9:30 am – 10:15 pm
Manuscripts
Ph Project
- reply to Ajaz and Nicole about modeling work
- send back comments on plan to add model figure
- should try to compute fraction of localizations/molecules in clusters over 30 nm as a function of total Ph concentration for all types. Try this later…
Oligo Secondaries project with Wu lab
- final comments for last round review / response to reviewers (hopefully) sent to BB
Chromatin scaling manuscript
- working on introduction
Discussions on HiC
- Questions for Max and Geoff:
- evidence of domain switching (looking at the large scale, off diagonal interaction preferences, change a domain from repressed to active (in a different cell line or by stimulation) and show that it switches from compartment B to compartment A).
- supposedly this is clear from Dixon 2012 and Nora 2012 data
Other notes
- 3C / 4C / 5C hard to have a simple and accurate normalization — not clear what’s visibility vs. contacts
- linker domains hard to formalize
- domains follow epigenetic marks but not dependent on them
- CTCF / cohesin not yet shown to have a role in metazoan genomes but maybe that’s an assay problem: sufficient time for domains to re-equilibrate after knockdown? sufficient knockdown?
- supposedly removing a CTCF (or cohesin) loader is sufficient to cause more substantial changes?
improving 3D data
- looking for better correction factor (see RecomputeChromatinVolumes_150330).
- simple attempts at linear rescaling based on radius of gyration, computed volume, rg ratio, don’t suggest that such an approach is promising.
- not sure the z-data is quantitatively accurate enough for these measurements.
- blue data pretty reliably still for large regions in all dimensions, but for large black and large yellow there is a systematic depletion of the data at the z-extremes due to detection efficiency issues, which causes these trends to curve down. Images look okay but quantification not as good.