Fourth Annual PRIMES Conference. MAY 18, 2014 Loop Extruding Enzymes in Interphase: Dynamic Folding of Chromatin Domains

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1 Fourth Annual PRIMES Conference. MAY 18, 2014 Loop Extruding Enzymes in Interphase: Dynamic Folding of Chromatin Domains Carolyn Lu Professor Leonid Mirny Maxim Imakaev, Geoffrey Fudenberg

2 Characterizing Chromosomal Contacts: Contact maps and scalings contacts Contact maps many contacts Contact probability scalings: (contact probability vs. separation distance) distance few contacts

3 6.5 Mb 55.5 Mb TADs: Topologically Associated Domains few contacts many contacts Regions of increased interaction ~1.3Mb Decreased interaction across boundaries 62 Mb Region of Chromosome Mb 62 Mb

4 contact frequency TAD Scalings distance in kb Within TAD slope in log-log of contact probability over distance in kb is -0.5 Between TADs slope goes from around -0.5 at closer distances to -1.0 at further

5 What mechanisms can define TADs and TAD boundaries consistent with experimental data?

6 Methods: Polymer simulations Experimental Simulation? contact map? scaling???

7 Previously explored models: thick-thin RNA stiff-flexible

8 SMCs as loop-extruding proteins Alipour, Elnaz, and John F. Marko. "Self-organization of domain structures by DNA-loopextruding enzymes." Nucleic acids research (2012): Anton Goloborodko & Leonid Mirny (Unpublished)

9 Basic kinetic model of SMC Loop Extrusion SMC binds DNA SMC extrudes DNA SMC releases DNA

10 SMC loop extrusion + boundary TAD boundaries? TAD boundaries have been shown to be highly bound by a number of key epigenetic regulators. Hypothesis: Boundaries which halt SMC loop extrusion or release SMC loops can in turn create TAD boundaries boundary

11 Complications of the kinetic model 1. What happens when a loop meets a boundary? 2. What happens when a loop meets another loop?

12 Kinetic SMC model: Loop-boundary behavior Boundary Stall OR Release

13 Kinetic SMC model: loop-loop behavior Stall OR Cross

14 Four variations on the basic kinetic model of SMC loop extrusion Since details of SMC loop extrusion are unknown, we tested a number of possible variations: - Boundary stalling and loop-loop stalling (stalling/stalling) - Long boundary stalling and loop-loop stalling (long-stalling/stalling) - Boundary release and loop-loop crossing (release/crossing) - Boundary release and loop-loop stalling (release/stalling)

15 time SMC extrusion kinetic Model 1: Boundary stalling and loop-loop stalling monomer boundary

16 SMC extrusion kinetic model 1: Contact Map (stall/stall) Simulated TADs Experimental TADs

17 Stall-stall: Scalings contact frequency

18 time SMC extrusion kinetic Model 2: Long boundaries and loop-loop stalling monomer Point boundary stall/stall

19 Long boundary: Contact maps Loop density 20 Loop density 5 Experimental TADs

20 Long boundary: Scalings Loop density 20 Loop density 5

21 time SMC extrusion Model 3: Boundary release and loop crossing monomer Point boundary stall/stall

22 Release/cross: Contact map Simulated TADs Experimental TADs

23 contact frequency Release/cross: Scalings monomer distance

24 time SMC extrusion Model 4: Boundary release and loop stalling monomer Point boundary stall/stall Model 3: release/cross

25 Release-stall: Contact map Simulated TADs Experimental TADs

26 contact frequency Release-stall: Scalings monomer distance

27 contact frequency experimental Comparison of models monomer distance

28 Conclusions and Discussion Our models of SMC loop extrusion can reproduce some features of TAD contact maps but do not completely reproduce TAD scalings Details of SMC behavior strongly affect simulated contact maps and scalings o Release at boundaries / stalling between loops best reproduced experimental data Further biological experiments are necessary to determine detailed mechanisms of SMC action & TAD formation

29 Thanks to PRIMES alum/mit student Boryana Doyle, awesome mentors Geoffrey Fudenberg and Maxim Imakaev, Prof. Leonid Mirny, and MIT PRIMES.