Recent Publications

  • Pioneer Factors: Nature or Nurture?
    Stoeber S, Godin H, Xu C, Bai L (2024)
    Critical Reviews In Biochemistry & Molecular Biology, Invited Review, 1–15,
  • Transcription Factor Condensates Mediate Clustering of MET Regulon and Enhancement in Gene Expression.  
    Lee J, Simpson L, Li Y, Becker S, Zou F, Bai L (2024)
    Elife, Accepted
  • Systematic Dissection of Sequence Features Affecting the Binding Specificity of a Pioneer Factor Reveals Binding Synergy Between FOXA1 and AP-1.
    Xu C*, Godin H*, Yang JY, Leith E, Johnson J, Tan S, Mahony S, Bai L (2024)
    Molecular Cell, Accepted
  • DNA Methylation-Based High-Resolution Mapping of Long-Distance Chromosomal Interactions in Nucleosome-Depleted Regions. 
    Li Y, Lee J, Bai L (2024)
    Nature Communications, 15(1):4358
  • Using Integrated Synthetic Oligo (ISO) library to systematically interrogate the activities of pioneer factors and their coordination with chromatin remodelers. 
    Chen HY, Yan C, Dhasarathy A, Kladde M, Bai L (2023)
    Star Protocols, DOI: 10.1016/j.xpro.2023.102279
  • Using Synthetic DNA Library to Investigate Chromatin and Gene Regulation.
    Kleinschmidt H, Xu C, Bai L (2023)
    Chromosoma, Invited Review, DOI: 10.1007/s00412-023-00796-5
  • Basic helix-loop-helix pioneer factors interact with the histone octamer to invade nucleosomes and generate nucleosome depleted regions.
    Donovan BT, Chen HY, Eek P, Meng ZY, Jipa C, Tan S†, Bai L†, Poirier MG† (2023)
    Molecular Cell, 83: 1251.
  • Predicting Nucleosome Positioning Using Statistical Equilibrium Models in Budding Yeast
    Kharerin H & Bai L (2023) 
    Star Protocols: 4 (1): 101926.
  • Origin recognition complex harbors an intrinsic nucleosome remodeling activity
    Li S, Wasserman MR, Yurieva O, Bai L, O’Donnell ME, Liu S (2022)
    PNAS, 119 (42): e2211568119
  • Nucleosome-directed replication origin licensing independent of a consensus DNA sequence
    Li S*, Wasserman MR*, Yurieva O, Bai L, O’Donnell ME, Liu S (2022)
    Nature Communications, 13:4947.
  • Partitioned Usage of Chromatin Remodelers by Nucleosome-Displacing Factors
    Chen HY, Kharerin H, Dhasarathy A, Kladde M, Bai L (2022)
    Cell Reports, 40(8): 111250.
  • EOMES expression bypasses WNT signaling input in human mesendoderm specification
    Yoney A*, Bai L*, Brivanlou AH, Siggia ED (2022)
    Development, 149(20):dev200335.
  • Chemically Induced Chromosomal Interaction (CICI): A New Tool to Study Chromosome Dynamics and Its Biological Roles
    Du MY*, Zou F*, Yan YJ, Bai L (2022) 
    Nat Communication, 13: 757.
  • Thermodynamic Modeling of Genome-wide Nucleosome Depleted Regions in Yeast
    Kharerin H & Bai L (2021) 
    Plos Computational Biology, 17(1): e1008560.
  • Ash1 and Tup1 Dependent Repression of the Saccharomyces cerevisiae HO promoter Requires Activator-Dependent Nucleosome Eviction
    Emily J. Parnell, Timothy J. Parnell, Chao Yan, Lu Bai, David J. Stillman (2020) 
    Plos Genetics, 16(12): e1009133.
  • A Role for Mediator Core in Limiting Coactivator Recruitment in Saccharomyces cerevisiae
    Yarrington R, Yu Y, Yan C, Bai L, Stillman D (2020)
    Genetics, 215:407-20. [PDF]
  • Existence, Transition, and Propagation of Intermediate Silencing States in rDNA
    Zou F, Du MY, Chen HY, Bai L (2019)
    Mol. Cell. Biol, pii: MCB.00146-19[PDF]
  • Enhancement of LacI Binding in vivo
    Du MY, Kodner S, Bai L (2019)
    Nucleic Acid Research, 47:9609-18[PDF]
  • Dissociation rate compensation mechanism for budding yeast pioneer transcription factors
    Donovan BT, Chen HY, Jipa C, Bai L, Poirier MG (2019)
    Elife, pii: e43008[PDF]
  • Using Time-lapse Fluorescence Microscopy to Study Gene Regulation
    Zou F & Bai L (2018)
    Methods, 159-160:138-145. Review. [PDF]
  • Modulation of fluorescent protein chromophores to detect protein aggregation with turn-on fluorescence
    Liu Y, Wolstenholme C, Carter G, Liu H, Hu H, Grainger L, Miao K, Fares M, Hoelzel C, Yennawar H, Ning G, Du MY, Bai L, Li X, Zhang X (2018)
    J. Am. Chem. Soc., 140:7381-7384. [PDF]  [F1000 recommended]
  • Systematic Study of Nucleosome-Displacing Factors in Budding Yeast.
    Yan C, Chen HY, Bai L (2018)
    Molecular Cell, 71(2): 294–30. [PDF]  (Read Highlight in Molecular Cell here) [F1000 recommended]
  • 3D clustering of co-regulated genes and its effect on gene expression.
    Du MY & Bai L (2017)
    Current Genetics, doi: 10.1007/s00294-017-0712-9. Review. [PDF]
  • Three distinct mechanisms of long-distance modulation of gene expression in yeast.
    Du MY, Zhang Q, Bai L (2017)
    PLOS Genetics, 13(4):e1006736. [PDF]
  • Inter-allelic interaction and gene regulation in budding yeast.
    Zhang DY & Bai L (2016)
    PNAS, 113:4428-33. [PDF]
  • Regulation of cell-to-cell variability in divergent gene expression.
    Yan C, Wu S, Pocetti C, Bai L (2016)
    Nature Communications, 7: 11099. [PDF]
  • Decoupling of divergent gene regulation by sequence-specific DNA binding factors.
    Yan C, Zhang DY, Garay JA, Mwang MM, Bai L (2015)
    Nucleic Acid Research, 43: 7292-305. [PDF]
  • The Rts1 regulatory subunit of PP2A phosphatase controls expression of the HO endonuclease via localization of the Ace2 transcription factor.
    Parnell EJ, Yu Y, Lucena R, Yoon Y, Bai L, Kellogg DR, Stillman DJ (2014)
    JBC, 289:35431-35437. [PDF]
  • Stochastic expression and epigenetic memory at the yeast HO promoter.
    Zhang Q, Yoon Y, Yu Y, Parnell EJ, Garay JA, Mwangi MM, Cross FR, Stillman DJ, Bai L (2013)
    PNAS, 110: 14012-14017. [PDF] (Read Comments in PNAS here)
  • Transcription under torsion
    Ma J, Bai L, Wang MD. (2013)
    Science, 28:1580-1583. [PDF]
  • Kinetic competition between elongation rate and binding of NELF controls promoter proximal pausing.
    Li J, Liu Y, Rhee HS, Ghosh BS, Bai L, Pugh BF, Gilmour DS. (2013)
    Molecular Cell, 50: 711–722. [PDF]


Before 2012

  • Nucleosomes and the accessibility problem
    Wang X, Bai L, Bryant GO & Ptashne M (2011)
    Trends Genet, 27: 487-92. Review. [PDF]
  • Multiple sequence-specific factors participate in the formation of nucleosome-depleted-region on the CLN2 promoter.
    Bai L, Ondracka A & Cross FR. (2011)
    Mol. Cell. 42:465-76. [PDF]
  • Comparison of pause predictions of two sequence-dependent transcription models.
    Bai L & Wang MD. (2010)
    Journal of Statistical Mechanics. P12007. [PDF]
  • Gene regulation by nucleosome positioning.
    Bai L & Morozov AV. (2010).
    Trends Genet. 26:476-83. Review. [PDF]
  • Nucleosome depleted regions in cell-cycle-regulated promoters ensure reliable gene expression in every cell cycle.
    Bai L, Charvin G, Siggia ED & Cross FR. (2010)
    Developmental Cell. 18:544-55. [PDF] [F1000 Recommended]
  • Overcoming the nucleosomal barrier during transcription elongation.
    Jin J, Bai L, Johnson DS, Fulbright RM, Kireeva ML, Kashlev M, Wang MD (2010)
    Nature Structural and Molecular Biology. 17:745-52. [PDF]
  • High resolution dynamic mapping of histone-DNA interactions in a nucleosome.
    Hall MA, Shundrovsky A, Bai L, Fulbright RM, Lis JT & Wang MD (2009).
    Nature Structural and Molecular Biology 16:124-129. [PDF] [F1000 Recommended]
  • Single molecule studies reveal dynamics of DNA unwinding by the ring-shaped T7 helicase.
    Johnson DS, Bai L, Smith B, Patel S & Wang MD (2007).
    Cell. 129:1299-309. [PDF] [F1000 Recommended]
  • Mechanochemical kinetics of transcription elongation.
    Bai L, Fulbright RM & Wang MD (2007).
    Phys Rev Lett. 98:068103. [PDF]
  • Single molecule analysis of RNA polymerase transcription.
    Bai L, Santangelo T & Wang MD (2006).
    Annu. Rev. Biophys. Biomol. Struct 35:343-360. Review. [PDF]
  • Detection of high affinity mismatch binding and sliding clamp modes for the MSH2-MSH6 mismatch recognition complex by single-molecule unzipping force analysis.
    Jiang J*, Bai L*, Surtees J, Gemici Z, Wang MD & Alani E (2005).
    Mol. Cell. 20:771-81. [PDF]
  • Sequence-dependent kinetic model for transcription elongation by RNA polymerase.
    Bai L, Shundrovsky A. & Wang MD (2004).
    J. Mol. Biol. 344:335-349. [PDF]

News and views:

  • Bind at your own RSC:  Nucleosome phasing and occupancy in a eukaryotic promoter
    Buchler NE & Bai L (2011).
    Current Biology. 21:223-225 [PDF]
  • Nucleosome-depleted regions in promoters: consequences on robustness of transcriptional activation
    Bai L & Charvin G (2010)
    Med Sci (Paris). 26:1035-1037. [PDF]