Our preprint reporting the absolute quantification of CTCF (~217k proteins per cell) of cohesin (through Rad21; ~109k proteins per cell) in mouse embryonic stem cells has now been published in eLife.
We use these measurements to estimate constraints on models of 3D genome organization: the time-averaged occupancy of an average CTCF binding site is ~50% and the density of putatively loop extruding cohesins is 5.3 per Mb (if monomeric).
We also present biochemical evidence for cohesin-cohesin interactions and we report a very simple, convenient and easy method for absolute abundance quantification of any Halo-tagged protein of interest.
The full paper is here: https://elifesciences.org/articles/40164
And a back-to-back complementary paper in HeLa cells is here: https://elifesciences.org/articles/46269

We just posted a new preprint "Promoters adopt distinct dynamic manifestations depending on transcription factor context".
Find it here: https://www.biorxiv.org/content/10.1101/650762v2
In this work with Christoph Zechner, we study how promoters responds to different patterns of dynamic transcription factor input in budding yeast. Surprisingly, we find that promoters can exhibit qualitatively distinct scaling behaviors depending on TF input. We refer to this observation as context dependent "manifestations".

New preprint from Stanley Hsieh. Using Micro-C to generate 3D contact maps of mouse embryonic stem cells, we see a whole new level of genome organization below the levels of TADs.
This includes enhancer-enhancer, promoter-promoter and enhancer-promoter interactions and stripes/flames. We also find a new type of small domains. We call these microTADs.
Moreover, it seems like besides CTCF/Cohesin, these microTADs are often demarcated by the transcriptional machinery.
Read the full story here on BioRxiv.

And see also a back-to-back preprint from Oliver Rando's lab with the Mirny and Dekker labs on BioRxiv.

The lab website is live. The lab will officially open its doors at MIT BE on Feb 1st, 2020, but we will be setting up before then and are already recruiting. Please see Join for more information.