Lu Bai

Mailing Address:

406 South Frear Building, University Park, Pa 168602

About Me

Dr. Bai is a 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 and postdoctoral training at Rockefeller University. Dr. Bai moved to the Penn State University as an assistant professor in 2012, was promoted to associate professor in 2018, and then full professor in 2023. 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

Editorial Boards

Centers

Research Interest

The mechanism of gene regulation by chromatin 

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.

Selected Recent Publications

Lee J, Simpson L, Li Y, Becker S, Zou F, & Bai L^† (2024) Transcription factor condensates, 3D clustering, and gene expression enhancement of the MET regulon. eLife 13: RP96028.

Xu C*, Godin H*, Yang JY, Leith E, Johnson J, Tan S, Mahony S, and & Bai L^† (2024) Systematic Dissection of Sequence Features Affecting the Binding Specificity of a Pioneer Factor Reveals Binding Synergy Between FOXA1 and AP-1. Mol Cell, 84(15):2838-2855.

Li Y, Lee J, & Bai L^† (2024) DNA Methylation-Based High-Resolution Mapping of Long-Distance Chromosomal Interactions in Nucleosome-Depleted Regions. Nat Commun. 15(1):4358.

Donovan BT, Chen HY, Eek P, Meng ZY, Jipa C, Tan S^†, Bai L^†, Poirier MG^† (2023) Basic helix-loop-helix pioneer factors interact with the histone octamer to invade nucleosomes and generate nucleosome depleted regions. Mol Cell, 83(8):1251-1263.

Chen HY, Kharerin H, Dhasarathy A, Kladde M, & Bai L^† (2022) Partitioned usage of chromatin remodelers among genome-wide nucleosome displacing factors. Cell Reports. 40: 111250.

Du MY*, Zou F*, Li Y, Yan YJ, & Bai L^† (2022) Chemically-induced chromosomal interactions (CICI) method to perturb chromosomal conformation and study its functions. Nat Commun. 13: 757.

Kharerin H & Bai L^† (2021) Thermodynamic Modeling of Genome-wide Nucleosome Depleted Regions in Yeast. PLOS Comp Biol, 17(1): e1008560.

Du MY, Kodner S, & Bai L^† (2019) Enhancement of LacI Binding Affinity in vivo. Nucleic Acids Res, 47(18): 9609–9618.

Donovan BT, Chen HY, Jipa C, Bai L, & Poirier MG (2019) Dissociation rate compensation mechanism for budding yeast pioneer transcription factors. Elife, pii: e43008.

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, 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.

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.