Chromosomes, chromatin and the 3d organisation of the nucleus

Question 1

Describe bacterial chromosomes

Answer 1

1. <10Mb DNA
2. approx. 3mm
3. > 1000x linear compaction

Question 2

bottlebrush nucleoid model

Answer 2

interwound supercoiled loops emanate from dense core

Question 3

Smc proteins

Answer 3

• ## “chromosomal glue”

Question 4

Smc1/3

Answer 4

ring-like structure around sister chromatids

Question 5

Smc2/4

Answer 5

stabilise 300nm fibre

Question 6

interchromatin compartment

Answer 6

non-chromatin domains

Question 7

non-chromatin domains

Answer 7

• transcription
• splicing
• dna rep and rep

Question 8

chromosome territories

Answer 8

gene positioning correlates with transcriptional status

Question 9

TADs

Answer 9

• less pronounced boundaries in plants
• CTCF and cohesion boundary elements

Question 10

Hubs

Answer 10

for the purposes of transcription

Question 11

eukaryotic cell

Answer 11

• NE
• 1000x more dna
• sub-nuclear compartments (nucleolus)
• 2m dna/cell
• 150millkm/body
• 9.5trill km lifetime synthesis

Question 12

hydrogen hypothesis

Answer 12

• takes up: organics and oxygen
• gives off: water
• transfers: H2, CO2, acetate
• increased exchange SA = internalisation
• NE protects against protomitochondrion ROS

Question 13

genetic perspective

Answer 13

• recombination

Question 14

inside-out hypothesis

Answer 14

blebs emerging from host prokaryote engulf epizootic alphaproteobacterium; weakens the S-layer

Question 15

EEE

Answer 15

• Prometheum syntrophicum MK-D1
• Halodesulfubrio
• Methanogenium

Question 16

why so much more ?

Answer 16

• more bioenergetic membranes

Question 17

chromosome condensation

Answer 17

histones phosphorylated by sdks

Question 18

FISH

Answer 18

sequence proximity

Question 19

3c, HiC

Answer 19

1. crosslink HindIII onto DNA
2. restrict
3. fill
4. biotin
5. ligate
6. purify and shear
7. pull down biotin
8. paired-end sequence
9. shows proximity
10. diagonal = high organisation

Question 20

CHiP

Answer 20

• mapping chromatin state
• binding regulatory proteins

Question 21

DNAse hypersensitivity

Answer 21

unprotected by DNA BPs

Question 22

Chromosome painting

Answer 22

probes for active transcription

Question 23

loop extrusion in yeast

Answer 23

1. condensin binds tethered dna
2. atp hydrolysis extrudes a loop
3. 1 condensin complex = 1kbs-1 dna loops
4. asymmetric

Question 24

loop size

Answer 24

1. convergent CTCF binding

Question 25

CTCF

Answer 25

- CCCTC binding factor - 11 zinc fingers - 50-60bp range

Question 26

convergent CTCF binding

Answer 26

1. Nipbl loads condensin onto chromatin 2. atp-dependent cohesion movement; loop extrusion 3. convergent antiparallel CTCF BSs stall movement 4. WapI unloads cohesin

Question 27

WapI depletion

Answer 27

vermicelli chromosomes: extended loops

Question 28

TADs

Answer 28

- basic unit of chromosome folding - approx. 1Mb loops - syntenic conserved genomic location - multiple promotor/repressor/enhancer complices as co-regulatory units for spatial control

Question 29

LADs

Answer 29

enriched in methylated histones

Question 30

TFies

Answer 30

- foci in permeabilised cells - approx. RNAPs specialised for gene subsets

Question 31

DNA moves?

Answer 31

- Pol activity retained

Question 32

Genome organisation wrt transcription

Answer 32

- clusters of active Pols and TFs - gene tethering near TFies

Question 33

chromosome compartments

Answer 33

transcriptionally (in)active chromatin regions segregates subnuclearly

Question 34

TAD