The pan-genomic model:

8  FAQs

[This is mainly text; this pdf provides it's text in searchable form]

Answers illustrate how comprehensive the model is,

including discussion of:

Transcription factories, TADs, A/B compartments, micro-compartments, phase-separated condensates, intrinsically-disordered regions, nucleoli.

Detecting DNA:DNA contacts

(Hi-C, ChIA-PET, GAM, SPRITE, RCMC, multiplexed DNA FISH, seq-FISH).

Live-cell microscopy, super-resolution microscopy, photobleaching, resolution limits, expansion microscopy, electron microscopy, cryo-electron microscopy.

Numbers of RNA polymerases transcribing a typical gene, whether polymerases form convoys, how much transcription occurs in factories, the number of factories/cell, evidence for the transient immobility of active polymerases, how adjacent and convergent genes are transcribed, transcriptional interference.

What energy inputs are needed to form factories, kinetic proof-reading, how transcription factors find binding sites, forces maintaining factory structure, the importance of entropic forces like the depletion attraction and bridging-induced attraction.

Where capping, splicing, poly-adenylation, and nonsense-mediated decay occur.

Position effects.

Chromosome databases.

Whether genes on different chromosomes are transcribed in the same factory.

What happens to loops/factories during mitosis.

What fraction of loops are anchored by active RNA polymerases (using inhibitors to assess this).

How factories form during development.

Transvection and the structure of polytene chromosomes.

How chromosomes pair during meiosis.

Speculations on how/when factories might have evolved.