cell nucleus; chromatin structure

Question 1

what is the chromatin?

Answer 1

2m of DNA packed, wrapped around histones in cell nucleus of 10-20 micrometres but still accessible for all nuclear functions (replication, transcription, repair)

Question 2

early models of interphase

Answer 2

• Rabl’s model (1885); threads that each represents an individual chromosome territory
• Coming’s model (1968); attachment sites for chromosome, non-territorial

Question 3

electron micrograph

Answer 3

can visualise nuclear, nucleolus, heterochromatin and euchromatin

Question 4

FISH

Answer 4

visualise location of genes & chromosomes in nucleus

Question 5

limitations of electron micrograph and FISH

Answer 5

• sensitivity; how small a single copy genomic region can be visualised
• resolution; minimum distance between two genomic regions that can be distinguished as two separate signals (super resolution)
• single cell analysis; snapshot only of what is happening in a cell population

Question 6

gene locations

Answer 6

• genes have preferential locations at surface of chromosome terrritory
• can dynamically loop out in response to transcriptional activation
• correlates with gene density

Question 7

structure of nucleosome core particle at 2.8A resolution in 1997;

Answer 7

• revealed by X-ray crystallography of nucleosome crystals
• 1.65 turn, 147 bp DNA
• DNA show up white, histones H2A, H2B H3 & H4 are yellow, red, blue & green

Question 8

what are the structure states of the nucleosome?

Answer 8

• tetrasome
• hexasome
• hemisome
• lexasome

Question 9

tetrasome

Answer 9

H3-H4 tetramer; missing H2A and H2B

Question 10

hexasome

Answer 10

H3-H4 tetramer + 1 x H2A - H2B hetradimer
- intermediate states during nucleosome assembly and during transcription

Question 11

hemisome

Answer 11

half nucleosome

Question 12

lexasome

Answer 12

transcriptionally poised nucleosome

Question 13

transcriptionally silent

Answer 13

highly packaged chromatin basedon 30nm fibre

Question 14

transcriptionally active

Answer 14

more open chromatin

Question 15

models of 30nm fibre from electron micrography and crystal studies

Answer 15

1. solenoid model
2. zigzag model

Question 16

solenoid model

Answer 16

coiled around a central axis of symmetry, 6-7 nucleosomes per turn.
- nucleosomes follow one another along same helical path

Question 17

zigzag model

Answer 17

two rows of two nucleosomes with linker DNA crisscrossing between

Question 18

recent progress in understanding of 3D chromosomes folding looks at:

Answer 18

• library of ligation products representing chromatin structure
• frequency at which 2 genetic loci are in close proximity
• one to one between specific genomic regions