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lola chat

May 15, 2013

lola chat

stumpf lab work


May 15, 2013

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  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) ?