Manyu Du

About Me

I joined Penn State University in Feb 2025 as a faculty at the Department of Biochemistry and Molecular Biology, Eberly College and the Huck Institutes of Life Sciences. I also obtained my PhD in Biochemistry, Molecular and Microbiology in Dec 2019 at Penn State! Before returning, I was a postdoctoral researcher at Massachusetts Institute of Technology from 2020 to 2021 and at the Max Planck Institute of Immunobiology and Epigenetics, Germany from 2021 to 2024. Originally from China, I obtained my bachelor's degree in Life Sciences at Wuhan University, China in 2013.

Research Summary

The Du lab is interested in understanding how transcription machineries and regulatory DNA elements organize in 3D in the nucleus to regulate gene expression. Both healthy and cancerous cells acquire functional genomic features, including super-enhancers (SEs) to drive expression of prominent oncogenes and developmentally important genes. Mechanistically, how such super-enhancers control gene expression to affect different outcomes in development and cancer related diseases is not understood. Recent models evoking phase separation and gene control suggest that SEs are multimolecular assemblies or condensates that provide a way to concentrate transcription cofactors (such as Mediators) and Pol II to regulate gene activation. 

We leverage single-molecule super-resolution imaging, advanced lattice light sheet microscopy and other state of the art biophysical approaches to study molecular mechanisms of transcription and genome organization. We are using mouse embryonic stem cells and mouse erythroid leukemia cells to investigate the dynamics and function of transcriptional condensates in health and disease. Other than imaging, we are also interested in biochemical, genetic and sequencing approaches to understand gene regulation.

Selected Publications

1. Du M, Stitzinger S H, Spille J H, Cho W, Lee C, Hijaz M, Quintana A, Cisse I I (2024). Direct observation of a transcriptional condensate effect on super-enhancer controlled gene bursting. Cell. 187(2):331-344.e17.

2. Zolotarev N, Wang Y, DuM, Bayer M, Cisse I I, Grosschedl R (2024). EBF1 function

requires spatially distributed tyrosines that favor phase separation and subnuclear

cluster formation. Genes Dev. doi: 10.1101/gad.350828.123. Epub ahead of print. PMID:38233109. 

3. Du M*, Zou F*, Li Y, Yan Y, & Bai L (2022). Chemically Induced Chromosomal Interaction (CICI) method to study chromosome dynamics and its biological roles. Nat Communications 13, 757.

4. Du M, Kodner S, & Bai L (2019) Enhancement of LacI Binding Affinity in vivo. Nucleic Acid Research. Volume 47, Issue 18, 10 October 2019, Pages 9609–9618.

5. Du M, Zhang Q, & Bai L (2017). Three distinct mechanisms of long-distance modulation of gene expression in yeast. PLOS Genet, 13(4):e1006736.

6. Asimi V, Kumar A S, Niskanen H, Riemenschneider C, Hetzel S, Naderi J, Fasching N, Popitsch N, Du M, Kretzmer H, Smith Z D, Weigert R, Walther M, Mamde S, David M, Wittler L, Buschow R, Timmermann B, Cisse I I, Ameres S L, Meissner A, Hnisz D (2022). Hijacking of transcriptional condensates by endogenous retroviruses. Nat Genet. https://doi.org/10.1038/s41588-022-01132-w

7. Zou F, Du M, Chen H and Bai L (2019) Existence, Transition, and Propagation of Intermediate Silencing States in rDNA. Molecular and Cellular Biology.

https://doi.org/10.1128/MCB.00146-19

*Co-first author