VL 3: Chromatin (III) Flashcards
How do modified histones affect DNA-templated processes?
Direct and indirect mechanisms (histone modifikations) can both be causative.
Direct: change chromatin sturture (acetylation)
Indirect: includes binding of other protein/ factor and promotes or revents binding (methylation)
What is the role of Heterochromatin Protein 1 (HP1)?
HP1 (reader) is recruited via its chromodomain (domain) to H3K9me2 or H3K9me3 marks, interacting with SUV39n histone methyltransferases (writer) to create a positive feedback loop of H3K9 methylation,
-> leading to heterochromatin formation.
(there is no eraser)
What is histone acetylation and which enzymes are involved?
Histone acetylation involves the addition of acetyl groups to lysine residues, reducing histone-DNA interactions and promoting chromatin accessibility.
* many lysins can be acetylated, mostly at the endterminal of histone (kleiner schwanz deer rausguckt)
The enzymes involved are Histone Acetyl Transferases (HATs) and Histone Deacetylases (HDACs).
* oftern multi enzyme complexes
* reader domain: bromodomain
How does histone acetylation affect chromatin and gene expression?
Histone acetylation:
* opens up chromatin by reducing positive charge interactions with DNA,
* preventing chromatin compaction,
* recruiting bromodomain proteins,
* and is highly correlated with active transcription, especially at transcription start sites.
* competitive antagonism with methylation
How to study histne modifikations
Gene Knockout:
* Pros: Rapid (CRISPR), identifies essential functions.
* Cons: Doesn’t distinguish catalytic/non-catalytic, lethal phenotypes.
Catalytic Point Mutant:
* Pros: Isolates catalytic functions, maintains stability.
* Cons: Requires detailed knowledge, affects stability unpredictably.
Oncohistone Transgene:
* Pros: Rapid, single transgene, applicable to many models.
* Cons: Limited to HMTases, incomplete activity abolition, pathway interference.
Histone Gene Replacement:
* Pros: Definitive for specific residues.
* Cons: Model-specific, doesn’t distinguish modifications.
Small-Molecule Inhibitor:
* Pros: Kinetic analysis, useful for tissue culture.
* Cons: Extensive R&D, limited in vivo use.
What are the different types of lysine methylation and their roles?
Lysine residues can be mono-, di-, or tri-methylated, with roles varying by location and methylation level.
* H3 hotspot of methylation (on Lysin or Arginin)
* Lysin Methyltransferases: KMT’s (ZMT’s) -> highly specific readout and puts on mono, di or tri methyl
Roles:
1. Recruitent of other chromatn proteins through specific domains “Royal family”
2. Transcriptoinal activation (e.g. H3K4me3)
3. Trascriptional repression (e.g. H3K9me)
Wat is the function of H3K4me3?
One of the best characterized post- translational modifikations (PTMs) but the function is still unclear. Maybe it is transcriptional consistecy.
- H3K4me3 is enriched in the promoters of most active genes in eukaryotes, peaking around the transcription start site (TSS)
- enables the recruitment of transcriptional machinery and thus potentially facilitates transcription
But.. - Studies suggest that H3K4me3 is not essential for most transcription, indicating its role may be more nuanced
- local writing of H3K4me3 modestly activates gene expression in a strictly context-dependent manner
- remarkably conserved
- Transcription-dependent recruitment
- Maybe: transcriptional consistency, as H3K4me3 is inversely correlated with stochastic variation (noise) in gene expression levels.
- In mammals, maintained during transcriptionally quiescent states, such as in mature oocytes and sperm, and in fertilized embryos before zygotic genome activation -> maybe longterm funtion like epigenetic memory
(Epigenetic Memory: There is a hypothesis that H3K4me3 plays a role in long-term epigenetic memory, as initially suggested for the Trithorax complex in Drosophila.)
What marks active enhancers and their significance?
Active enhancers are marked by H3K4me1 and H3K27ac, which are associated with cell-type-specific gene regulation and contribute to the activation of target genes.
What is the role of H3K36me3 in post-transcriptional control?
- correlated with actively transcribed regions
- recruitment of the H3K36 methyltransferase SETD2
by elongating RNA polymerase II. - not required for transcriptional elongation
- inhibits cryptic transcription via deacetylation of histones and DNA methylation
- regulates splicing and guides co-transcriptional N6- methyladenosine methylation of mRNA
How does H3K27me3 contribute to gene regulation?
- Together with monoubiquitylation of histone 2A
(H2Aub) feature of facultative heterochromatin - produced by distinct activities of Polycomb repressive complexes PRC2 and PRC1
- is associated with genes (not reperat region)
How do histone modifications interact in crosstalk?
Mutually exclusive: a position can be modified either with an activating or repressive mark (competitive antagonism)
* H3K9ac vs. H3K9me
One modification recruits a modifying enzyme that places/removes another modification on the same/different histone tail
* H3S10P recruits GCN5 H3K14ac
The binding of a protein may be disrupted by modification of an adjacent position
* HP1 (binds to H3K9me) by H3S10P : “phospho switch”
What are the functions of histone variants H2A and H3 variants?
** H2A.Z **
* Gene activation,
* promotes transcription and is incorporated into nucleosomes by SWR1/SRCAP complexes,
* is more loosely bound to chromatin (although NCP structure very similar)
H3 variants like H3.1, H3.3, and CENH3 have specific roles in chromatin structure, transcription regulation, and centromere function.
What is the significance of H3.1 and H3.3 distribution in chromatin?
H3.1 is associated with heterochromatin, while H3.3 is found in actively transcribed genes. These variants influence nucleosome stability and chromatin properties.
What is H3K9me2, and what is the role of KYP in its regulation?
H3K9me2 (Histone H3 Lysine 9 Dimethylation):
* Role in Gene Silencing: H3K9me2 is a histone modification associated with gene repression and the formation of heterochromatin. It plays a critical role in maintaining the silent state of specific genomic regions.
* This mark is typically found in pericentromeric heterochromatin and other repressive chromatin regions.
KYP (Kryptonite)
- is a hsitone methyltransefrase enzym -> adding methyl groups to lysn 9 of histone H3 (specifically forming H3K9me2)
- By methylating H3K9, KYP helps establish and maintain the repressive chromatin state, ensuring stable gene silencing across cell generations.
