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Lu Bai

Associate Professor of Biochemistry and Molecular Biology and of Physics
Lu Bai

About Me

Dr. Bai is an associate professor in the Department of Biochemistry and Molecular Biology and Department of Physics at Penn State University. She received her PhD in biophysics from Cornell University (supervisor: Dr. Michelle Wang). For her thesis work, she combined single molecule experimental approaches with theoretical modeling to understand the thermodynamic and kinetic properties of a variety of biomolecules. She then worked as a postdoctoral fellow at Rockefeller University (supervisors: Dr. Fred Cross and Dr. Eric Siggia), using cell-cycle genes as a model to understand how promoter architecture and nucleosome positioning regulate gene expression in single cells. Dr. Bai moved to the Penn State University as an assistant professor in 2012, and was promoted to associate professor in 2018. Besides her dual appointment at BMB and Physics, her group is also part of the Penn State Center for Eukaryotic Gene Regulation, which provides a highly interactive environment for the study of chromatin and gene regulation.


Program or Departmental Affiliations

The BMMB Graduate Program The Center for Eukaryotic Gene Regulation The Department of Physics



Editorial Boards

Editorial board member, Current Opinion in Genetics & Development




The Center for Eukaryotic Gene Regulation



Research Interest

The mechanism of gene regulation by chromatin structure at different levels


Research Summary

The Bai Lab uses a variety of strategies to understand the mechanism of gene regulation by chromatin structure at different levels. Currently, we are working on two main projects: (1) to identify and characterize “pioneer factors” that can lead to nucleosome depletion and (2) to mechanistically dissect long-distance chromosomal interactions that regulate gene expression. We measure gene expression in single live cells to probe how these chromatin features affect gene expression in terms of the average level, cell-to-cell variability (noise), and dynamics. We are using budding yeast as our primary model system, but we are venturing into the mammalian cells as well. Method-wise, we are using a combination of imaging, genetics, genomics, and computational methods. We are also developing new genetics and genomics tools for the projects above.


Honors or Awards

  • 2008-2010, Suzanne & Bob Wright Fellow of the Damon Runyon Cancer Research Foundation 

  • 2007, Woman and Science Fellowship

  • 2006, Cornell University Liu Memorial Award


Selected Publications

  • Du MY, Fan Z, & Bai L† (2019) Chemically-induced chromosomal interactions: a new tool to perturb chromosomal conformation and study its functions. Manuscript in preparation
  • Yarrington RM, Yu Y, Yan C, Bai L, & Stillman DJ (2019) Independent Recruitment of the Mediator Tail Module Helps Overcome Coactivator Interdependence and Repressive Chromatin at the HO promoter. Under Revision in Genetics.
  • Zou F, Du MY, Chen HY, & Bai L† (2019) Existence, Transition, and Propagation of Intermediate Silencing States in rDNA. Mol Cell Biol, pii: MCB.00146-19.
  • Du MY, Kodner S, & Bai L† (2019) Enhancement of LacI Binding Affinity in vivo. Nucleic Acids Res, 47(18): 9609–9618.
  • Donovan B, Jipa C, Chen HY, Yan C, Bai L & Poirier MG (2019) Dissociation rate compensation mechanism for budding yeast pioneer transcription factors. Elife. pii: e43008. 
  • Zou F & Bai L† (2018) Using Time-lapse Fluorescence Microscopy to Study Gene Regulation. Methods. 159–160: 138–45. Review. 
  • Liu Y, Wolstenholme C, Carter G, Liu H, Hu H, Grainger L, Miao K, Fares M, Hoelzel C, Yennawar H, Ning G, Du M, Bai L, Li X & Zhang Xin (2018) Modulation of Flu
  • Yan C, Chen HY & Bai L† (2018) Genome-wide Study of Nucleosome-Depleting Factors in Budding Yeast. Mol Cell. 71(2): 294–30.
  • Du MY & Bai L† (2017) 3D clustering of co-regulated genes and its effect on gene expression. Curr Genet, 63:1017-21. Review.
  • Du MY, Zhang Q, & Bai L† (2017) Three distinct mechanisms of long-distance modulation of gene expression in yeast. PLOS Genet, 13(4):e1006736.
  • Zhang DY & Bai L† (2016) Inter-allelic interaction and gene regulation in budding yeast. Proc Natl Acad Sci, 113:4428-33.
  • Yan C, Wu S, Pocetti C, & Bai L† (2016) Regulation of cell-to-cell variability in divergent gene expression. Nat Commun, 7: 11099.
  • Yan C, Zhang DY, Garay JA, Mwang MM, & Bai L† (2015) Decoupling of divergent gene regulation by sequence-specific DNA binding factors. Nucleic Acids Res, 43: 7292-305.
  • Parnell EJ, Yu Y, Lucena R, Yoon Y, Bai L, Kellogg DR, & Stillman DJ (2014) The Rts1 regulatory subunit of PP2A phosphatase controls expression of the HO endonuclease via localization of the Ace2 transcription factor. J Biol Chem, 289:35431-35437.
  • Zhang Q, Yoon Y, Yu Y, Parnell EJ, Garay JA, Mwangi MM, Cross FR, Stillman DJ, & Bai L† (2013) “Stochastic expression and epigenetic memory at the yeast HO promoter.” Proc Natl Acad Sci, 110: 14012-14017.
  • Ma J, Bai L, & Wang MD. (2013) “Transcription under torsion”. Science, 28:1580-1583.
  • Li J, Liu Y, Rhee HS, Ghosh BS, Bai L, Pugh BF, & Gilmour DS. (2013) “Kinetic competition between elongation rate and binding of NELF controls promoter proximal pausing.” Mol Cell, 50: 711–722. 
  • Wang X, Bai L, Bryant GO & Ptashne M (2011) “Nucleosomes and the accessibility problem.” Trends Genet, 27: 487-92. Review.
  • Bai L†, Ondracka A & Cross FR†. (2011) “Multiple sequence-specific factors participate in the formation of nucleosome-depleted-region on the CLN2 promoter.” Mol Cell, 42:465-76.
  • Bai L† & Wang MD. (2010) “Comparison of pause predictions of two sequence-dependent transcription models.” J Stat Mech, P12007. 
  • Bai L† & Morozov AV. (2010). “Gene regulation by nucleosome positioning.” Trends Genet, 26:476-83. Review.
  • Bai L†, Charvin G, Siggia ED & Cross FR. (2010) “Nucleosome depleted regions in cell-cycle-regulated promoters ensure reliable gene expression in every cell cycle.” Dev Cell, 18:544-55.
  • Jin J, Bai L, Johnson DS, Fulbright RM, Kireeva ML, Kashlev M, Wang MD (2010) “Overcoming the nucleosomal barrier during transcription elongation.” Nat Struct Mol Biol, 17:745-52.
  • Hall MA, Shundrovsky A, Bai L, Fulbright RM, Lis JT & Wang MD (2009). “High resolution dynamic mapping of histone-DNA interactions in a nucleosome.” Nat Struct Mol Biol, 16:124-129. 
  • Johnson DS, Bai L, Smith B, Patel S & Wang MD (2007). “Single molecule studies reveal dynamics of DNA unwinding by the ring-shaped T7 helicase.” Cell, 129:1299-309.
  • Bai L, Fulbright RM & Wang MD (2007). “Mechanochemical kinetics of transcription elongation.” Phys Rev Lett, 98:068103.
  • Bai L, Santangelo T & Wang MD (2006). “Single molecule analysis of RNA polymerase transcription.”  Annu Rev Biophys Biomol Struct, 35:343-360.  Review.
  • Jiang J*, Bai L*, Surtees J, Gemici Z, Wang MD & Alani E (2005). “Detection of high affinity mismatch binding and sliding clamp modes for the MSH2-MSH6 mismatch recognition complex by single-molecule unzipping force analysis.” Mol Cell, 20:771-81.
  • Bai L, Shundrovsky A. & Wang MD (2004). “Sequence-dependent kinetic model for transcription elongation by RNA polymerase.” J Mol Biol, 344:335-349.