lo 4 4. How do histone variants contribute to chromatin architecture?

What are the core histones?

H2A, H2B, H3, and H4 [answer] The core histones are Histone 2A (H2A), Histone 2B (H2B), Histone 3 (H3), and Histone 4 (H4).

What is the linker histone?

Histone H1 [answer] The linker histone is Histone 1 (H1).

What forms the nucleosome core particle?

Two of each core histone (octamer) wrapping ~147bp of DNA [answer] Two of each core histone (H2A, H2B, H3, H4) form an octameric nucleosome core particle wrapping ~147bp of DNA.

When was the nucleosome hypothesis proposed?

1974 [answer] Roger Kornberg's nucleosome hypothesis was proposed in 1974.

What happens when three Histone H1 coding genes are knocked out?

Global chromatin decompaction [answer] Knockout of three Histone H1 coding genes causes global chromatin decompaction, visible in electron microscopy images of nuclei.

What changes in histone modifications occur upon Histone H1 loss?

Depletion of repressive H3K27me3 and gains in active H3K36me3 [answer] ChIP-seq shows global depletion of repressive histone modifications (H3K27me3) and gains in active histone modifications (H3K36me3) at large scales across chromosomes.

What happens to A and B compartments when Histone H1 is lost?

Gains in active A compartments and reductions in repressive B compartments [answer] Loss of Histone H1 corresponds with gains in active A compartments and reductions in repressive B compartments from Hi-C experiments.

How does Histone H1 facilitate spreading of repressive histone modifications?

Through compaction of nucleosomal structure at the dyad [answer] Histone H1-mediated compaction of nucleosomal structure at the dyad is essential for normal deposition and maintenance of histone modification landscapes after cell division.

In which cancer type are Histone H1 mutations recurrent?

B-cell lymphomas [answer] Mutations in Histone H1 coding genes (HIST1E, HIST1C, and HIST1D) are recurrent events in B-cell lymphomas.

Where do Histone H1 mutations cluster in lymphoma?

In the globular domain [answer] Mutations in Histone H1 tend to cluster in the globular domain of the protein and affect dyad formation in the nucleosome.

What is the effect of Histone H1 mutations in lymphoma?

Dysregulation of 3D genome architecture and loss of normal histone modification deposition [answer] Histone H1 mutations are thought to drive cancer development through dysregulation of 3D genome architecture and loss of normal histone modification deposition throughout the genome.

Can Histone H1 mutations drive cancer formation alone?

Yes, in mouse models [answer] Mouse models of Histone H1 mutations show that they can drive cancer formation alone.

How many genes encode canonical H3 proteins in humans?

15 different genes [answer] In humans, 15 different genes encode one of 3 canonical histone proteins (H3.1, H3.2, and H3.3).

What is H3.1?

Canonical H3 incorporated genome-wide without site-specific preferences [answer] H3.1 is incorporated into nucleosomes genome-wide without site-specific preferences.

What is H3.3?

Canonical H3 incorporated selectively at actively transcribed regions and heterochromatin [answer] H3.3 is incorporated selectively at actively transcribed regions (promoters and enhancers) and heterochromatin.

What is CENP-A?

A non-canonical H3 variant found at centromeres [answer] CENP-A is a histone H3 variant selectively found at centromeres and is crucial for kinetochore assembly during mitosis.

What chaperone protein incorporates CENP-A at centromeres?

HJURP [answer] CENP-A is selectively incorporated into chromatin at centromeres through the chaperone protein HJURP.

How does CENP-A differ structurally from canonical H3?

It has a shorter N-terminal alpha-helix and weaker DNA-nucleosome interactions [answer] CENP-A has variations in an N-terminal region that result in a shorter alpha-helix and weaker DNA-nucleosome interactions.

What happens when the CENP-A N-terminus is replaced with the canonical H3 N-terminus?

Major defects in mitosis [answer] Replacing the CENP-A N-terminus with the canonical H3 N-terminus results in major defects in mitosis, showing the shortened N-terminal helix is critical for CENP-A function.

What are the epigenetic features of centromeres?

Low DNA methylation and low H3K9me3 [answer] Centromeres (CENP-A bound sites) are low in DNA methylation and H3K9me3.

What are the epigenetic features of peri-centromeric regions?

Highly enriched in DNA methylation and H3K9me3 [answer] Peri-centromeric regions flanking centromeres are highly enriched in DNA methylation and H3K9me3.

What is macro-H2A?

A non-canonical H2A variant with a bulky C-terminal domain linked to transcriptional repression [answer] Macro-H2A contains a bulky C-terminal domain and is linked to transcriptional repression.

What is H2Ax?

A non-canonical H2A variant enriched at sites of DNA damage [answer] H2Ax is enriched at sites of DNA damage, and its phosphorylation (γH2Ax) is a marker of double-strand breaks and plays a role in directing DNA repair.

How many genes encode canonical H2A proteins in humans?

17 different genes encoding 10 canonical H2A proteins [answer] In humans, 17 different genes encode one of 10 canonical H2A proteins.

What is the function of non-canonical H2A variants?

They have distinct functions in transcriptional control and DNA repair [answer] Non-canonical H2A variants have key functional differences in chromosome structure and transcriptional control, such as macro-H2A for repression and H2Ax for DNA repair.

What is the role of H3.3 in gene regulation?

It is incorporated at actively transcribed regions [answer] H3.3 is incorporated selectively at actively transcribed regions (promoters and enhancers) and heterochromatin, playing a role in active transcription.

What is the function of histone chaperones?

They incorporate histone variants into specific chromatin locations [answer] Histone chaperones incorporate histone variants into specific chromatin locations, such as HJURP incorporating CENP-A at centromeres.

What happens to CENP-A function if its N-terminal helix is extended?

Major defects in mitosis [answer] Introducing an extended N-terminal helix into CENP-A results in major defects in mitosis, demonstrating the importance of the shortened helix for proper centromere function.

How do histone variants contribute to chromatin architecture beyond the core histones?

They provide functional diversity and specialised roles in chromosome structure, transcriptional control, DNA repair, and mitotic function [answer] Histone variants provide functional diversity by replacing canonical histones at specific genomic locations, allowing specialised functions such as CENP-A for centromere function, H2Ax for DNA repair, and macro-H2A for transcriptional repression