$30 off During Our Annual Pro Sale. View Details »

lola chat

elipapa
May 15, 2013

lola chat

stumpf lab work

elipapa

May 15, 2013
Tweet

More Decks by elipapa

Other Decks in Science

Transcript

  1. That was way too complicated! • Well studied pathway, suited

    to study stress response • What does the bug do under N limitation? • We are interested in two TFs: NtrC(glnG) and Nac • genes regulated by Nac are transcribed via σ70 • Ntr is σ54 dependent • Nac transcription is activated by NtrC
  2. More on ntrC and nac • To the last count

    nac regulated 25 genes / 10 transcription units • ntrC thought to regulate up to 2% of genome • under N limiting conditions: ↑ N assimilation and tries to keep the bacteria growing • Part of glnALG operon (also glutamine synthetase, NtrB sensor kinase) • ntrC (and nac) bind to an inverted repeat sequence which can be far from TSS
  3. Experimental setup time N spike t0 tOD t3 t9 N

    limited • Can bacteria sense N limitation and prepare the Ntr response? • What happens when it’s shocked back to N abundance? • “inverse” response? or does a different initial state matter ?
  4. Chip-Seq analysis • Tells us where does the Tf protein

    binds on the genome • correlates with regulation
  5. ChipSeq analysis 1. peak calling - Find the peaks 2.

    motif analysis - Does the binding sequence make sense? 3. annotation - Where do the peaks lie? Which genes could they be regulating?
  6. Annotation • not so trivial in bacteria • ntrC can

    act from far (but we don’t know just how far) • lots of overlapping genes
  7. We need more (for modelling) • ntrC exerts its effect

    when phosporilated • Can we use a time series of Tf binding data and transcriptomics data to obtain a proxy of Ntr(P) ?