Findings:
(1) looping is frequently rate limiting for transcription (see manuscript draft).
(2) Bcd activates transcription by affecting promoter priming, not pol II recruitment (unlike most activators from yeast).
(3) hb proximal enhancer required for normal levels of total mRNA (as well as lower noise expression).
Goals:
(1) 6x bcd, count hb mRNA
(2) counting controls: competing probes (single mRNA per dot?)
(3) total mRNA levels for paused and unpaused genes (ths vs sog, pnr vs tup).
I disagree that too much snail creates a problem. Our 4x snail flies are perfectly happy.
Too much hb creates a problem. We can hardly keep even 3x hb alive and 4x is definetely dead.
Sog is probably more sensitive to levels. See the sog figs I sent.
I think knowing the repressor(s) for snail is necessary to properly nail down the snail patterning canalization / phenotypes.
I’ve been testing candidates for 4 years (they hardly ever make my progress reports because they hardly ever show any promise). I got 6 more fly lines I’m playing with at the moment. Much more of a gamble than the hb stuff.