Lecture 1- 3D organisation of the nucleus

Question 1

what is the hydrogen hypothesis?

Answer 1

hypothesis that the mitochondrion developed from hydrogen-producing archaea, inside hydrogen-dependent archaeal hosts, and that the partnership was initially based on nutrition

Question 2

what is syntrophy (general term)?

Answer 2

one organism feeding on the metabolic products of another, in order to cope with energy limitations- such as that discussed in the hydrogen hypothesis

Question 3

inside out hypothesis of nuclear formation

Answer 3

extracellular protrusions, or ‘blebs’, eventually created the nuclear membrane, as they acted as a starting point for other cell material to join the cell (see pictures- it’s easier)

Question 4

syntrophy hypothesis of nuclear origin

Answer 4

nucleus and mitochondria formed from 2 different endosymbionts

Question 5

entangle-engulf-endogenise (E3) model

Answer 5

symbiotic bacteria were ‘entangled’ by an ancestral archaeon under the conditions where one produced hydrogen created by the other, oxygen-consuming partner was ‘engulfed’, metabolism became more entwined- ‘endogenise’

Question 6

Lane and Martin hypothesis for why eukaryotes have more DNA

Answer 6

mitochondria > nucleus no longer in charge of respiration > able to support a larger genome, so diversification

Question 7

proteins which need to be phosphorylated to facilitate chromatin condensation

Answer 7

cdk, SMC proteins such as condensin and cohesin

Question 8

what does SMC mean

Answer 8

stable maintenance of chromosomes- proteins such as condensin

Question 9

how are chromosomes organised in bacteria?

Answer 9

no histones, but there is still protein-mediated compacting by condensin etc

Question 10

how would you visualise specific sequences within a chromosome

Answer 10

FISH to look at specific sequences

Question 11

how would you look at crosslinked, ligated DNA etc

Answer 11

chromosome conformation capture (3C/HiC)- this involves cutting crosslinks, marking the ends, and sequencing to see where the ligation etc occurs

Question 12

how would you map chromatin state

Answer 12

immunoprecipitation (ChIP)

Question 13

how would you look at chromosome positioning within the nucleus

Answer 13

chromosome paiunting

Question 14

different levels of organisation within the chromosome

Answer 14

-chromosome territories
-chromosome compartments, which are segregated into nuclear locations
-topologically associated domains- TADs- regions of the genome which interacts heavily with itself
-loops

Question 15

mechanism of loops

Answer 15

anchor holds DNA to a condensin loop, and the DNA gets pushed out if there is ATP- also happens around histones

Question 16

how are loop sizes controlled?

Answer 16

CTCFs are present along the DNA, which can be pulled together- they act as ‘start’ and ‘stop’ signals for loop formation

Question 17

why do TADs exist

Answer 17

form the basic unit of chromosome folding, as they allow the formation of ~1MB loops.

Question 18

name of a region that can silence chromatin, and how

Answer 18

lamina-associated domains (LADs)- these associate chromatin with lamin proteins at the nuclear periphery, which leads to gene silencing

Question 19

organisation of transcription machinery

Answer 19

discrete ‘transcription factories’, which contain 8ish RNAPs each, and can specialise in different genes

Question 20

difference between fixed and tracking pol

Answer 20

fixed pol- the pol is attached to the rest of the machinery, so activity is always retained at the protein site