W3L1 Nuclear architecture and chromatic

Question 1

Nuclear structure

Answer 1

The nucleus condensate
! Liquid-liquid phase separation
! Separation of nuclear components into non-membrane bound domains
! Condensate contain Low-complexity domains (LCDs) or intrinsically disordered regions (IDRs)
! Increase the local concentration of components required for transcription initiation

Question 2

Nuclear organization

Answer 2

! The nucleus is not homogenous
! Position of genes can affect expression
-Nuclear scaffold
- Chromosome territories (more transcription in the middle, less to the periphery )
- Active and inactive

Question 3

Sub nuclear localisation

Answer 3

• the position of the gene in the nuclear might lead to expression or no expression
  -after a cell receive a signal, inactivate gene is then moved into the nuclear neighborhood for gene expression from the repressive domain in the lamia
  -location can affect expression but there are other factor and gene dependent

Question 4

Chromsome structure and gene regulation

Answer 4

! Position of genes on chromosomes can affect expression
! Gene in Heterochromatin region– silenced (darker colour when stained)
!gene in Euchromatin – potentially active
-barrier prevent heterochromatin bleed into euchromatin, occur via DNA methylation
! Position effect variegation is when gene is inserted into the heterochromatin due to rare chromosome inversion

Question 5

DNA methylation

Answer 5

-the process is gene dependenti
-in mammal, it occur at CpG doublet
! Two classes of DNA methylases
! De novo methylase which methylase un methylase strand
! Maintenance methylase which return the methylation pattern state of the newly produce strand (inheritable)
-DNA demethylase reverse the methylase state

Question 6

DNA methylation and turning gene expression off

Answer 6

• a naked DNA can still be express when it is bind by regulator
  -methylation occur on the naked gene due to binding of CpG
  -protein bind to the methylated DNA, regulatory factor cannot bind to it

Question 7

Methylation and histone modification

Answer 7

-DNA methylation can affect the recruitment of histone modifying enzymes
- the histone modifying enzymes can affect DNA methylation, still allow for regulatory protein to bind

Question 8

Histone type

Answer 8

! Core histones
! H1, H2A, H2B, H3 and H4
! Histone variants
! H2A.X, H2A.Z, CENPA, H5

Question 9

Histone variants

Answer 9

-histone have different variant that have different histone fold

Question 10

Arrangement of DNA and histone

Answer 10

-Not randomly distributed along DNA
Some position can look like random positioning, nucleoside free region, identical position in the population or having histone variant

Question 11

Nucleosome free region

Answer 11

-We need binding sites for regulatory proteins
-nearby nucleosome contain H2A.Z which define a NFR

Question 12

What is a driving factor behind nucleosome (histone dna ball) location

Answer 12

-DNA protein interaction
-nucleosome position can be directed, driven by DNA binding protein