1. Noise and Variability in Gene Expression Presenting: Tal Ashuah Advisor: Dr. Alon Zaslaver 10/05/15

2. Outline Introduction – what is noise? Researching Noise – ◦ Intrinsic Noise vs. Extrinsic Noise ◦ Measuring and Classifying noise Regulating Noise – ◦ Promotor Architecture ◦ MicroRNA Regulation Conclusions

3. Sources for Heterogeneity Genetic Diversity Environmental, Historical Differences Noise

4. Sources of Noise What can cause variability in a population of genetically identical organisms in an identical environment?

5. Sources of Noise Extrinsic Noise: variation between separate individual organisms ◦ Different amount of RNAP, Ribosome, etc. ◦ Cellular cycle stage ◦…◦… Intrinsic Noise: variation within the single organism ◦ RNAP binding randomness ◦ mRNA degradation ◦…◦…

6. Measuring Noise 2002, Michael B. Elowitz, Rockefeller U., NY Goals: ◦ Measure noise levels in a population ◦ Differentiate between intrinsic and extrinsic noise

7. Experimental System Strains of E. coli incorporating two distinguishable fluorescent proteins Identical promotors

8. Classifying Noise

9. Phenotypic Results

10. Computational Results

11. So far Noise is the source of heterogeneity in homogeneous populations Noise can be divided to: ◦ intrinsic noise - stems from stochastic processes in the cell ◦ extrinsic noise – stems from differences between individual cells in the population Questions?

12. Noise – limitation or feature? All biological systems must face a certain degree of randomness What could be the advantages of having more or less noise? Can noise be regulated?

13. Promoter Architecture and Noise Jones, Brewster, Phillips (Caltech) Published Dec. 2014 Goal - Determine if noise is: o Universal and invariant of regulatory mechanisms or o Tunable and subject to evolutionary selective pressures

14. Mathematical Model

15. Model vs. Experimental Data

16. Systematically Tunable Repression

17. Adjusting the Mathematical Model

20. Results

21. Conclusions The suggested model is not necessarily a good predictor of noise levels A systematic change of promotor architecture results in a distinct change of the variation profile Thus, noise can be regulated by the promotor architecture, and is subject to evolutionary selective pressures

22. so far Noise is the source of heterogeneity in homogeneous populations Noise can be divided to intrinsic, extrinsic Noise is subject to evolutionary selection pressure Questions?

23. Regulating Noise We saw that noise can be regulated by adjusting transcriptional parameters Can noise be regulated post- transcriptionally as well?

24. MicroRNA control of Noise Schmiedel, …, Van Oudenaarden (Hubrecht inst.) Published in Science, April 2015 Could miRNA be used to regulate noise levels?

25. MicroRNA – extended introduction Accelerate mRNA degradation and inhibit translation Very common in many living organisms Only slightly reduce mean expression levels, knockouts rarely show phenotypes Genes are often regulated by multiple miRNAs

26. The Hypothesis – Intrinsic Effect Reminder:

27. The Hypothesis – Extrinsic Effect miRNA transcription, maturation and effectiveness are noisy Intrinsic noise for the miRNA is extrinsic noise to the regulated mRNA miRNA increase extrinsic noise

28. The Hypothesis – Total Effect miRNA decrease intrinsic noise miRNA increase extrinsic noise Effect on total noise depends on expression levels

29. Experimental System

30. Results

31. Results

32. Results

33. Verifying Hypothesis ` Measure intrinsic noise separately to verify the separate effects

34. Results II

35. Multiple Regulatory miRNA Assuming the different miRNAs aren’t co-regulated Independent acceleration of degradation – further decrease intrinsic noise miRNA expression noise cancels out – diminish additional extrinsic noise

36. Meaning of Results miRNAs decrease intrinsic noise, increase extrinsic noise Multiple independent miRNA can mitigate noise more effectively, at higher expression levels (back to last week) – Noise regulation offers a possible explanation to the incoherent feed-forward-loop we saw

37. Conclusions Noise is a significant part of gene expression and a useful feature for living organisms The cell regulatory mechanisms regulate both mean and variance of gene expression levels Much is still unknown