10:00 A – 7:20P, 8:30P – 11:30P
Fly Work
- collect virgin MTDs. (progeny of MTD x TRIP -> collection cage. These embryos should lay infertile offspring / transformed embryos). Let’s do Psc; MTD first, see if structure of K27me3 but not presence of K27me3 changes ?
- 8:30 PM collection of virgin MTDs. Espl, Sim and more recent MTDs not yet emerging.
Other
- Aligning steering mirrors on STORM2 rebuild. Too many builders, task aborted.
- Working on presentation for meeting with Xiaowei tomorrow.
- Zeiss 700 now has motorized stage and transmitted light PMT.
Coding
- fixed bug in application of filters
- added new filter ‘select region’
- wrote new conventional chromatic warp function, integrated into STORManalyzer. multifunctional
Image Analysis — see post
Literature
- Hou et al Mol Cell on physical partitioning of the genome by gene density, transcription, and insulators. Bioinformatics ‘resource’.
- Approach: Hi-C of Kc167 cells
- Claims: physical domains of chromosomes are distinct from epigenetic domains (defined by histone modifications)
- higher-order compaction of chromatin within physical domains is independent of silencing chromatin marks on the 10nm chromatin fiber: insertion into domain is less common than insertion into boundary, claim therefore that domain is less compact.
- domain boundaries are gene dense, actively transcribed. contain RED/YELLOW chromatin little BLUE (Pc) chromatin rarely BLACK. Large domains correspond to BLACK chromatin, medium domains to BLUE H3K27me3 chromatin.
- contrary to embyro cells, Kc cells show no increase in intrachromosomal interarm interactions (e.g. 2L to 2R).
- most transgene insertions map close to domain boundaries (correspondingly into RED/YELLOW chromatin regions). Expression level (eye-color) is highest for those at boundary, decreases as moves away. distance from repressive chormatin correlates with lower expression, distance from active chromatin correlates with higher expression.
- Propose transcription defines physical domain boundaries. All insulator proteins except Su(Hw) preferentially associate with promoters.