[mtekman]

This is really amazing. I wonder if confounders such as transcriptional bursting[1] are modelled too? I did not check but I assume cell-cycle is readily modelled.

1: The tendency of a single cell to perform transcription in bursts of activity/inactivity, which averages in bulk tissue as a continuous variable.

[bglazer]

They use a master equation for transcription, so they could theoretically get bursty behavior. But, my understanding is that the most well understood cause of burstiness is caused in eukaryotic cells by rearrangement of histones allowing transcription. Since this happens on a slower timescale than transcription you get bursts when the histones periodically get out of the way.

Bacteria (like this minimal cell) don’t have histones but they do have bursty transcription, which is weird. Apparently it might be caused by DNA supercoiling and uncoiling [1], which is weird and cool. That said, they definitely don’t model that, so I’d be surprised if they got bursting transcription. If they did, I’d be interested in knowing what mechanism is causing the transcription bursts in the model.

1. https://www.cell.com/cell/pdf/S0092-8674(14)00739-9.pdf