VL 2 Chromatin (II)

Question 1

What are the roles of chromatin remodelers?

Answer 1

Inserting, sliding, and evicting nucleosomes are roles of chromatin remodelers. These processes modify chromatin structure to regulate access to DNA and facilitate transcription and ensure packaging of genome.

Question 2

What are shared characteristics of chromatin remodeling complexes?

Answer 2

• bind nucleosomes
• are DNA-dependent ATPases
• recognize histone modifications
• ATPase activity can be regulated
• interact with other proteins

Each family of chromatin remodelers carries out specialized functions.

Question 3

Family of chromatin remodelers and their functions

Answer 3

1. SWI/SNF (SWI/SNF and RSC) nucleosome depleted regions, position +1 nucleosome for transcription initiation
2. ISWI (Isw1a, Isw1b, and Isw2) and CHB nucleosome maturation and spacing to
   create nucleosomal arrays
3. INO80 (INO80 and SWR1) nucleosome editing by exchanging histone variants

Question 4

What are the detailed roles of ISWI chromatin remodelers?

Answer 4

ISWI (limitation switch)
* nucleosome spacing,
* creating regular nucleosomal arrays,
* facilitating chromatin assembly during replication,
* contributing to heterochromatin formation, and
* regulating transcription by positioning nucleosomes on DNA.

They do not strictly colocalize with RNA Polymerase II but play a crucial role in maintaining chromatin structure.

Question 5

Types of Histone Modifications

Answer 5

Histone proteins can be modified to affect chromatin structure. The amino terminal regions of the histone monomers extend beyond the nucleosome and are accessible for modification (covalently attached groups).
H3 and H4 have long tails -> good excessiblility,
Lysin often targeted because oft its H3N+ End

1. methlyation (mono-, di- or tri-) just on H3 &H4
2. acetylation (genetic function-> not so important)
3. phosphorylation (negatively charged (less then acetyl) -> everything moves away -> opening up)
4. ubiquitinlation (very large, half as big as histone)

all are dynamic and reversable (in response to signals),
serve diverse biological functions

Question 6

Histone code hypthesis and different readers

Answer 6

The idea that specific combinations of histone modifications can be “read” by proteins, leading to distinct biological outcomes.
-> a given combination of histone modifications read by a combination-specific protein or protein complex and thereby leads to a downstream event distinct from the readouts resulting from one modification alone

different readers e.g.
1. acetylation (red triangle): read by Bromodomain
2. methylation: a lot of readers, but tudor & PHD are most common

sometimes more than 2 different proteins are needed

Question 7

What are the roles of writers, erasers, and readers in chromatin modification?

Answer 7

Writers are enzymes that add chemical marks to histones (e.g., acetyltransferases, methlase, phosphorylase)

Erasers remove these marks (e.g., deacetylases, demethylases, phosphatase)

Readers are proteins that recognize and interpret these marks.
(bromodomain, chromodomain, PHDfinger, WD40repeat)

Question 8

How to analyze histone modifications? ChIP

Answer 8

ChIP is a technique used to analyze protein-DNA interactions.
1) It involves cross-linking proteins to DNA,
2) shearing the DNA into smaller pieces, and using specific antibodies to isolate DNA-protein complexes.
3) The precipitated DNA is then analyzed by methods like PCR, ChIP-chip, or ChIP-seq to identify binding sites of proteins on the genome.

Question 9

How do histone modifications relate to gene locations?

Answer 9

Different histone modifications occur at specific locations within genes and transpososn, influencing chromatin structure and gene expression.

Certain modifications are associated with active gene regions, while others are linked to repressed areas, contributing to the regulation of transcription.

e.g.
H3K9me strongly assosciated with Heterochromatin. Mediates repression -> silenced all the time