Quantitative analysis of gene expression in single molecule and single cell

Our research is focused on dissecting biological pathways that control and modulate gene expression profiles that are pertinent to human diseases. We develop single molecule and single cell platforms to examine potential rate-limiting steps that contribute to modulating transcription and translation. In particular, we investigate RNA interference pathway and G-quadruplex DNA mediated promoter activity. In collaboration, we are also studying telomeric DNA processing and chromatin remodeling. Together, we seek to shed light on molecular orchestration and mechanism that govern the Central Dogma of Biology.

Our research interests involve developing and applying single molecule and single cell approaches to acquire quantitative understanding of biology and to find ways to improve human medicine. Single molecule platform offers an exquisite capability to detect molecular interactions and dynamics in real time. We devise sequential experimental stations that measures reactions at the molecular, biophysical and cellular levels. Our laboratory consist of scientists trained in molecular biology, physics, physical chemistry, bioengineering and chemical engineering, which is an ideal team setting for carrying out a highly interdisciplinary research.

The current directions of our research include the following. (i) DNA recombination and repair in which we study proteins involved in homologous recombination and trinucleotide repeat processing (collaborate with Patrick Sung and Timothy Lohman; Nat Comms 2013); (ii) Telomere and telomerase processing where we investigate the Shelterin protein components and their interaction with telomerase (collaborate with Patricia Opresko; Structure 2012, Structure 2014, Scientific Reports 2014); (iii) RNA interference mechanism for which we devised stepwise testing platforms to quantitatively analyze RNAi silencing efficiency (collaborate with Jennifer Doudna; PNAS, 2013, NAR 2014) (iv) Ribonucleoprotein assembly and dynamics where we seek to understand the role of RNA helicases in nucleating and forming granules in vitro and in cells (collaborate with Clifford Brangwynne and Christian Eckmann;PNAS, 2015); (v) G quadruplex (GQ) DNA mediated gene regulation where we investigate the role of GQ in altering transcription and translation (NAR 2014; NAR 2015). 

In technical front, we have pioneered a new method for single molecule fluorescence imaging termed PIFE for protein induced fluorescence enhancement (PNAS 2011). This method offers a unique opportunity of performing single molecule experiment without having to fluorescently label the protein under study, thus expanding the capability of the current single molecule imaging. Recently, we established a real-time single molecule assay for detecting telomerase extension activity (Scientific Report, 2015) and GQ conformation probing assay by induced fluorescence of GQ ligands (NAR, 2015) We expect the outcome of our studies to uncover molecular details that govern cellular responses. This can open a new way of drug targeting, provide drug screening platforms and help optimize drug efficiency. In addition, our capability to perform single cell measurements will lead to better understanding about the cell to cell heterogeneity, which poses a challenging problem in research and biomedicine.

Visit  https://myonglab.jhu.edu/research.html for more detailed information on current research projects going on in the Myong Lab

Niaki, A.G.*, Sarkar, J.*, Cai, X., Rhine, K., Vidaurre, V., Guy, B., Hurst, M., Lee, J.C., Koh, H.R., Guo, L., Fare, C.M., Shorter, J., Myong, S. "Loss of dynamic RNA interaction and aberrant phase separation induced by two distinct types of ALS/FTD-linked FUS mutations", Molecular Cell

Rhine, K., Vidaurre, V., Myong, S. "RNA Droplets", Ann Rev Biophys

Sarkar, J., Lee, J.C., Myong, S. "Biophysics of RNA-Protein Interactions", Biol Med Physics Biomed Engineer, David Rueda and Chirlmin Joo (Editors): 978-1-4939-9724-4,214752_1_En.

2019

Lee, C., McNerney, C. Myong, S. "G-Quadruplex and Protein Binding by Single-Molecule FRET Microscopy", Methods Mol Biol, 2019 Aug 23;2035:309-322.

Kukura, P., Myong, S. "Editorial overview: Advances and future prospects of molecular imaging for studying and quantifying biological processes", Curr Opin Chem Biol, 2019 July 13;51:A4-A5.

Tippana, R., Chen, M. C., Demeshkina, N. A., Ferré-D’Amaré,A. R., Myong, S. "RNA G-quadruplex is resolved by repetitive and ATP-dependent mechanism of DHX36", Nat Commun., 2019 Apr 23;10(1):1855.

2018

Alexander E., Niaki A. G., Zhang T., Sarkar J., Liu Y., Nirujogi R. S., Pandey A., Myong S., Wang J. "Ubiquilin 2 Modulates ALS/FTD-linked FUS-RNA Complex Dynamics and Stress Granule Formation",PNAS, 2018. (2018)

Voter A., Qiu Y., Tippana R., Myong S., Keck J. "A guanine-flipping and sequestration mechanism for G-quadruplex unwinding by RecQ helicases",Nat Commun., 2018 Oct 10;9(1):4201. (pdf )

Sarkar J., Myong S. "Single-Molecule and Ensemble Methods to Probe Initial Stages of RNP Granule Assembly", Methods Molecular Biology, 2018;1814:325-338. ( pdf)

Koh H., Myong S. “Single-cell imaging approaches for studying small RNA induced gene regulation”, Biophysical Journal, 2018 Jul 17;115(2):203-208. ( pdf)

Sarkar J., Lee J.C., Myong S. “Evolving methods in defining the role of RNA in RNP assembly“, Springer book"Biophysics of RNA-Protein Interactions", D. Rueda & C. Joo Editors, 2018 ( in press ) 

Chen M. C., Tippana R., Demeshkina N. A., Murat P., Balasubramanian S., Myong S., Ferré-D'Amaré A. R., “Structural basis of G-quadruplex unwinding by the DEAH/RHA helicase DHX36”,Nature,2018 Jun;558(7710):465-469. ( pdf) 

Langdon E. M., Qiu Y., Niaki A. G., McLaughlin G. A., Weidmann C., Gerbich T. M., Smith J. A., Crutchley J. M., Termini C. M., Weeks K. M., Myong S., and Gladfelter A. S., “mRNA structure determines specificity of a polyQ-driven phase separation” Science, 2018 May 25;360(6391):922-927. ( pdf)

Qiu Y., Koh H.R., Myong S. "Probing Dynamic Assembly and Disassembly of Rad51 Tuned by Srs2 Using smFRET", Methods Enzymol., 2018;600:321-345. (pdf ) 

Zhang T., Wu YC., Mullane P., Ji Y. J., Liu H., He L., Arora A., Hwang HY., Alessi A. F., Niaki A. G., Periz G., Guo L., Wang H., Elkayam E., Joshua-Tor L., Myong S., Kim J., Shorter J., Ong SE., Leung A. K. L., Wang J. "FUS Regulates Activity of MicroRNA-mediated Gene Silencing", Molecular Cell, 2018 Mar 1;69(5):787-801.e8. (pdf ) 

2017

Koh H., Niaki A. G., Myong S. “RNA Stem Structure Governs Coupling of Dicing and Gene Silencing in RNA interference”, PNAS, 2017 Nov 28;114(48):E10349-E10358. ( pdf) 

Lee H. T., Bose A., Lee C. Y., Opresko P. L., Myong S. "Molecular mechanisms by which oxidative DNA damage promotes telomerase activity", Nucleic Acid Research, 2017 Nov 16;45(20):11752-11765. ( pdf)

Qiu Y., Levendosky R., Chakravarthy S., Bowman G., Myong S. "The Chd1 chromatin remodeler shifts nucleosomal DNA bidirectionally as a monomer", Molecular Cell, 2017 Oct 5;68(1):76-88.e6. ( pdf) 

Koh H., Kidwell M., Doudna J., Myong S. "RNA scanning of a molecular machine with a built-in ruler", Journal of the American Chemical Society, 2017, 139 (1), pp 262–268. ( pdf)

2016

Koh H., Wang X., Myong, S., “Visualizing repetitive diffusion activity of double-strand RNA binding proteins by single molecule fluorescence assays”, Methods 2016 Mar 21 pii: S1046-2023(16)30043-3. ( pdf )

Kim M., Kreig A., Lee C., Rube T., Calver J., Song J., Myong S., "Quantitative analysis and prediction of G-quadruplex forming sequences in double-stranded DNA", Nucleic Acid Research 2016 ( in press ) 

2015

Kreig, A., Calvert, J., Sanoica, J., Cullum, E., Tippana, R., Myong, S., “ G-quadruplex Formation in Double Strand DNA probed by NMM and CV Fluorescence”, Nucleic Acid Research 2015 Sep 18;43(16):7961-70. ( pdf )

Wang, X., Vukovic, L., Koh, H., Schulten, K., Myong, S., “Dynamic profiling of double-stranded RNA binding proteins”,Nucleic Acid Research 2015 Sep 3;43(15):7566-76. ( pdf )

Bell R.J.A., Rube H.T., Kreig A., Mancini A., Fouse S.F., Nagarajan R.P., Choi S., Hong C., He D., Pekmezci M., Wiencke J.K., Wrensch M.R., Chang S.M., Walsh K.M., Myong S., Song J.S., Costello J.F., “The transcription factor GABP selectively binds and activates the mutant TERT promoter in cancer” Science 2015 May 29;348(6238):1036-9. (pdf )

Elbaum-Garfinkle S., Kim Y., Szczepaniak C., Eckmann C., Myong S., Brangwynne CP., “The disordered P granule protein LAF-1 drives phase separation into droplets with tunable viscosity and dynamics” PNAS 2015 Jun 9;112(23):7189-94. ( pdf )

Qiu Y., Niu H., Vukovic L., Sung P., Myong S., “Molecular Mechanism of Resolving Trinucleotide Repeat Hairpin by Helicases” Structure 2015 Jun 2;23(6):1018-27. ( pdf )

Shim J., Kim Y., Humphreys GI., Nardulli AM., Kosari F, Vasmatzis G, Taylor WR., Ahlquist DA., Myong S, Bashir R., “Nanopore-Based Assay for Detection of Methylation in Double-Stranded DNA Fragments” ACS Nano 2015 Jan 27;9(1):290-300. ( pdf )

2014

Hwang, H., Opresko, PL., Myong, S., “Single-molecule real-time detection of telomerase extension activity” Scientific Reports 2014 Sep 29;4:6391. ( pdf )

Koh H., Xing L., Kleiman L., Myong S., “Repetitive RNA unwinding by RNA helicase A facilitates RNA annealing” Nucleic Acid Research 2014 Jul;42(13):8556-64. ( pdf )

Tippana R., Xiao W., Myong S., “G-quadruplex conformation and dynamics are determined by loop length and sequence”Nucleic Acid Research 2014 Jul;42(12):8106-14. ( pdf )

Hwang H., Kreig A., Calvert J., Lormand J., Kwon Y., Daley JM., Sung P., Opresko PL., Myong S., "Telomeric Overhang Length Determines Structural Dynamics and Accessibility to Telomerase and ALT-Associated Proteins" Structure 2014 Jun 10;22(6):842-53. ( pdf ): Highlight Preview Hopfner, K-P., “Single Molecule Choreography between Telomere Proteins and G Quadruplexes” Structure. 2014 Jun 10;22(6):801-2.

Vukovic L., Koh H., Myong S., Schulten K. “Substrate recognition and specificity of double-stranded RNA binding proteins” Biochemistry 2014 Jun 3;53(21):3457-66. ( pdf )

Lytle A. K., Origanti S. S., Qiu Y., VonGermeten J., Myong S. and Anthony E. "Context dependent remodeling of Rad51-DNA complexes by Srs2 is mediated by a specific protein-protein interaction" J. Mol. Biol. 2014 May 1;426(9):1883-97. (pdf )

Hwang H., and Myong S. “Protein induced fluorescence enhancement (PIFE) for probing protein–nucleic acid interactions” Chem. Soc. Rev., 2014 Feb 21;43(4):1221-9. ( pdf )

Qiu Y., and Myong S. "Single Molecule Imaging of proteins that recognize and repair DNA damages" Selected Topics in Quantum Electronics, IEEE Journal of , vol.20, no.2, pp.223,231, March-April 2014. ( pdf )

2013

Qiu Y., Antony E., Doganay S., Koh H., Lohman T. M., and Myong S. "Srs2 prevents Rad51 filament formation by repetitive motion on DNA". Nat Commun. 2013 Aug 13;4:2281. ( pdf )

Bruns A.M., Pollpeter D., Hadizadeh N., Myong S., Marko J.F., Horvath C.M., "ATP Hydrolysis Enhances RNA Recognition and Antiviral Signal Transduction by the Innate Immune Sensor", Laboratory of Genetics and Physiology 2 (LGP2). J Biol Chem. 2013 Jan 11;288(2):938-46. ( pdf )

Koh H., Kidwell M., Ragunathan K., Doudna J., and Myong S., "ATP independent diffusion of double stranded RNA binding protein". Proc Natl Acad Sci. 2013 Jan 2;110(1):151-6. ( pdf )

2012

Hwang H., Buncher N., Opresko P. L., and Myong S., "POT1-TPP1 regulates telomeric overhang structural dynamics".Structure. 2012 Nov 7;20(11):1872-80. ( pdf )

Jia H., Korolev S., Niedziela-Majka A., Maluf N. K., Gauss G.H., Myong S., Ha T., Waksman G., Lohman T.M. "Rotations of the 2B sub-domain of E. coli UvrD helicase/translocase coupled to nucleotide and DNA binding". J Mol Biol. 2011 Aug 19;411(3):633-48. Erratum in: J Mol Biol. 2012 May 4;418(3-4):264-5. ( pdf )

2011

Torbeev, V. Yu., Myong, S., Ha, T. and Kent, S. B. H. “Single-Molecule Studies of HIV-1 Protease Catalysis Enabled by Chemical Protein Synthesis” Isr. J. Chem. 51: 960–967. November 2011 ( pdf )

Ha T, Myong S. "A single-molecule view of chaperonin cooperativity". Proc Natl Acad Sci. U S A. 2011 Oct 11;108(41):16865-6. ( pdf )

Balci H., Arslan S., Myong S., Lohman T.M., Ha T. "Single-molecule nanopositioning: structural transitions of a helicase-DNA complex during ATP hydrolysis". Biophys J. 2011 Aug 17;101(4):976-84. ( pdf )

Hwang H., Kim H. and Myong S. "Protein induced fluorescence enhancement as a single molecule assay with short distance sensitivity" Proc Natl Acad Sci. 108(18):7414-8 (2011) ( pdf )

Qiu Y. and Myong S. "Single molecule detection of one, two and multiplex proteins involved in DNA/RNA transaction"Cellular and Molecular Bioengineering 4, 2, 125-137 (2011) ( pdf )

BEFORE 2011                          

Park J., Myong S., Niedziela-Majka A., Yu J., Lohman T. M. and Ha T."Reeling in DNA One Base at a Time: PcrA translocation coupled to DNA looping dismantles RecA filaments" Cell 142, 4, 544-555, (2010) ( pdf )

Myong, S. and Ha T., "Stepwise translocation of nucleic acid motors", Current Opinion in Structural Biology 20 (1), 121-127 (2010) ( pdf )

Okumus, B., Arslan S., Fengler S., Myong S. and Ha T., "Single Molecule Nanocontainers Made Porous Using a Bacterial Toxin", J. Am. Chem. Soc. 131, 14844–14849 (2009) ( pdf )

Myong, S., Cui S., Cornish P. V., Kirchhofer A. , Gack M. U., Jung J. U., Hopfner K. P. and Ha T., "Cytosolic viral sensor RIG-I is a 5 prime - triphosphate-dependent translocase on double-stranded RNA", Science 323(5917), 1070-1074 (2009) ( pdf )

Gack, M. U., Kirchhofer A., Shin Y. C., Inn K. S., Liang C., Cui S., Myong S., Ha T., Hopfner K. P. and Jung J. U., "Roles of RIG-I N-terminal tandem CARD and splice variant in TRIM25-mediated anti-viral signal transduction", Proc Natl Acad Sci, USA 105(43), 16743-16748 (2008) ( pdf )

Myong, S., Bruno M. M., Pyle A. M. and Ha T., "Spring-loaded Mechanism of DNA Unwinding by HCV NS3 Helicase",Science 317, 513-516 (2007) ( pdf )

Rasnik, I., Myong S., and Ha T., "Unraveling Helicase Mechanisms One Molecule at a Time", Nucleic Acid Research 34, 4225-4231 (2006) ( pdf )

Joo, C., McKinney S. A., Nakamura M., Rasnik I., Myong S., and Ha T., "Real Time Observation of RecA Filament Dynamics with Single Monomer Resolution", Cell 126, 515-527 (2006) ( pdf )

Myong, S., Stevens B., and Ha T., "Bridging Conformational Dynamics and Function using Single-Molecule Spectroscopy", Structure 14, 633-643 (2006) ( pdf )

Myong, S., Rasnik I., Joo C., Lohman T. M., and Ha T., "Repetitive Shuttling of a Motor Protein on DNA", Nature 437, 1321-1325 (2005) ( pdf )

Rasnik, I., Myong S., Cheng W., Lohman T. M., and Ha T., "DNA-binding Orientation and Domain Conformation of the E. Coli Rep Helicase Monomer Bound to a Partial Duplex Junction: Single-molecule Studies of Fluorescently Labeled Enzymes", J. of Mol. Biology 336(2), 395-408 (2004) ( pdf )