MT1 Fricker- Chromosomes, chromatin and 3D organisation of the nucleus

how did the eukaryotic nucleus originate?

the hydrogen/syntrophy hypothesis:

• metabolic symbiosis between an archaeal host and an alpha-proteobacteria leads to gene transfer to the host

• the nuclear envelope might have formed to separate transcription from translation- either to protect the dna from reactive oxygen species (from the mitochondrion) or to ensure translation doesn’t start without introns being spliced out

the inside-out hypothesis:

• instead of an endosymbiosis event, engulfment via protrusions occurred, in a manner that could lead to nuclear pore and endoplasmic reticulum formation (with the mitochondria escaping from this ER)

the developed syntrophy hypothesis:

• in this ecological system, cyanobacteria were producing oxygen needed for the mitochondria, but the archaeal host need a more anoxic environment (for methane metabolism)

• a third organism, a delta-proteobacteria could have been the true host, which engulfed both the alpha-protobacteria that became the mitochondrion, and the asgard archaea that became the nucleus within this host

• (supporting evidence- asgard archaea could not be cultured without also coming with two other organisms in some syntrophy, and they have histones + SMC proteins)

these theories could be combined together

why do eukaryotes have so much dna?

• the presence of the mitochondria, and its increase in efficiency due to genome reduction, permitted a massive increase in the number of genes that could be expressed due to increased energy availability

• this increased innovation of the protein folding toolkit

• the mitochondria were a prerequisite to this level of complexity and genome size

how are chromosomes organised in bacteria and archaea?

• bacteria has a ‘bottlebrush model’ nucleoid (supercoiled loops radiate out from a dense core)- no histones but the chromosome is organised via stable maintenance of chromosome (SMC) proteins

• archaea have histones as well as SMC proteins- this supports the idea that archaea were a precursor to the nucleus as we know it

how are chromosomes organised in 3D within the nucleus?

in order of decreasing scale:

level 1: there are distinct chromosome territories within the nucleus but these are not constant/are somewhat ambiguous

level 2: the chromosomes are least active nearest the nuclear envelope (in transcriptionally silent laminar associated domains of chromatin, LADs)- this seems counterintuitive because it means mRNA have to travel further to leave the nucleus, but it may be a method of UV protection

level 3: topologically associated domains (TADs) form between chromosomes, partitioning the nucleus into distinct co-regulatory units (multiple promoter/enhancer/repressor complexes)

level 4: chromosome loops of transcriptionally active regions

how are chromosome loops formed?

• cohesin (an SMC protein) can bind tethered DNA and extrude a loop of DNA through the ring, actively driving the movement using ATP hydrolysis

• the ring is big enough for nucleosomes to remain bound at their original locations

• this is a self-organising system, the extrusion is stopped by convergent CTCF binding:

• CCCTC binding factor (CTCF) can recognise and bind two CCCTC motifs 50-60 bases apart in the DNA

• this CTCF stalls extrusion of the loop until the SMC is unloaded

why and how is DNA organised into functional clusters in the nucleus?

• loops of transcriptionally active DNA are formed through extrusion by SMC proteins

• these are clustered into topologically associated domains (TADs) within/between chromosomes based on similar function

• this increases efficiency in transcription, because the transcription machinery stays stationary while the DNA moves, and so clustering genes near the machinery increases firing frequency