Chromatin and Molecular Mechanisms of Transcription Repression and Activation Flashcards
There are positions within genomes where large heterochromatin blocks are built called _______. Genes that are close to or within these areas are strongly repressed.
Silencers
The repression of genes by silencers depends on their ________, depending on whether they are close to or within heterochromatin. This does not depend their promoters.
Position
List two examples of positional repression from the model organism S. cerevisiae?
- Mating type loci
- Sub-telomeric genes
Describe main points surrounding the mating type loci in yeast, HML and HMR.
- HML and HMR are constantly repressed.
- Genetic studies have showed several proteins that regulate this repression.
- Rap1 binds next to the repressed loci and recruits Sir proteins
- Sir proteins (Silent Information Region) proteins spread over the repressed locus
- Sir is a histone DEACETYLATES the histones at HML and HMR
- The deacetylated histones bind tighter to DNA, form heterochromatin and prevent the association of transcriptional activators to the promotors
- Histone hypo-acetylation is necessary for gene repression
Sir2 is a histone deacetyase. What does this mean?
It deacetylates the histones at HML and HMR.
Describe positional repression at the telomeres.
- Rap1 and Sir proteins bind to the telomeres.
- Sir proteins spread in the sub-telomeric regions of the chromosomes.
- Many telomeres cluster at the periphery of the nucleus and are covered with condensed hypoacetylated nucleosomes
Describe the mutational analysis conducted on histones: Lysine –> Arginine
- These mutants MAINTAIN gene repression at telomeres.
- Arg retains the positive charge, can not be acetylated to lose its positive charge
- The DNA-histone interaction is strong, chromatin is compact
- Gene repression cannot be reversed by acetylating the histones
Describe the mutational analysis conducted on histones: Lysine –> Glutamine
- These mutations ABOLISH repression at the telomeres
- Glutamine has a neutral charge (resembling acetylated Lysine)
- Glutamine cannot be deacetylated to gain a positive charge
- Chromatin is decondesnsed
- Gene cannot be repressed
Does the Lysine –> Glutamine mutation abolish or maintain gene repression at the telomeres?
Abolish -> Can not be deacetylated to gain a positive charge
Does the Lysine –> Arginine mutation abolish or maintain gene repression at the telomeres?
Maintains- Arginine retains the positive charge
In the case of positional repression, describe the role of Rap1, th telomere, Sir3/Sir 4, and Sir 2.
Rap1 - The repressor.
The telomere - The “Silencer”
Sir 3/Sir 4 - Co-repressors
Sir 2 - Histone-Deacetylase
The Sir2/3/4 complex binds Rap 1 and then spreads away from the telomere.
In the case of promoter-dependent repression and activation, ______ and ______ bind to promoters and enhancers and recruit the co-repressors or co-activators.
Repressors and activators (THESE DO NOT SPREAD)
In the case of promoter-dependent repression and activation, is the position of the gene a critical factor?
No.
Describe Ume6 and Sin3/Rpd3.
Ume6- Transcription repressor
Sin3/Rpd3 - Complex is a co-repressor
Rpd3- Histone deactylase
Transcriptional repressors often ______ interact with a histone deactylase.
Directly
Transcriptional repressors often ______ interact with a histone acetyl-transferase.
Indirectly
Describe Gcn4, SAGA and Gcn5.
Gcn4 - Transcription activator
SAGA - Complex co-activator
Gcnc5 - Histone acetyl-transferase
Ayceylated histones can recruit more co-activators via _______.
Bromo-domains
Transcriptional activators de-condense chromatin via 1. ________ and 2. ___________.
- Histone acetylation
- Chromatin remodelling
What are the two types of co-activators brought in by transcriptional activators?
- Histon acetyl-transferases
- Chromatin-remodelling complexes
All chromatin remodelling complexes are homologous to the yeast ________ complex
SWI/SNF
Once histones are acetylated, nucleosomes- DNA interaction become _________.
Loose
What do chromatin-remodelling complexes use to push nucleosomes along DNA to “open” promoters?
ATP (energy source)
How do SWI/SNF ATPases function?
They move nucleosomes along the DNA by sliding or transferring them. They shift nucleosomes away from the promoter/enhancer sites and gives transcription factors access to the DNA.
The mediator is an examples of a co-activator. The mediator is a huge complex containing a variety of proteins including enzymes and proteins that recognize ______, _______, and ______.
They recognize activators, GTFs, and other coactivators.
True or False. Different mediators contain proteins required for all the same/every type of gene.
False - Different mediator complexes contain proteins required for specific genes.
The Mediator directly interacts with ____________. One mediator complex can interact with multiple transcriptional activators.
Transcriptional activators.
Cells differentiate and select the genes they ________.
Express
Cells divide multiple times and express the ____ genes after each cell division.
Same
True or False? DNA replication is a major disruptor of chromatin and bound transcription factors.
True.
How do cells remember which genes to express?
The epigenetic memory of transcription. The “memory of gene expression is achieved through reconstitution of the same chromatin structure after the passage of the replication fork.
How is epigenetic control of transcription maintained?
Through DNA methylation and methylation and acetylation of histones.
When are epigenetic marks rebuilt?
Epigenetic marks are rebuilt during and/or soon after the passage of the replication fork.
Name the three types of histone post-translational modifications?
- Methylation
- Acetylation
- Phosphorylation
Methylation of CpG islands leads to ________.
Condensation of chromatin.
How does methylation of the CpG islands lead to condensation of chromatin?
- Methylated DNA recruits special classes of Me-DNA-biding proteins (MeBPs).
- MeBPs recruit factors that deacetylates histones and condense chromatin.
Unmethylated CpG islands recruit proteins that methylate a specific position on histones: ___________.
Histone 3-Lysine 4 (H3-K4). This is an epigenetic mark that dictates gene expression.
The methylation of DNA is rebuilt _______ after the passage of replication forks.
Immediately
Example: Methylation of the CpG islands in the promotors of tumour suppressor genes 1. ___________ their expression and 2. _______ cancer.
- Block
- Promote
When the replication fork passes through the condensed chromatin, the cell _________ condensed chromatin.
Replicates or rebuilds
When the fork passes through open chromatin, the fork rebuilds what kind of chromatin?
Open chromatin.
What is the effect on transcription at the H3 (K4) site of modification with methylated lysine?
Activated transcription.
What is the effect on transcription at the H3 (K9, K27) site of modification with methylated lysine?
Repression of transcription.
Cells express the same genes after DNA replication and cell division through reconstitution of the same type of chromatin after the passage of the fork. How?
- Reconstitution of the H3-K9Me after the passage of the replication fork
(old histones with marks are recycled and assembled in the nucleosomes behind the replication form, while histone-methyl-transfereases recognize the H3-K9Me marks and methylate new histones re the site to build the same epigenetic mark)
- Reconstitution of H3-K27Me after the passage of the replication fork.
(Polycomb repression complex 2 is a H3-K27 methyl transferase that acts as a co-repressor and associates with heterochromatin, while the transcription repressors and PRC2 are recycled and rebuild behind the form the methylate H3-K27).
Polycomb Repression Complex 2 (PRC2) maintains repression by associating with target loci and continually methylating ________.
H3-K27
Polycomb Repression Complex 1 (PRC1) recognizes H3-K27-Me and _______ chromatin.
Compacts
What is the role of trithorax function during chromosome replication?
It opposes repression by Polycomb complexes by METHYLATING H3 at lysine 4 and maintaining this activity during chromosome replication.
Therefore, methylating = activating transcription
