Eukaryote genome and the cell cycle 3

How are interphase chromosomes organised within the nucleus ?

Although chromatin can appear as disordered chains of nucleosomes, chromosomes are organised into functional and structural domains, including:

TADs (topologically associating domains)

A/B compartments

LADs (lamina-associated domains)

Active enhancer regions and sub-TADs

What is the difference between euchromatin and heterochromatin TADs ?

Euchromatin TADs: generally associated with active genes (ON)

Heterochromatin TADs: generally associated with inactive genes (OFF)

Are all genes within a TAD necessarily co-regulated ?

No. TADs often contain multiple genes that are not tightly co-regulated. However, genes within a TAD are generally in a similar ON or OFF state in a particular tissue or cell type.

Are TADs found throughout the animal kingdom ?

Yes. TAD-level and cis-regulatory element (CRE)-to-CRE contacts have been detected across much of the animal kingdom. Some TAD arrangements are also conserved between related species, such as homologous regions in mouse and human genomes

Do organisms without conventional histones from TADs ?

Yes. The lecture highlights dinoflagellates, which have very large genomes, liquid-crystalline DNA and lack conventional histones, yeast still form TADs

Do plants have TAD organisation ?

Yes although it varies between species

Many plants show TAD-level and CRE-to-CRE interactions

Rice displays relatively conventional TAD organisation

Arabidopsis has little evidence of TAD-like interactions and is considered unusual, possibly partly because of its relatively small genomes

Does budding yeast have TADs ?

No clear TAD-like organisation has been identified in budding yeast. However, Micro-C experiments show that the chromatin within individual gene-coding regions can aggregate with itself.

What is RabI arrangement ?

A polarised chromosomes arrangement found in some plants with large genomes and many chromosomes, including wheat, barley and maize.

Centrosomes cluster towards one nuclear pole

Telomeres cluster towards the opposite pole

Chromosomes arms lie alongside one another

Why is the RabI arrangement useful ?

It helps prevent large numbers of chromosomes from becoming tangled during mitosis and meiosis, keeping chromosomes organisation manageable

What are chromocentres in plant nuclei ?

Chromocentres are visible aggregates of DNA formed by clustered centromeres regions.

In some plants:

Centromeres aggregate into chromosomes

Telomeres aggregate in the surface of the nucleolus

How do mouse rod photoreceptor cells reorganise their chromatin ?

As rod photoreceptor cells differentiate, they invert their normal nuclear chromatin arrangement:

In typical fibroblasts, heterochromatin is mainly at the nuclear periphery and euchromatin towards the interior

In mouse rod cells, heterochromatin and the nucleolus move towards the interior, while euchromatin is positioned towards the periphery

Why do mouse rod photoreceptor cells have inverted chromatin architecture ?

The inverted arrangement helps intensify light transfer towards rhodopsin in the outer segment of the photoreceptor, improving night vision

What is NETosis ?

NETosis is a process in which neutrophils release their nuclear contents to form nuclear extracellular traps (NETs)

NETs help capture and kill bacteria and fungi during infection

What happens to chromosomes during M-phase ?

Following DNA replication, each pair of sister chromatids becomes highly compacted. This chromosome-wide remodelling allows accurate chromosome separation during cell division

What are the two main stages of M-phase chromosome compaction ?

1) Linear compression: chromatin forms loops around a scaffold within each chromatid

2) Axial shortening: the chromosome becomes shorter and more compact

What happens to transcription machinery during M-phase chromosome condensation?

Virtually all transcription ceases. RNA polymerases, most co-activators and repressors, and most transcription factors are evicted from M-phase chromosomes.

However, some regulatory information is retained

Does chromosome condensation completely areas gene-regulatory information ?

No. Some pioneer transcription factors, chromatin regulatory proteins (CRAs), nucleosomes and previous histone post-translational modification patterns persist.

These retained features act as chromatin bookmarks, helping cells restore gene expression patterns after division.

Which histone modifications are associated with entry into mitosis ?

On entry to mitosis:

Aurora kinases phosphorylate histone H3 at serines 10 and 28 (H3S10 and H3S28)

Haspin kinase phosphorylates histone H3 at threonine 3 (H3T3)

These changes create an M-phase-specific histone modification pattern

How does H3S10 phosphorylation contribute to chromosome condensation?

H3S10 phosphorylation recruits a histone deacetylase (HDAC)

The HDAC removes the acetyl group from H4K16 (H4K16Ac). Loss of this acetylation promotes interactions between nucleosomes, encouraging chromatin aggregation and condensation.

Which proteins form the main scaffold involved in M-phase chromosome compaction ?

The main enzyme scaffold consists of:

Topoisomerase Ila (Topo Ila)

Condensin I

Condensin II

Condensins I and II belong to the structural maintenance of chromosomes (SMC) protein family, as does cohesin.

What are the proposed roles of Condensin I and Condensin II ?

The two condensins have distinct roles in the two stages of chromosome compaction:

Condensin II is associated with the initial linear compression and loop formation

Condensin I contributes to subsequent axial shortening and further compaction

How do condensins and Topoisomerase Ila compact chromatin ?

They manipulate chromatin loops containing ~ 100 kbp of DNA

Using ATP hydrolysis, they trap, extrude, encircle and manipulate chromatin loops to produce compact chromatin supercools

Supercools are more compact than open chromatin loops

What is the role of Ki-67 during mitosis ?

Ki-67 forms a capsule-like coating around mitotic chromatids

This helps keep chromosomes physically separated during anaphase. Deleting Ki-67 causes mitotic chromosomes to clump together.

How are TADs and chromatin domains re-established after mitosis ?

After chromosome and cell division, chromatin decondenses. Retained chromatin bookmarks, including CTCF-bound insulators, help re-establish TADs and chromatin domains during the transition into G1.

What is the overall relationship between chromatin organisation and gene expression?

Chromatin organisation is both ordered and dynamic. Genome and epigenome structures regulate gene expression over different timescales, from relatively stable chromosome domains to rapid changes during cell division and differentiation.