the final method developed for 3D genome mapping and how does it work
how do chromosomes fold?
example of the consequences of the disruption of TADs
experiment done to see the differences in maternal and paternal inherited imprinting patterns
what are imprinted genes, what do they control and how are they silenced
one mechanism with which methylation prevents transcription is that it prevents the binding of CTCF to the ICR
how does CTCF form maternal specific chromatin loops
what happens on the paternal allele at the IGF2 locus
the ICR and two distal iDMRs are methylated such that CTCF cannot bind and form chromatin loops
