Mustafa Mir

faculty photo
Assistant Professor of Cell and Developmental Biology
Department: Cell and Developmental Biology

Contact information
Colket Translational Research Building
3501 Civic Center Boulevard
Room 9030
Philadelphia, PA 19104
Lab: 2674253938
B.Sc. (Electrical Engineering)
University of Illinois at Urbana-Champaign, 2008.
M.Sc. (Electrical Engineering)
University of Illinois at Urbana-Champaign, 2010.
Ph.D. (Electrical Engineering)
University of Illinois at Urbana-Champaign, 2013.
Post-Graduate Training
Postdoctoral Fellow, California Institute of Regenerative Medicine, University of California, Berkeley, 2014-2014.
Postdoctoral Scholar, Department of Molecular and Cell Biology, University of California, Berkeley, 2015-2020.
Permanent link
> Perelman School of Medicine   > Faculty   > Details

Description of Research Expertise

The goal of our lab is to develop and apply advanced microscopy technologies to visualize and quantify the dynamic processes that underly the regulation of gene expression during early embryonic development. Our favorite tool is high-resolution light-sheet microscopy which allows us to probe a vast range of spatial and temporal scales within living embryos (so far in Mice, Drosophila, and C. elegans). For example, we can acquire data on patterns of gene expression at embryonic scales, high-speed and multi-color volumetric data to quantify chromatin dynamics and the distribution of protein domains associated with gene activation or repression, and single molecule tracking data to quantify the kinetics of individual transcription factors as they search for and bind to their genomic targets. We apply these advanced imaging approaches along with biophysical modelling, genomics, and gene editing to studies within the areas of: (1) How protein-protein interactions shape nuclear organization and the ability of transcription factors to find their targets efficiently, (2) How nuclear organization changes during embryonic development and how this influences gene expression, and (3) How different disordered domains within proteins enable specialized functions. Our vision is to utilize quantitative data in combination with mechanistic modelling to develop new strategies to specifically manipulate nuclear organization and transcriptional regulation to achieve desired phenotypes. The insights gained through these projects will not only lead to an improved understanding of one of life’s fundamental processes, transcription, but will also open new doors for correcting transcription when it goes awry.

Selected Publications

M. Mir, A. Reimer, J. E. Haines, X.-Y. Li, M. Stadler, H. Garcia, M. B. Eisen, X. Darzacq: Dense Bicoid hubs accentuate binding along the morphogen gradient. Genes Dev. 31: 1784-1794 2017.

Alan P. Boka, Apratim Mukherjee, Mustafa Mir: Single-molecule tracking technologies for quantifying the dynamics of gene regulation in cells, tissue, and embryos. Development 148(18): dev199744, September 2021.

M. Mir, M. R. Stadler, S.A. Ortiz, X. Darzacq, M. B. Eisen: Dynamic Multifactor hubs transiently interact with sites of active transcription in Drospophila embryos. eLife 7(e40497 ), 2018.

M. Woringer, X. Darzacq, C. Zimmer, and M. Mir: Faster and less phototoxic 3D fluorescence microscopy using a versatile compressed sensing scheme. Optics Express 25(12): 13668-13683, 2017.

M. Mir, W. Bickmore, E. E. M. Furlong, G. J. Narlikar: Chromatin topology, condensates, and gene regulation: shifting paradigms or just a phase? Development 146(dev182766), 2019.

D. T. McSwiggen, M. Mir, X. Darzacq, R. Tjian: Evaluating phase separation in live cells: diagnosis, caveats, and functional consequences. Genes Dev gad.331521.119, 2019.

S. Chong and M. Mir: Towards decoding the sequence-based grammar governing the functions of intrinsically disordered protein regions. J Mol Biol 2021.

M. Mir, A. Reimer, M. Stadler, A. Tangara, A. S. Hansen, D. Hockemeyer, M. B. Eisen, H. Garcia, X. Darzacq: Chapter 32 – Single Molecule Imaging in Live Embryos using Lattice Light-Sheet Microscopy, Nanoscale Imaging: Methods and Protocols. Methods in Molecular Biology. Nanoscale Imaging: Methods and Protocols 2018.

M. Mir, Z. Wang, Z. Shen, M. Bednarz, R. Bashir, I. Golding and G. Popescu: Optical Measurement of Cell Cycle Dependent Growth. Proceedings of the National Academies of Sciences (PNAS) 108 (32): 13124-13129, 2011.

M. Mir, D. Babacan, M. Bednarz, M. N. Do, I. Golding and G. Popescu: Visualizing Escherichia coli Sub-Cellular Structure Using Sparse Deconvolution Spatial Light Interference Tomography. PLoS ONE 7 (6)(e38916 ), 2012.

back to top
Last updated: 06/14/2022
The Trustees of the University of Pennsylvania