Visualizing RNA Dynamics in the Cell

Dr. Grigory Filonov is a postdoctoral associate in the Department of Pharmacology at the Weill Medical College of Cornell University. He received a Ph.D. from the School of Chemistry of M.V. Lomonosov Moscow State University. Dr. Filonov conducted his first postdoctoral training at Albert Einstein College of Medicine of Yeshiva University where he engineered fluorescent proteins that can be used to visualize processes in live animals. Dr. Filonov then joined the laboratory of Dr. Jaffrey at Weill Cornell Medical College. Here Dr. Filonov is working on expanding the “RNA mimics of fluorescent proteins” technology. In particular, Dr. Filonov focuses on developing novel high-throughput screening approaches to isolate RNA-based fluorescent probes that have different spectral and photophysical properties. Additionally, Dr. Filonov is addressing the problem of robust expression of functional synthetic RNAs in live cells and organisms. Dr. Samie Jaffrey is a Professor of Pharmacology at the Weill Medical College of Cornell University. He received an M.D. and Ph.D. from Johns Hopkins School of Medicine where he also conducted postdoctoral work. Dr. Jaffrey’s laboratory focuses on identifying novel RNA regulatory pathways the control protein expression in normal cellular function and in disease processes. His research uses novel imaging, sequencing, microfluidic, and chemical biology approaches to address these questions. Dr. Jaffrey’s laboratory developed a novel class of RNAs referred to as “RNA mimics of green fluorescent protein,” which are used to image RNA localization and monitor RNA processing in living cells. The Jaffrey laboratory extended this technology to create a new class of genetically encoded biosensors composed of RNA that allows signaling molecules to be imaged in living cells.

1. RNA Imaging with Multiplexed Error Robust Fluorescence in Situ Hybridization
J.R. Moffitt and X. Zhuang
2. Imaging Single mRNA Dynamics in Live Neurons and Brains
H.C. Moon and H.Y. Park
3. Monitoring of Rna Dynamics in Living Cells Using Pum-Hd and Fluorescent Protein Reconstitution Technique
H. Yoshimura and T. Ozawa
4. Applications of Hairpin DNA Functionalized Gold Nanoparticles for Imaging mRNA in Living Cells
S.R. Jackson, A.C. Wong, A.R. Travis, I.E. Catrina, D.P. Bratu, D.W. Wright and A. Jayagopal
5. In Vivo RNA Visualization in Plants Using MS2 Tagging
E.J. Peña and M. Heinlein
6. Trick: A Single-Molecule Method for Imaging the First Round of Translation in Living Cells and Animals
J.M. Halstead, J.H. Wilbertz, F. Wippich, T. Lionnet, A. Ephrussi and  J.A. Chao
7. Fluctuation Analysis: Dissecting Transcriptional Kinetics with Signal Theory
A. Coulon and D.R. Larson
8. IMAGEtags: Quantifying mRNA Transcription in Real Time with Multiaptamer Reporters
J. Ray, I. Shin, M. Ilgu, L. Bendickson, V. Gupta, G.A. Kraus and M. Nilsen-Hamilton
9. A Method for Expressing and Imaging Abundant, Stable, Circular Rnas in Vivo Using Trna Splicing
C.A. Schmidt, J.J. Noto, G.S. Filonov and A.G. Matera
10. RNA-ID, A Powerful Tool for Identifying and Characterizing Regulatory Sequences
C.E. Brule, K.M. Dean and E.J. Grayhack
11. Fluorescent Protein-Based Quantification of Alternative Splicing of a Target Cassette Exon in Mammalian Cells
N.G. Gurskaya, D.B. Staroverov and K.A. Lukyanov
12. Iras: High-Throughput Identification of Novel Alternative Splicing Regulators
S. Zheng
13. Analysis of Nonsense-Mediated mRNA Decay at the Single Cell Level using Two Fluorescent Proteins
N.G. Gurskaya, A.P. Pereverzev, D.B. Staroverov, N.M. Markina and K.A. Lukyanov
14. Developing Fluorogenic Riboswitches for Imaging Metabolite Concentration Dynamics in Bacterial Cells
J.L. Litke, M. You and S.R. Jaffrey