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REST regulatory networks

REST regulatory networks. Gene Yeo 1,2 Stefan Aigner 2 , Eric Van Nostrand 1,2 , Fred H. Gage 2 1 Crick-Jacobs Center of Theoretical and Computational Biology 2 Laboratory of Genetics The Salk Institute for Biological Studies, La Jolla, CA.

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REST regulatory networks

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  1. REST regulatory networks Gene Yeo1,2 Stefan Aigner 2, Eric Van Nostrand1,2, Fred H. Gage2 1Crick-Jacobs Center of Theoretical and Computational Biology 2Laboratory of Genetics The Salk Institute for Biological Studies, La Jolla, CA

  2. REST repressor/silencing complex silences neuronal genes in non-neuronal cells Histone K4 Demethylase HDAC HDAC MeCP2 SCP mSin3 CoREST DNMT1 REST HMT K9 HP1 MeCP2 RE1 mCpG Methyl H3K9 mK9 mK9 mK9 mK9 mK9 mK9 mK9 mK9 mK9 m m m m m m m m m m Differentiated non-neuronal cells REST binds to a ~20 bp sequence REST levels decrease during neuronal differentiation Slide courtesy of XC

  3. REST sites are highly-conserved across evolution Superiorcervical ganglion neural-specific 10 Synaptosomal-associated protein 25 Brain-derived neurotrophic factor

  4. Algorithm to identify conserved REST sites Converged motif

  5. Several REST sites are proximal to microRNAs

  6. REST-regulated microRNAs are neuronal

  7. REST binds in vivo to predicted sites

  8. REST occupancy near microRNA genes decreases during neural differentiation Anti-REST chromatin immunoprecipitation/qPCR for candidate REST sites in P19 cells upon neural induction

  9. Neural-specific microRNAs and REST co-repressors during mouse stem cell neuronal differentiation d0 d5 d7 d9 d11 d0 d5 d7 d9 d11 Neural differentiation of P19 mouse embryonic carcinoma cells RA induction Western blots Northern blots REST miR-9 msin3A SCP-1 miR-124a CoREST U6 Neuronal marker TUJ1

  10. Neural-specific microRNAs likely target com-ponents of the REST co-repressor complex mCpG Methyl H3K9 mK9 mK9 mK9 mK9 mK9 mK9 mK9 mK9 mK9 m m m m m m m m m m mir-9 and mir-124a downregulate mSin3a and SCP-1, respectively Plasmid transfected: Plasmid transfected: mir324 mir124 empty GFP empty mir-9 mir1 msin3A SCP-1 Loading control -actin Histone K4 Demethylase HDAC HDAC MeCP2 SCP mSin3 CoREST DNMT1 REST HMT K9 HP1 MeCP2 RE1

  11. Neural-specific microRNAs likely target com-ponents of the REST corepressor complex A sensor assay confirms predicted target sites for miR-124a in the 3’UTR of SCP-1 SCP-1 3’UTR SCP-1 sensor ADAR1 3’UTR Control sensor Control sensor SCP1 sensor + mir124

  12. Enhancing neurogenesis

  13. A model for REST regulation to enhance neurogenesis Neurons Neuronal progenitors REST high REST low REST-regulated microRNAs ON REST-regulated microRNAs downregulate components of the REST repressor complex REST-regulated microRNAs OFF REST-regulated protein coding genes OFF REST-regulated protein coding genes ON Supported by Crick-Jacobs Center, NSF Acknowledgements: Eunice Meija, Xinwei Cao

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