Chromatin Modifications

Question 1

What do chromatin modifications imply?

Answer 1

Modification of histones

Question 2

Most common histone modifications

Answer 2

Acetylation
Methylation
Ubiquitination
Phosphorylation
Isomerisation

Question 3

How do we identify which modifications are present?

Answer 3

using mass spectrometry

Question 4

How do we determine the position of a histone mark?

Answer 4

By performing ChIP-Seq

Question 5

Where is K27 enriched?

Answer 5

Both at enhancer and promoter

Question 6

Writers

Answer 6

Enzymes adding specific modifications to amino acids in specific positions of specific histones

Question 7

Readers

Answer 7

Regulatory proteins recognising a specific combination of histone modifications and attracting additional proteins

Question 8

How do readers function?

Answer 8

Can cause sliding of a histone, making the piece of DNA accessible to other regulatory proteins

Question 9

Erasers

Answer 9

Enzymes removing specific modifications from specific amino acids in specific positions of specific histones

Question 10

What do transcription activators do?

Answer 10

Provide specificity and regulate access to RNA polymerase by triggering changes to the promoter chromatin structure

Question 11

4 ways to make chromatin more accessible

Answer 11

1. A TF bind at a specific location and recruits chromatin-remodeling complexes
2. The TF can recruit an enzyme that removes nucleosomes completely giving a nucleosome-free region
3. Recruiting of enzymes that modify chromatin
4. Recruitment of TF that causes the recruitment of enzymatic activity that switches the type of histone making it less compact

Question 12

Chromatin-remodeling complexes

Answer 12

SLide around nucleosomes starting from compact chromatin regions they will open it up

Question 13

Glucocorticoid receptor

Answer 13

Its activity is regulated by dexamethasone: this TF can interact with a protein CBP which is an enzyme able to acetylate lysine residues

Question 14

How do transcriptional regulators work?

Answer 14

1. Compete with transcriptional activators recognising the same sequence; if the repressor is more abundant, it will win the competition
2. Blocking activator function by having a domain that interacts with the transcription activation domain
3. Blocking assembly of general TFs
4. Recruiting CRCs
5. Recruitment of histone deacetylases

Question 15

Histone deacetylases

Answer 15

Remove acetly groups and repress transcription and gene expression by depositing other markers

Question 16

Epigenetic inheritance

Answer 16

a form of inheritance superimposed on the genetic inheritance bases on DNA

Question 17

How can epigenetic inheritance happen?

Answer 17

Can be due to feedback loops of TRs or hereditable modification on chromatin proteins

Question 18

Which is the most famous example of epigenetic transmission?

Answer 18

DNA methylation

Question 19

When does DNA methylation take place?

Answer 19

Only when a C is followed by a G

Question 20

What is DNA methylation associated by?

Answer 20

Repression of gene expression

Question 21

How does DNA methylation prevent binding of TFs?

Answer 21

1. Methylation interfers with the ability of TFs to recognise their sequence and activate genes
2. Recruits histone modifying proteins

Question 22

Hypomethylated regions in cancer

Answer 22

Contain oncogenes

Question 23

Hypermethylated regions in cancer

Answer 23

Contain tumor suppressor genes

Question 24

How are new methylation patterns established later in development?

Answer 24

de novo DNA methyltransferases DNMTs

Question 25

When is there genome-wide demethylation?

Answer 25

After fertilisation