Base-pair Conformational Switch Modulates MiR-34a Targeting of Sirt1 MRNA

Overview

Journal Nature

Specialty Science

Date 2020 May 29

PMID 32461691

Citations 29

Authors

Lorenzo Baronti

Ileana Guzzetti

Parisa Ebrahimi

Sarah Friebe Sandoz

Emilie Steiner

Judith Schlagnitweit

Bastian Fromm

Luis Silva

Carolina Fontana

Alan A Chen

Katja Petzold

Affiliations

Soon will be listed here.

Abstract

MicroRNAs (miRNAs) regulate the levels of translation of messenger RNAs (mRNAs). At present, the major parameter that can explain the selection of the target mRNA and the efficiency of translation repression is the base pairing between the 'seed' region of the miRNA and its counterpart mRNA. Here we use R relaxation-dispersion nuclear magnetic resonance and molecular simulations to reveal a dynamic switch-based on the rearrangement of a single base pair in the miRNA-mRNA duplex-that elongates a weak five-base-pair seed to a complete seven-base-pair seed. This switch also causes coaxial stacking of the seed and supplementary helix fitting into human Argonaute 2 protein (Ago2), reminiscent of an active state in prokaryotic Ago. Stabilizing this transient state leads to enhanced repression of the target mRNA in cells, revealing the importance of this miRNA-mRNA structure. Our observations tie together previous findings regarding the stepwise miRNA targeting process from an initial 'screening' state to an 'active' state, and unveil the role of the RNA duplex beyond the seed in Ago2.

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References

Bartel D . Metazoan MicroRNAs. Cell. 2018; 173(1):20-51. PMC: 6091663. DOI: 10.1016/j.cell.2018.03.006. View

Marusic M, Schlagnitweit J, Petzold K . RNA Dynamics by NMR Spectroscopy. Chembiochem. 2019; 20(21):2685-2710. PMC: 6899578. DOI: 10.1002/cbic.201900072. View

Ebrahimi P, Kaur S, Baronti L, Petzold K, Chen A . A two-dimensional replica-exchange molecular dynamics method for simulating RNA folding using sparse experimental restraints. Methods. 2019; 162-163:96-107. DOI: 10.1016/j.ymeth.2019.05.001. View

Wang Y, Juranek S, Li H, Sheng G, Wardle G, Tuschl T . Nucleation, propagation and cleavage of target RNAs in Ago silencing complexes. Nature. 2009; 461(7265):754-61. PMC: 2880917. DOI: 10.1038/nature08434. View

Sheng G, Zhao H, Wang J, Rao Y, Tian W, Swarts D . Structure-based cleavage mechanism of Thermus thermophilus Argonaute DNA guide strand-mediated DNA target cleavage. Proc Natl Acad Sci U S A. 2013; 111(2):652-7. PMC: 3896195. DOI: 10.1073/pnas.1321032111. View

Elkayam E, Kuhn C, Tocilj A, Haase A, Greene E, Hannon G . The structure of human argonaute-2 in complex with miR-20a. Cell. 2012; 150(1):100-10. PMC: 3464090. DOI: 10.1016/j.cell.2012.05.017. View

Schirle N, MacRae I . The crystal structure of human Argonaute2. Science. 2012; 336(6084):1037-40. PMC: 3521581. DOI: 10.1126/science.1221551. View

Nakanishi K, Weinberg D, Bartel D, Patel D . Structure of yeast Argonaute with guide RNA. Nature. 2012; 486(7403):368-74. PMC: 3853139. DOI: 10.1038/nature11211. View

Grimson A, Farh K, Johnston W, Garrett-Engele P, Lim L, Bartel D . MicroRNA targeting specificity in mammals: determinants beyond seed pairing. Mol Cell. 2007; 27(1):91-105. PMC: 3800283. DOI: 10.1016/j.molcel.2007.06.017. View

10.

Nielsen C, Shomron N, Sandberg R, Hornstein E, Kitzman J, Burge C . Determinants of targeting by endogenous and exogenous microRNAs and siRNAs. RNA. 2007; 13(11):1894-910. PMC: 2040081. DOI: 10.1261/rna.768207. View

11.

Klum S, Chandradoss S, Schirle N, Joo C, MacRae I . Helix-7 in Argonaute2 shapes the microRNA seed region for rapid target recognition. EMBO J. 2017; 37(1):75-88. PMC: 5753032. DOI: 10.15252/embj.201796474. View

12.

Schirle N, Sheu-Gruttadauria J, MacRae I . Structural basis for microRNA targeting. Science. 2014; 346(6209):608-13. PMC: 4313529. DOI: 10.1126/science.1258040. View

13.

Filipowicz W, Bhattacharyya S, Sonenberg N . Mechanisms of post-transcriptional regulation by microRNAs: are the answers in sight?. Nat Rev Genet. 2008; 9(2):102-14. DOI: 10.1038/nrg2290. View

14.

Sheu-Gruttadauria J, Xiao Y, Gebert L, MacRae I . Beyond the seed: structural basis for supplementary microRNA targeting by human Argonaute2. EMBO J. 2019; 38(13):e101153. PMC: 6600645. DOI: 10.15252/embj.2018101153. View

15.

Wee L, Flores-Jasso C, Salomon W, Zamore P . Argonaute divides its RNA guide into domains with distinct functions and RNA-binding properties. Cell. 2012; 151(5):1055-67. PMC: 3595543. DOI: 10.1016/j.cell.2012.10.036. View

16.

He L, He X, Lim L, de Stanchina E, Xuan Z, Liang Y . A microRNA component of the p53 tumour suppressor network. Nature. 2007; 447(7148):1130-4. PMC: 4590999. DOI: 10.1038/nature05939. View

17.

Yamakuchi M, Ferlito M, Lowenstein C . miR-34a repression of SIRT1 regulates apoptosis. Proc Natl Acad Sci U S A. 2008; 105(36):13421-6. PMC: 2533205. DOI: 10.1073/pnas.0801613105. View

18.

Vecenie C, Serra M . Stability of RNA hairpin loops closed by AU base pairs. Biochemistry. 2004; 43(37):11813-7. DOI: 10.1021/bi049954i. View

19.

Ulrich E, Akutsu H, Doreleijers J, Harano Y, Ioannidis Y, Lin J . BioMagResBank. Nucleic Acids Res. 2007; 36(Database issue):D402-8. PMC: 2238925. DOI: 10.1093/nar/gkm957. View

20.

Parisien M, Major F . The MC-Fold and MC-Sym pipeline infers RNA structure from sequence data. Nature. 2008; 452(7183):51-5. DOI: 10.1038/nature06684. View