Genome Architecture -> Chromatin

Question 1

topologically associated domains (TADs)

Answer 1

Regions in close proximity

Question 2

chromosome conformation capture (3C)

Answer 2

Used to study TADs
- formaldehyde to induce formation of covalent crosslinks between DNA and proteins in close proximity
- If 2 chromosomal regions are adjacent, they get crosslinked
DNA is then digested into smaller fragments with restriction - enzymes
- Ends of fragments are joined by a DNA ligase enzyme
- Crosslinking is reverted
- The resulting circular DNA molecule is sequenced, or
analyzed by PCR

Question 3

Constitutive heterochromatin

Answer 3

Regions of the DNA that do not contain any gene (i.e. centromeric and telomeric DNA), that are constitutively kept in a compacted form

Question 4

Facultative heterochromatin

Answer 4

Regions of the DNA that contain genes and that get dynamically compacted only during specific stages of the cell’s life (e.g. differentiation)

Question 5

Insulators

Answer 5

prevent cross-talk between TADs, so that each TAD remains transcriptionally independent
Regulatory elements (e.g. enhancers) cannot regulate a distal gene if an insulator is present in between

Question 6

Histone acetylation

Answer 6

(occurring on Lys residues), usually reduces the affinity of DNA for histones, reducing compaction (it is in fact associated with actively transcribed genes)

Question 7

Histone acetyltransferases (HATs)

Answer 7

add the acetyl group

Question 8

Histone deacetylases (HDACs)

Answer 8

remove the acetyl group

Question 9

De novo methyltransferase

Answer 9

De novomethyltransferases recognize something in the DNA that allows them to newly methylate cytosines. These are expressed mainly in early embryo development and they set up the pattern of methylation.De novomethyltransferases are also active when a signal-responsive cell, such as aneuron, needs to alter protein expression

Question 10

Maintenance methyltransferase

Answer 10

add methylation to DNA when one strand is already methylated. These work throughout the life of the organism to maintain the methylation pattern that had been established by the de novo methyltransferases.

Question 11

Chromatin

Answer 11

A complex of DNA and protein found in eukaryotic cells. The primary function is to package long DNA molecules into more compact, denser structures.

Question 12

Histones

Answer 12

Positively charged proteins that form basic subunit of chromatin. 8 histone proteins (2xH2A, H2B, H3 and H4)) form the nucleosome

Question 13

Linker histone

Answer 13

A 5th histone type (H1) that acts as a clamp to prevent DNA from detatching from the nucleosome.

Question 14

Nucleosome

Answer 14

Basic structure of chromatin, around which DNA wraps twice.
150 bp of DNA is wounded around nucleosome and 50-70 bp of ‘‘naked” DNA link two consecutive nucleosomes (linker DNA)

Question 15

centromere

Answer 15

2 copies of chromosomal DNA are held together

Question 16

Chromatids

Answer 16

Arms of the chromosome

Question 17

euchromatin

Answer 17

Open chromatin (light areas under electron microscope)

Question 18

Heterochomatin

Answer 18

closed chromatin (dark areas under electron microscope)