ELOWITZ, Michael, Cellular Signaling Circuits, Caltech, Jan 26, 2015
<p class="MsoNormal" >ELOWITZ, Michael, Cellular Signaling Circuits, Caltech, Jan 26, 2015</p>
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this is at Stanford in Clark Aud at 4PM in Dept of Biology.</p>
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Mike is at Caltech and is an HHMI investigator.
intro: many awards including MacArthur Genius Award.
was a post-doc at Princeton.</p>
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his full title: signaling and memory circuits from an operational point of view.</p>
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topics: Notch signaling and chromatin regulation</p>
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the challenge of gene circuit design...</p>
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can draw circuit diagrams...
but what does the circuit do and how does it do it?</p>
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what does the circuit do (function?)
and how... its mechanism?
and why that particular way.</p>
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approaches of our lab:</p>
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synthetic biology and single cell dynamics...</p>
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control: design and BUILD circuits...</p>
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The Repressilator...</p>
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a 3 limb circuit was sufficient to build this</p>
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from TetR to lambdacl to Lac...
he shows a video</p>
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from Elowitz and Leibler in 2000 and J Stricker in Nature in 2008;</p>
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today: first: Notch signaling</p>
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NOTCH...</p>
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canonical highly conserved signaling pathways...</p>
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like hedgehog. TGF EGF, Notch, Wnt and others...</p>
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but why?</p>
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he shows complex diagram of Wnt
TF-beta and Notch...</p>
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how do they work?</p>
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Notch signaling from the bottom up...</p>
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NOTCH:</p>
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notch signaling is used in diverse develop patterning processes...</p>
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eg used in inner ear develp and also
in retinal angiogensis...</p>
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idea is there is a delta ligand that binds to notch receptor that release something in t he cell.</p>
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we made a minimal notch signaling pathway that can be reconst in cells (CHO cells)</p>
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see Sprinzak in Nature in 2010...</p>
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he shows movie: at start Notch is totally off then totally on after a while...</p>
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notch and delta inactivate oneantohe in the same cell (in cis)</p>
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notch is like a walkie talkie... either send or receive but not but simultaneously.</p>
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Notch is a walkie talkie...</p>
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cuz of binding of delta and notch... depends on which one you have an excess of.</p>
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eg lateral inhibition...
two cells are in a see-saw state... one goes up, the other goes down.</p>
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if more notch than delta... then you are in receive state and vice versa for send state.</p>
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but this is not the whole story...</p>
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there are 4 notches and 5 ligands... and they interact...</p>
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and fringes: lunatic , manic and radical etc. that modualte.</p>
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examples from immune system, angiogenesis,and neurogenesis...</p>
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so, what kind of commun channels are possible?</p>
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eg Luantic fringe strengthens trans Delta-Notch interactions and weakens trans Jagged-Notch interactions...</p>
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how does Lunatic Fringer affect cis interactions?</p>
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new assy: Notch availability...</p>
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Lauren showed that Luntic Fringe reduces cis interacitons with Jagged1 but not Delta1.</p>
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we teamed up with Hamed Jafar-Nejad at Baylor ... fly lab.</p>
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see a Notch in the fly wings (why notch is called notch)</p>
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fringe can suppress interaciton of jagge dand notch.</p>
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creates a TABLE of interactions
with detla, jagged and lunatic ( 8 entries... 8 binary terms... eg 010 etc)</p>
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get pure senders, specific receviers, and universal receiver.</p>
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so, notch signaling stts predic tpossible communic channels...</p>
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this is a DAG = directed acyclic graph...</p>
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no muti-state cyles</p>
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alll communic is heterotypic... cells cannot talk toc ells like themselves....</p>
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talks about fly wing.. vetnral surface vs dorsal...</p>
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so, can we move from molec view to an abstract view with just states and channels.</p>
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so, new issues/ quesitons:
who can talk to whom in develp embryos and tissues?</p>
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* story #2 epigenetic regulation </p>
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usual view is that if you incr the TF = transcrip factor then it upregs the gene and get more gene expresiswon as TF goes up...
in sigmoid process.</p>
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BUT, epigenetic memoeyr is asso cwith chromatin-based regulation...</p>
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regulating histones...</p>
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shows an abcam illustration that shows many point sof regulation of this...</p>
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Vernalization... must expose plant to cold to get it to flower...</p>
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as cold goes on get more PRC2 based silencing and then get more flowering...</p>
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synthetic systgem enables controleld recrutiment and de-recruit of chromatin regulators...</p>
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uses rTetR...</p>
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whichc hromatin regulators did we look at?</p>
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EED protein... a par tof Polycomb Repressive Complex 2</p>
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and 2nd was KRB a histone methylation present in zinc finger TFs</p>
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and Dnmt3b a DNA methlation factor</p>
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and HDAC4.. histone deacetylase...</p>
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we can add dox or remove dox to control these cells.</p>
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shows movie that shows silencing event after dox is added.</p>
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Toff = time duration until cells turns off after addition of doxycycline.</p>
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epigenetic silencing is abrupt, all-or-none, and stochastic.</p>
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same pattern in both EED and KRAB systems.</p>
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and Dnmt3b....now slower and stochastic...</p>
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HDAC4... same but slow.</p>
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but all cells get silenced... but are they alll in same or in difft states when silenced?</p>
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A: difft chromatic regulators produce distinct molec states.</p>
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gene expression is off but molec the cells are difft.</p>
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reactivation events are stochastic andall-or-none...</p>
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even tho cells are off, their differing states leads to changes in reactivation.</p>
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we can have reversible silent states and irreversible silent states.</p>
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he shows that his 3 state model nicely fits his data...
with 3 rates...</p>
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active to reversible to inactive (and back from reversible to active)</p>
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3 factors are rate of reactivation,,, rate of inactivation and rat eof ermanent inactivaion.</p>
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EED commitment issues.. takeslots of effot; it is slow-responding and has limtied ocmmitemtn</p>
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KRAB fast responding and limited commitment</p>
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and DNMT3b slow responding perfect committer</p>
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HDAC4 fast-resonding... but no commitment... a "player"</p>
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analogy to a grad studnet aht you're trying to recruit...</p>
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some, take long courtship andmay change their minds depsite that...</p>
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he calls this quantum chromatodynamics</p>
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both silencing and re-activ are stochastic, abrupt, and all-or-none at the single cell level</p>
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bottom line: synthetic operation approaches can provide higher-level reprs of compelx genetic circits...</p>
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from molecules to DAGs...</p>
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done by John Yong and Lacra Bintu...</p>
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